[English] 日本語
Yorodumi
- PDB-3p8c: Structure and Control of the Actin Regulatory WAVE Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p8c
TitleStructure and Control of the Actin Regulatory WAVE Complex
Components
  • Abl interactor 2
  • Cytoplasmic FMR1-interacting protein 1
  • Nck-associated protein 1
  • Probable protein BRICK1Probability
  • Wiskott-Aldrich syndrome protein family member 1
KeywordsPROTEIN BINDING / actin polymerization
Function / homology
Function and homology information


peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone / modification of postsynaptic actin cytoskeleton / dendrite extension / lens fiber cell morphogenesis / regulation of translation at postsynapse, modulating synaptic transmission / filopodium tip / regulation of modification of postsynaptic actin cytoskeleton / cytoskeletal anchor activity / regulation of dendritic spine morphogenesis / regulation of actin filament polymerization / RNA 7-methylguanosine cap binding / ruffle organization / actin polymerization or depolymerization / cell projection assembly / axon extension / proline-rich region binding / positive regulation of ruffle assembly / positive regulation of dendrite development / lamellipodium assembly / protein kinase A binding / regulation of myelination / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / Rac protein signal transduction / protein kinase A regulatory subunit binding / dendritic growth cone / filamentous actin / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of axon extension / positive regulation of lamellipodium assembly / signaling adaptor activity / axonal growth cone / response to electrical stimulus / translation repressor activity / cellular response to brain-derived neurotrophic factor stimulus / cytoskeleton organization / ruffle / RAC1 GTPase cycle / actin filament polymerization / viral process / mitochondrion organization / receptor-mediated endocytosis / neuron projection morphogenesis / central nervous system development / actin filament organization / axon guidance / cell motility / positive regulation of protein-containing complex assembly / FCGR3A-mediated phagocytosis / adherens junction / cell morphogenesis / terminal bouton / Regulation of actin dynamics for phagocytic cup formation / cognition / small GTPase binding / VEGFA-VEGFR2 Pathway / kinase binding / SH3 domain binding / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / specific granule lumen / positive regulation of fibroblast proliferation / cell migration / actin filament binding / actin cytoskeleton / regulation of translation / tertiary granule lumen / lamellipodium / nervous system development / actin binding / regulation of cell shape / fibroblast proliferation / actin cytoskeleton organization / postsynapse / protein-containing complex assembly / secretory granule lumen / in utero embryonic development / mitochondrial outer membrane / dendritic spine / cytoskeleton / neuron projection / focal adhesion / neuronal cell body / synapse / apoptotic process
Similarity search - Function
Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / ABL interactor 2 / Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain ...Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / ABL interactor 2 / Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain / Abl-interactor, homeo-domain homologous domain / SCAR/WAVE family / ABI family / CYRIA/CYRIB Rac1 binding domain / Abl-interactor HHR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Wiskott Aldrich syndrome homology region 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / WH2 motif / WH2 domain / WH2 domain profile. / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix Hairpins / SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Abl interactor 2 / Cytoplasmic FMR1-interacting protein 1 / Protein BRICK1 / Actin-binding protein WASF1 / Abl interactor 2 / Nck-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.29 Å
AuthorsChen, Z. / Borek, D. / Padrick, S.B. / Gomez, T.S. / Metlagel, Z. / Ismail, A.M. / Umetani, J. / Billadeau, D.D. / Otwinowski, Z. / Rosen, M.K.
CitationJournal: Nature / Year: 2010
Title: Structure and control of the actin regulatory WAVE complex.
