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- PDB-6uxo: Crystal structure of BAK core domain BH3-groove-dimer in complex ... -

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Basic information

Entry
Database: PDB / ID: 6uxo
TitleCrystal structure of BAK core domain BH3-groove-dimer in complex with DDM
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Pore-forming Protein
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / negative regulation of peptidyl-serine phosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / apoptotic signaling pathway / response to gamma radiation / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like ...Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
ACETATE ION / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.799 Å
AuthorsCowan, A.D. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1059290 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: BAK core dimers bind lipids and can be bridged by them.
Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / ...Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / Smith, B.J. / Reid, G.E. / Dewson, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
I: Bcl-2 homologous antagonist/killer
J: Bcl-2 homologous antagonist/killer
K: Bcl-2 homologous antagonist/killer
L: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,531102
Polymers114,00812
Non-polymers17,52390
Water5,873326
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A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,54118
Polymers19,0012
Non-polymers2,54016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-106 kcal/mol
Surface area10910 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,83715
Polymers19,0012
Non-polymers2,83613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-116 kcal/mol
Surface area9320 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,52820
Polymers19,0012
Non-polymers3,52718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-98 kcal/mol
Surface area10990 Å2
MethodPISA
4
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,96217
Polymers19,0012
Non-polymers2,96015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-116 kcal/mol
Surface area9870 Å2
MethodPISA
5
I: Bcl-2 homologous antagonist/killer
J: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,43818
Polymers19,0012
Non-polymers3,43716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-111 kcal/mol
Surface area11360 Å2
MethodPISA
6
K: Bcl-2 homologous antagonist/killer
L: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,22514
Polymers19,0012
Non-polymers2,22312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-90 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.941, 91.835, 95.716
Angle α, β, γ (deg.)90.000, 107.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 36 molecules ABCDEFGHIJKL

#1: Protein
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 9500.688 Da / Num. of mol.: 12 / Fragment: Core/dimerisation domain, residues 68-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q16611
#2: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 4 types, 392 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium sulfate, n-Dodecyl-b-D-maltoside, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.799→45.92 Å / Num. obs: 121101 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.833.62.9022038656760.21.7513.3960.595
9.85-45.923.30.01724297350.9990.0110.02151.593.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å39.45 Å
Translation1.8 Å39.45 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXM

6uxm


Resolution: 1.799→39.454 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2499 1993 1.65 %
Rwork0.2123 --
obs0.2129 120589 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.36 Å2 / Biso mean: 45.523 Å2 / Biso min: 17.16 Å2
Refinement stepCycle: final / Resolution: 1.799→39.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 1089 326 9054
Biso mean--75.96 47.96 -
Num. residues----955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.799-1.84360.36671300.3489774692
1.8436-1.89350.35741430.34038491100
1.8935-1.94920.36421440.33128485100
1.9492-2.01210.33371420.27978495100
2.0121-2.0840.28361430.25138513100
2.084-2.16740.25261420.22628481100
2.1674-2.26610.23451430.20988495100
2.2661-2.38550.24541430.20058511100
2.3855-2.5350.23451440.19868563100
2.535-2.73060.24961420.19418494100
2.7306-3.00530.2491440.20158571100
3.0053-3.440.25991430.19198526100
3.44-4.33320.21361450.18688589100
4.3332-39.4540.24311450.2157863699
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)
12.7808-0.54960.22353.80271.00812.9732-0.1034-0.2087-0.37670.32990.3327-0.34770.10890.3128-0.27050.26550.0240.01310.23730.00510.283234.769145.783543.8764
22.4782-0.9789-0.05172.68510.63277.1025-0.0191-0.31620.42150.04440.3333-0.7143-0.09250.2189-0.26530.22420.0656-0.06460.2768-0.10460.457740.933555.81747.587
38.1377-1.75013.53742.6142-0.833.6921-0.0390.18950.0339-0.10570.057-0.3307-0.23040.2552-0.02780.34390.0260.06550.27070.00260.292735.540550.41232.5896
42.7448-0.77892.27798.6667-3.47733.7657-0.246-0.0519-0.1007-0.0476-0.00680.037-0.11360.00620.20310.26360.0311-0.00590.1889-0.07120.237823.802253.09134.8019
54.52340.0031.14762.0563-0.41621.91410.2398-0.16520.13720.2297-0.07590.55490.1559-0.0597-0.10180.24360.00140.00930.3453-0.06760.217549.808733.450943.561
63.96850.91061.80862.83342.48289.71040.2671-0.3831-0.45160.2797-0.1717-0.16560.2893-0.2733-0.0510.1748-0.0471-0.03810.31340.02550.299455.199622.937448.0534
75.96672.0509-1.75083.7416-2.03292.88460.01310.6376-0.08790.0265-0.0431-0.07340.1190.15320.02030.28050.0122-0.04870.4134-0.06410.280853.574829.531732.7121
85.0941-1.6329-2.353.01861.37513.11260.05660.48740.551-0.0769-0.0801-0.2983-0.10380.0897-0.00370.1023-0.009-0.04450.37450.06090.227362.015538.321534.1573
95.0101-4.1721-4.00895.93375.09627.0516-0.20460.0260.15080.43310.2905-0.25040.37830.0343-0.14120.2832-0.05860.00080.29090.00420.320133.807125.767941.3574
101.88371.74311.33553.6611-0.22236.89040.0733-0.17050.08520.45130.03830.55980.0523-0.3539-0.09210.26750.00340.08360.18140.0070.268319.82527.055650.301
112.1742-0.3156-0.55275.21292.64482.2924-0.0720.29330.2798-0.41220.26890.3760.095-0.28980.11310.3161-0.0977-0.06780.22020.03780.185226.209525.134733.2333
123.65861.88583.47374.12961.94494.20810.03450.0819-0.2056-0.20180.02230.15790.3297-0.1709-0.08170.2754-0.0798-0.00710.22950.00780.245229.539713.599234.3919
133.9958-0.9107-0.13024.46951.35782.0720.26590.2325-0.034-0.1279-0.0921-0.5180.02820.1258-0.24590.2328-0.0101-0.0310.3490.03180.347515.489711.95511.4657
143.7536-0.16990.77931.6206-0.49254.29070.2530.178-0.7817-0.1629-0.06930.1512-0.08490.266-0.07210.11980.0577-0.07130.3042-0.06640.45379.85051.7836-2.7473
157.079-3.7767-2.88626.47953.05014.03560.0926-0.6614-0.35690.2619-0.0803-0.30710.11680.1256-0.01480.2321-0.0642-0.03660.36620.11960.347611.95988.106212.1683
166.4241.8537-3.13393.211-0.85054.30660.1722-0.2440.0010.2606-0.18330.2517-0.0519-0.34920.01380.1525-0.0398-0.03080.3464-0.00830.25923.559517.344310.8667
173.92360.3735-2.25274.2435-1.35324.8064-0.09770.12170.1181-0.47110.16820.1848-0.0071-0.2694-0.0940.21490.0019-0.05550.1938-0.02670.24833.54374.88461.7226
182.0034-1.2056-0.67013.75980.2827.6070.06230.02310.2185-0.3997-0.0724-0.36460.03160.00910.04470.23070.01470.0520.14030.00640.257345.39985.4776-2.416
192.36991.3144-1.04267.2622-1.8192.5288-0.0239-0.31530.06430.3564-0.0464-0.16350.02780.33390.00940.1980.0344-0.0290.2344-0.02870.193438.54943.648612.7982
203.6096-0.910.67215.6982-1.51924.6336-0.167-0.1885-0.24030.31210.09830.23920.21650.10530.02950.20810.06830.05510.1834-0.01430.176335.081-7.744610.9681
214.6291-0.38692.3743.5583-1.01654.18440.11260.4759-0.2207-0.09390.01320.31720.0178-0.1008-0.22330.2244-0.01360.03120.2457-0.03810.256230.496224.55761.6913
224.00922.0524-0.98714.591-0.08947.9734-0.11720.19760.2320.02190.1910.2978-0.005-0.0078-0.04420.1201-0.0451-0.00690.18450.02530.28424.338234.3386-2.6566
233.51521.75570.87092.49130.53881.49550.09310.09120.07770.4658-0.17760.2599-0.1044-0.09490.03880.2532-0.0640.05040.228-0.04570.199828.855229.424212.6005
243.95922.94172.11098.62733.72078.5128-0.13750.1624-0.04310.21360.1965-0.2912-0.10920.5771-0.04760.1544-0.0345-0.01360.2041-0.00290.224546.069529.07218.187
252.15462.01671.93849.57076.90478.5790.1678-0.4070.1230.5539-0.3221-0.1239-0.0885-0.57870.09980.2715-0.031-0.00770.24970.00850.247136.763635.145914.2872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 106 )A68 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 147 )A107 - 147
3X-RAY DIFFRACTION3chain 'B' and (resid 69 through 106 )B69 - 106
4X-RAY DIFFRACTION4chain 'B' and (resid 107 through 146 )B107 - 146
5X-RAY DIFFRACTION5chain 'C' and (resid 67 through 106 )C67 - 106
6X-RAY DIFFRACTION6chain 'C' and (resid 107 through 147 )C107 - 147
7X-RAY DIFFRACTION7chain 'D' and (resid 69 through 106 )D69 - 106
8X-RAY DIFFRACTION8chain 'D' and (resid 107 through 147 )D107 - 147
9X-RAY DIFFRACTION9chain 'E' and (resid 68 through 100 )E68 - 100
10X-RAY DIFFRACTION10chain 'E' and (resid 101 through 147 )E101 - 147
11X-RAY DIFFRACTION11chain 'F' and (resid 69 through 106 )F69 - 106
12X-RAY DIFFRACTION12chain 'F' and (resid 107 through 147 )F107 - 147
13X-RAY DIFFRACTION13chain 'G' and (resid 67 through 106 )G67 - 106
14X-RAY DIFFRACTION14chain 'G' and (resid 107 through 147 )G107 - 147
15X-RAY DIFFRACTION15chain 'H' and (resid 69 through 106 )H69 - 106
16X-RAY DIFFRACTION16chain 'H' and (resid 107 through 146 )H107 - 146
17X-RAY DIFFRACTION17chain 'I' and (resid 67 through 106 )I67 - 106
18X-RAY DIFFRACTION18chain 'I' and (resid 107 through 147 )I107 - 147
19X-RAY DIFFRACTION19chain 'J' and (resid 69 through 106 )J69 - 106
20X-RAY DIFFRACTION20chain 'J' and (resid 107 through 146 )J107 - 146
21X-RAY DIFFRACTION21chain 'K' and (resid 69 through 106 )K69 - 106
22X-RAY DIFFRACTION22chain 'K' and (resid 107 through 147 )K107 - 147
23X-RAY DIFFRACTION23chain 'L' and (resid 68 through 106 )L68 - 106
24X-RAY DIFFRACTION24chain 'L' and (resid 107 through 124 )L107 - 124
25X-RAY DIFFRACTION25chain 'L' and (resid 125 through 148 )L125 - 148