Authors: Chen, Z. / Borek, D. / Padrick, S.B. / Gomez, T.S. / Metlagel, Z. / Ismail, A.M. / Umetani, J. / Billadeau, D.D. / Otwinowski, Z. / Rosen, M.K.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytoplasmic FMR1-interacting protein 1
B: Nck-associated protein 1
D: Wiskott-Aldrich syndrome protein family member 1
E: Probable protein BRICK1
F: Abl interactor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,84317
Polymers333,1055
Non-polymers73912
Water17,240957
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41520 Å2
ΔGint-296 kcal/mol
Surface area111710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.013, 113.982, 327.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 5 types, 5 molecules ABDEF

#1: Protein Cytoplasmic FMR1-interacting protein 1 / Specifically Rac1-associated protein 1 / Sra-1 / p140sra-1


Mass: 145363.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYFIP1, KIAA0068 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L576
#2: Protein Nck-associated protein 1 / NAP 1 / Membrane-associated protein HEM-2 / p125Nap1


Mass: 128940.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKAP1, HEM2, KIAA0587, NAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2A7
#3: Protein Wiskott-Aldrich syndrome protein family member 1 / WASP family protein member 1 / Protein WAVE-1 / Verprolin homology domain-containing protein 1


Mass: 31930.779 Da / Num. of mol.: 1 / Mutation: prolin rich region deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WASF1, KIAA0269, SCAR1, WAVE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92558
#4: Protein Probable protein BRICK1 / Probability


Mass: 8756.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3orf10, HSPC300, MDS027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUW1
#5: Protein Abl interactor 2


Mass: 18112.561 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DSN1, UniProt: Q9NYB9*PLUS

-
Non-polymers , 4 types, 969 molecules

#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 957 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.28→47.98 Å / Num. all: 164128 / Num. obs: 144578 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 33.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 2.28→2.31 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1157 / Rsym value: 0.196 / % possible all: 28.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MLPHAREphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.29→47.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.763 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23704 7144 5 %RANDOM
Rwork0.18807 ---
all0.1905 155636 --
obs0.1905 135310 86.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21789 0 39 957 22785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02222499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.96530406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0852721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10524.0191080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.168154188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.69215159
X-RAY DIFFRACTIONr_chiral_restr0.0630.23416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02116796
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.387413575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.122622040
X-RAY DIFFRACTIONr_scbond_it7.10748924
X-RAY DIFFRACTIONr_scangle_it9.2368365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 192 -
Rwork0.225 3707 -
obs--32.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23482.39920.05361.92190.05960.02110.2236-0.51120.21270.2069-0.2177-0.0428-0.08220.065-0.00590.6491-0.07050.00520.658-0.01390.467246.816155.8169255.3159
22.93520.75160.62282.01470.35932.4363-0.076-0.23240.08150.0202-0.04640.23230.0182-0.33440.12240.55060.06620.07170.4850.01310.46572.081445.4123243.4625
36.3037-1.4849-0.32483.5453-1.7052.0679-0.1867-0.76920.45030.6646-0.0384-0.4609-0.41270.33510.22510.55290.0241-0.05560.5252-0.01370.416425.997352.2701249.8193
46.00380.7979-1.84253.07010.75544.6429-0.0926-0.57760.1210.5392-0.04050.73970.0875-0.57710.1330.60120.11560.03880.5556-0.01390.5657-5.86549.7097243.3687
51.21880.17280.20661.46390.20021.2275-0.0816-0.17810.24790.11580.0365-0.0982-0.26380.11460.0450.49770.0082-0.05610.4915-0.01080.446925.704958.7326239.9456
62.935-2.1964-0.98545.7971.81081.26940.05560.27230.2334-0.4376-0.0577-0.2414-0.27690.0720.00220.5715-0.034-0.08590.49330.01830.421923.235866.5813230.5205
76.5641-2.96993.48135.3369-4.05318.906-0.08590.03990.20920.1745-0.1723-0.47-0.0450.44030.25820.439-0.04070.01540.5299-0.03920.480143.647635.4281221.6051
84.0619-1.36981.85881.807-0.84952.56220.02310.30640.2628-0.116-0.15-0.0673-0.07240.13010.12690.4987-0.03340.03220.4672-0.01390.465327.280344.8177221.7031
91.1707-0.41150.92460.7712-0.4712.4782-0.0751-0.21180.11780.2292-0.0096-0.2077-0.09650.26550.08480.50960.0041-0.01160.55950.01020.548642.556236.9769243.2803
100.94960.28731.12744.42431.08121.67660.0276-0.1569-0.07960.74170.1559-0.74840.23620.2796-0.18350.4530.0833-0.18950.95290.09790.325349.949235.4231258.2994
113.31731.50012.25293.13912.44015.2616-0.062-0.33180.34030.2441-0.0541-0.2701-0.35380.23980.11610.50720.0287-0.0280.53420.04280.461641.881842.9778245.6066
120.6646-0.3718-0.50660.63530.771.35090.01980.00620.0342-0.0183-0.0074-0.0346-0.07670.0206-0.01240.419-0.0017-0.0120.41360.0190.434518.23233.328210.4389
130.34140.10350.33570.58381.14242.7168-0.06550.04030.071-0.03060.0084-0.0449-0.11980.15050.05710.45040.00580.02190.46030.02960.473619.750318.8724196.463
140.11390.0732-0.31820.33650.02032.1708-0.03110.02880.00670.00970.00980.06530.0183-0.15480.02130.46220.01060.02630.4532-0.00940.473516.145610.1941176.2515
1532.4065-5.4632-35.19055.84457.402938.73451.03871.4793-0.3831-0.0521-1.37290.3963-1.1272-1.74660.33420.15410.09040.0791.2314-0.34910.53913.016818.6834168.9379
160.44770.50330.36432.86251.78073.6798-0.0115-0.03740.08970.0298-0.1060.3926-0.2384-0.36330.11760.44060.01330.02010.49250.01650.499720.109918.414176.1732
170.4978-0.0427-0.22050.4233-0.36772.0423-0.04730.1221-0.0188-0.0644-0.01040.18720.0016-0.52650.05770.4927-0.02070.00920.5752-0.03840.52497.011-0.5446142.5086
180.6684-0.03520.40830.9609-0.3731.84060.08620.0049-0.17410.0703-0.0654-0.19620.32260.2515-0.02080.51250.00210.05480.4356-0.01410.455831.535-5.8186171.8597
190.8184-0.26320.03730.69560.45221.291-0.00640.09590.0357-0.1192-0.02510.0617-0.0339-0.11770.03150.4009-0.0127-0.00150.4507-0.00790.425213.65180.8359139.8172
201.97783.80434.435911.016110.840212.41680.2773-0.0455-0.43830.637-0.0005-0.0711.073-0.3326-0.27680.5304-0.07810.06420.58060.01190.584617.2326-25.7441136.7234
219.67420.787-0.6478.8236-2.63482.9182-0.00760.8035-1.0559-0.75070.07510.03040.5465-0.1312-0.06740.54870.0671-0.00430.5045-0.0050.498547.3266-39.7244110.2064
224.30080.022-0.85531.37670.06452.08260.1732-0.28330.57930.15210.0709-0.5129-0.2580.7615-0.24410.49260.00370.04460.6561-0.06390.548470.786-16.4851120.3789
234.7014-0.19492.25841.30920.37533.37470.08770.1975-0.0203-0.07190.0884-0.76470.03590.9844-0.17610.44360.11780.1130.6689-0.08770.632477.9874-23.9562116.6649
241.94720.31290.29050.82220.20040.7222-0.00780.1551-0.1656-0.10670.0286-0.06990.09430.0948-0.02080.49230.00870.02930.4468-0.00620.423648.7492-28.2539107.5174
255.9737-1.84173.59464.2201-1.23535.78750.11730.2439-0.23320.03780.0239-0.57190.4690.8306-0.14130.43750.0510.09040.5821-0.06830.497274.8546-25.6326111.7079
261.1003-0.1558-0.04580.77190.20590.71940.03840.1624-0.0115-0.1297-0.031-0.0437-0.0293-0.0086-0.00730.4778-0.00570.00570.43310.00550.412239.5909-15.5789107.7619
277.8113.530812.179723.707521.200319.0355-0.22290.3051-0.3979-0.97660.8613-0.8548-0.61180.5665-0.63841.3935-0.3570.40450.7611-0.08380.491150.4916-9.87789.7673
281.1030.1748-0.35570.8492-0.13540.67530.020.06170.0807-0.03640.00980.0026-0.0525-0.0395-0.02980.4391-0.0032-0.0040.4301-0.01080.419933.9182-8.5702119.3767
291.09630.24310.08331.60580.48781.3112-0.00640.042-0.0245-0.0009-0.00230.09540.0955-0.06690.00870.46580.03630.01120.51810.01620.456630.5214-19.9117125.5859
302.1657-0.1909-0.35681.8991-0.07572.8228-0.05010.0876-0.38450.0185-0.00960.0820.4812-0.12070.05970.5092-0.03420.0090.4128-0.00080.524631.1063-39.9198117.1737
3110.51865.1878-1.88088.58-6.53927.9134-0.0580.1957-0.7054-0.2561-0.0222-0.22510.56540.20680.08020.49690.01860.00640.4424-0.01950.441937.9107-23.372127.5591
320.5209-0.5021-0.75841.23061.47452.32190.0615-0.01610.0663-0.13280.0464-0.1365-0.13020.0584-0.10780.4163-0.02530.01770.44590.01440.44143.8081-2.1528142.8676
332.94613.7754-3.62924.856-4.66074.48360.13060.03550.34280.17790.19590.4251-0.2203-0.1096-0.32650.80910.152-0.38841.0434-0.00371.015423.938533.1594166.9092
340.2997-0.0544-0.13431.07150.51231.146-0.0044-0.00560.0320.04050.0276-0.0015-0.03650.0378-0.02320.4168-0.0180.0340.45060.01620.417939.10942.0912152.4579
351.94961.38181.98183.41062.95533.71820.00430.056-0.14380.04010.00610.05120.18120.0113-0.01050.4589-0.00310.04870.48930.01620.436937.42783.4389164.4582
361.25460.2802-0.00561.9350.29031.5960.00360.01470.0380.00320.0234-0.1253-0.01530.1617-0.0270.43480.00620.00920.50040.01980.414748.505814.9139180.5021
372.01040.63861.75711.21611.0952.55590.0166-0.24940.10960.25390.024-0.31150.1020.264-0.04060.47250.033-0.00390.57840.01380.436557.715915.9758202.3668
388.10991.49670.54674.87610.91495.7541-0.0142-0.756-0.15730.8387-0.0893-0.50710.04980.22170.10350.6493-0.00470.02430.4152-0.00610.494638.1793-4.2977194.2186
391.20780.90450.5591.53431.57821.94440.1091-0.1202-0.23810.24580.078-0.32630.40190.3392-0.18710.49120.0396-0.0170.55660.03940.439855.04611.7128202.9591
401.7864-0.8581-0.03581.14380.40462.4402-0.0312-0.09190.00560.13380.041-0.06080.02460.1796-0.00970.4401-0.01430.0010.5060.01570.446346.726221.9271208.4993
410.27270.84590.4463.20111.53910.7722-0.063-0.15080.13050.1337-0.11580.23990.0111-0.1520.17870.98950.29490.20820.74930.17960.490929.573129.7919261.6386
423.75313.57274.46034.51862.93666.8499-0.1583-0.14120.1626-0.0495-0.09120.1201-0.385-0.1810.24960.5380.01680.04280.51160.06510.393726.766719.3025253.314
434.0285-1.62315.44913.96625.081823.3685-0.04960.14210.1557-0.1873-0.2701-0.0063-0.5151-0.21260.31970.48650.01510.02860.48480.05190.611121.898512.8403239.0589
448.26343.44486.25737.84613.800414.2426-0.1548-0.03070.46870.043-0.1330.3524-0.4473-0.61770.28780.51110.020.05950.45170.0120.423418.54157.0035226.3968
453.5261-0.17972.02897.32663.63268.8317-0.0043-0.3741-0.27760.4468-0.20870.23360.4435-0.45510.21310.5702-0.01750.09170.49320.05520.436215.2378-2.5204214.4242
467.858513.80311.884931.9097-7.906816.89330.2769-0.49910.74290.4722-0.48831.30690.2164-0.73150.21130.7415-0.00050.21480.59120.12920.515913.608-9.8188205.2128
474.8817-0.23453.75415.93221.451614.13990.23890.1747-0.7206-0.0350.15750.16530.7061-0.3584-0.39640.9159-0.10490.12940.34080.01890.403315.1362-15.726192.0195
486.6374-8.7655.7409239.41691.6625.3489-1.0788-5.2312-1.6047-9.21132.1969.9822-1.2474-4.6536-1.11721.76761.3284-0.00335.07080.70710.90258.106-12.1192182.232
493.2762-3.59773.20111.60637.579623.35690.36380.2452-0.6827-0.7214-0.98831.28970.8083-1.16190.62460.6113-0.4101-0.0140.6819-0.09890.58941.0099-1.2126184.6205
500.08650.59870.53928.3678.43339.2244-0.14740.01730.0201-0.1535-0.34630.5507-0.1378-0.48630.49370.5003-0.01960.0460.5211-0.01280.43638.955914.4988206.1358
516.5308-3.5621-3.14086.85962.95399.2779-0.374-0.2415-0.34750.36030.12720.06780.70830.33240.24680.5327-0.02820.06190.51450.06410.50887.778422.2674231.0358
523.8698-2.0785-1.03832.43462.36222.9067-0.440.6626-0.26570.1141-0.24520.6391-0.0028-0.35260.68520.4628-0.0983-0.04750.84390.03420.533-13.368634.9192227.8537
531.5957-1.4552-4.16091.77223.044912.4501-0.00720.1957-0.24080.0974-0.03040.41740.1657-0.75650.03760.45410.00730.00570.5440.01730.5366-1.414234.5975220.2983
543.13581.183-0.7569.3106-8.97620.31040.18220.94060.5977-0.9185-0.20530.2262-0.3721-0.39870.02310.49930.1318-0.08660.71770.12060.42212.430438.473198.6456
550.7835-4.20980.335622.7067-1.81190.1486-0.23390.00010.10031.16280.2251-0.4057-0.07190.02090.00880.64090.0479-0.16541.0740.15310.30782.920745.4407182.6988
561.0072-0.46850.88190.2472-0.47030.89920.50320.1397-0.2127-0.0708-0.17320.15650.08950.3077-0.331.4698-0.1450.09880.855-0.42740.42310.39558.5019167.7376
578.4608-12.7813-9.839720.957816.288812.7835-0.09690.7935-0.1019-0.1496-0.96541.26280.1233-1.14111.06230.7911-0.9571-0.13341.82160.32030.8603-0.37543.881173.9898
583.571714.4202-0.947194.668213.51538.77410.09740.27990.52760.7262-0.72182.92030.3449-1.3430.62440.25-0.06840.26931.1529-0.57760.8332-0.884210.8916181.1717
598.14876.33956.957516.38369.13167.15120.16860.7381-0.4352-0.4161-0.09790.53850.01010.3841-0.07070.6287-0.30090.16420.6292-0.32410.53-2.528917.9381194.6764
603.7067-3.0839-5.385110.1837-2.797816.25890.44120.91560.6566-1.2814-0.4497-0.67740.0917-1.0680.00850.45230.02-0.06710.86520.26140.7196.99330.5942196.69
618.5244-7.01075.02395.7783-4.13032.9625-0.61290.27181.46790.5854-0.2452-1.1454-0.3160.16630.85821.41960.13260.01741.0570.02110.69242.334125.7331263.2652
6226.409511.9546-2.03347.44713.29088.97710.491-1.1277-0.66380.7383-0.2883-0.51510.92150.5102-0.20260.57660.1137-0.05310.61750.07780.518440.099423.2667257.2617
639.2766-7.9353-4.96769.71869.990413.9170.2343-0.11440.3508-0.06460.3244-0.51750.12550.4745-0.55870.50950.0107-0.00240.53390.08170.479737.823420.2845251.696
6418.6329-2.04698.49540.6147-3.038815.2948-0.2303-0.18681.16330.0503-0.0983-0.1094-0.13490.63670.32860.51170.0497-0.02370.5227-0.00210.632636.111518.0887244.8744
655.32683.72695.18357.2652-3.529419.1197-0.2228-0.07990.5975-0.0984-0.1405-0.4174-0.60860.67020.36330.48660.00860.0950.5463-0.13671.012932.337716.2447236.9822
666.22842.38782.765.15676.302414.1636-0.04670.12380.692-0.08710.02920.1448-0.7878-0.34240.01750.54550.01270.02630.49190.06170.424728.467112.4388227.3215
6710.13653.7215-1.83066.28171.848628.8429-0.32-0.0623-0.21810.1279-0.1028-0.52330.54550.77480.42280.52250.00590.03610.44120.05340.457925.06729.0158219.1122
683.23931.65942.0015.7520.854913.5829-0.02460.13870.1291-0.33980.008-0.44030.37540.41930.01670.51030.01660.05550.45070.04030.441922.3725.6142210.493
690.51610.640.84568.9518-1.30635.9494-0.0393-0.06250.0137-0.3068-0.0749-0.2610.27090.14860.11430.4901-0.00480.05490.46050.04110.430317.26981.5057202.6529
7015.53154.963910.841830.64475.925513.9016-0.2687-0.97770.26970.748-0.04340.72040.5009-0.78860.31210.5135-0.00170.04620.44940.01430.437913.0412-2.3346196.2901
7155.0951-29.2-10.359619.58463.46032.9756-2.09413.28660.91271.52742.1775-0.31180.2268-2.5634-0.08340.34560.2550.023.89720.0490.77135.4646-4.7659191.7762
728.1267-7.3094-0.116120.836910.987811.79780.06130.4554-0.9610.9812-0.12170.29871.14950.01840.06040.6691-0.03810.10790.44570.07980.390921.8578-8.8415223.6817
7310.08312.28760.88917.68422.888212.04710.31320.393-0.73890.0851-0.3243-0.14481.0885-0.11810.01120.5823-0.01640.07230.4710.05180.396518.9518-3.1246231.6617
746.76610.0318-4.673115.42255.954812.6464-0.08890.2241-0.0389-0.1164-0.20870.96220.5585-0.95610.29760.5478-0.01720.04420.55240.06450.423717.71185.199241.4053
7510.3825-3.0428-5.672523.544111.6529.6722-0.17590.0225-0.23530.1915-0.29651.62370.7719-1.37090.47250.5242-0.0310.08910.48710.02580.450219.08849.0086250.1217
765.45462.80494.0362.07224.51313.0839-0.1450.07670.10580.0458-0.16850.10060.3569-0.1610.31350.5589-0.00480.05020.58780.03040.408422.174214.5118259.12
775.9535-4.862-1.26237.4097.00510.859-1.0402-0.36411.11210.9250.6796-0.61080.05720.8310.36050.7304-0.0571-0.13010.79880.12460.462926.430115.9251266.8419
781.2628-5.85183.255435.8143-1.726528.96530.06540.05610.06530.7618-0.0212-0.41651.76960.6636-0.04420.54140.0563-0.00420.99210.37470.504631.016311.2809262.2433
792.1225-0.5693-2.98430.16831.218519.2094-0.0767-0.0844-0.29670.06670.0290.09930.605-0.00410.04770.60870.0363-0.01640.54590.09640.4930.61069.4582251.9482
800.6670.27792.10973.22935.278313.14780.1735-0.0488-0.07550.0051-0.0078-0.21960.5485-0.0434-0.16570.56290.04040.04760.45260.05570.482528.65562.822235.4375
8119.2377-4.83252.56665.56863.311623.7297-0.1101-0.5827-0.37460.24740.2085-0.34590.26370.9611-0.09840.584-0.00370.05430.48110.03890.383527.7527-0.4089222.14
822.41561.3935-3.00072.9013-0.23344.9112-0.09730.1029-0.06090.12490.0401-0.3420.3597-0.23740.05730.59490.03240.10870.4923-0.01490.473625.171-3.2296214.4994
8315.3346-0.5299.264414.72736.815227.3589-0.2192-0.33050.10170.529-0.207-0.57640.42720.98640.42620.61570.03260.06390.4660.03870.431226.2291-5.4642206.5815
841.60010.63340.62182.8133.4399.7522-0.0487-0.02450.04390.09950.0658-0.15740.01820.2741-0.01710.5176-0.00160.05130.41930.03410.425121.2755-8.5451190.3865
852.20250.482-0.41860.2059-1.083110.7476-0.20680.0898-0.1285-0.07170.04420.01440.7202-0.53360.16260.5714-0.04840.10880.4537-0.0420.541317.6742-11.1449172.5213
8642.5453-2.7207-15.95650.30640.47238.28650.02090.2359-0.99950.0521-0.05230.1344-0.1652-0.03420.03140.65960.01010.040.4978-0.06140.506633.0139-14.6012160.8974
874.8937-3.0174-0.27041.9255-0.30693.7681-0.0898-0.26290.09250.03580.1148-0.09550.3680.4433-0.0250.53430.03110.01920.55030.02770.493749.5491-20.5766151.0636
8810.1187.37386.50215.91296.605510.76390.2269-0.2761-1.19510.6620.12-0.78751.73320.8305-0.34690.67320.3034-0.05260.58230.02260.450860.6082-30.4034137.8004
8913.38063.1832-1.47183.45746.571319.32710.10830.1186-0.14280.51290.0974-0.15581.2854-0.8929-0.20580.60240.0177-0.00830.82450.09020.573963.5447-33.719124.8978
9012.61052.7673-3.51052.7370.41744.5116-0.0198-0.2296-0.50380.2170.001-0.04380.56530.12270.01880.56360.0736-0.03080.41070.02050.502451.1723-41.9695118.966
9138.21-1.4206-10.64614.8632-8.966921.18991.17141.6269-3.1464-0.2628-0.86790.71830.09531.1094-0.30350.58130.11580.00620.2571-0.09621.098144.5395-48.6599115.7307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 68
2X-RAY DIFFRACTION2A69 - 147
3X-RAY DIFFRACTION3A148 - 171
4X-RAY DIFFRACTION4A172 - 216
5X-RAY DIFFRACTION5A217 - 313
6X-RAY DIFFRACTION6A314 - 346
7X-RAY DIFFRACTION7A347 - 381
8X-RAY DIFFRACTION8A382 - 442
9X-RAY DIFFRACTION9A443 - 521
10X-RAY DIFFRACTION10A522 - 571
11X-RAY DIFFRACTION11A578 - 617
12X-RAY DIFFRACTION12A618 - 738
13X-RAY DIFFRACTION13A739 - 799
14X-RAY DIFFRACTION14A800 - 873
15X-RAY DIFFRACTION15A874 - 878
16X-RAY DIFFRACTION16A879 - 921
17X-RAY DIFFRACTION17A922 - 981
18X-RAY DIFFRACTION18A982 - 1094
19X-RAY DIFFRACTION19A1095 - 1222
20X-RAY DIFFRACTION20A1223 - 1247
21X-RAY DIFFRACTION21B7 - 21
22X-RAY DIFFRACTION22B22 - 61
23X-RAY DIFFRACTION23B62 - 103
24X-RAY DIFFRACTION24B104 - 150
25X-RAY DIFFRACTION25B151 - 186
26X-RAY DIFFRACTION26B187 - 313
27X-RAY DIFFRACTION27B314 - 320
28X-RAY DIFFRACTION28B321 - 389
29X-RAY DIFFRACTION29B390 - 449
30X-RAY DIFFRACTION30B450 - 528
31X-RAY DIFFRACTION31B529 - 538
32X-RAY DIFFRACTION32B539 - 638
33X-RAY DIFFRACTION33B639 - 661
34X-RAY DIFFRACTION34B662 - 731
35X-RAY DIFFRACTION35B732 - 769
36X-RAY DIFFRACTION36B770 - 853
37X-RAY DIFFRACTION37B854 - 929
38X-RAY DIFFRACTION38B930 - 960
39X-RAY DIFFRACTION39B961 - 1017
40X-RAY DIFFRACTION40B1018 - 1121
41X-RAY DIFFRACTION41D21 - 27
42X-RAY DIFFRACTION42D28 - 39
43X-RAY DIFFRACTION43D40 - 49
44X-RAY DIFFRACTION44D50 - 59
45X-RAY DIFFRACTION45D60 - 70
46X-RAY DIFFRACTION46D71 - 75
47X-RAY DIFFRACTION47D76 - 86
48X-RAY DIFFRACTION48D87 - 91
49X-RAY DIFFRACTION49D92 - 100
50X-RAY DIFFRACTION50D101 - 113
51X-RAY DIFFRACTION51D114 - 131
52X-RAY DIFFRACTION52D132 - 145
53X-RAY DIFFRACTION53D146 - 160
54X-RAY DIFFRACTION54D161 - 176
55X-RAY DIFFRACTION55D177 - 183
56X-RAY DIFFRACTION56D184 - 221
57X-RAY DIFFRACTION57D222 - 228
58X-RAY DIFFRACTION58D229 - 234
59X-RAY DIFFRACTION59D235 - 250
60X-RAY DIFFRACTION60D251 - 264
61X-RAY DIFFRACTION61E10 - 13
62X-RAY DIFFRACTION62E14 - 18
63X-RAY DIFFRACTION63E19 - 22
64X-RAY DIFFRACTION64E23 - 28
65X-RAY DIFFRACTION65E29 - 34
66X-RAY DIFFRACTION66E35 - 42
67X-RAY DIFFRACTION67E43 - 47
68X-RAY DIFFRACTION68E48 - 54
69X-RAY DIFFRACTION69E55 - 61
70X-RAY DIFFRACTION70E62 - 66
71X-RAY DIFFRACTION71E67 - 73
72X-RAY DIFFRACTION72F0 - 8
73X-RAY DIFFRACTION73F9 - 16
74X-RAY DIFFRACTION74F17 - 24
75X-RAY DIFFRACTION75F25 - 29
76X-RAY DIFFRACTION76F30 - 37
77X-RAY DIFFRACTION77F38 - 44
78X-RAY DIFFRACTION78F45 - 49
79X-RAY DIFFRACTION79F50 - 58
80X-RAY DIFFRACTION80F59 - 72
81X-RAY DIFFRACTION81F73 - 77
82X-RAY DIFFRACTION82F78 - 83
83X-RAY DIFFRACTION83F84 - 89
84X-RAY DIFFRACTION84F90 - 104
85X-RAY DIFFRACTION85F105 - 114
86X-RAY DIFFRACTION86F115 - 120
87X-RAY DIFFRACTION87F121 - 130
88X-RAY DIFFRACTION88F131 - 135
89X-RAY DIFFRACTION89F136 - 139
90X-RAY DIFFRACTION90F140 - 149
91X-RAY DIFFRACTION91F150 - 155

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more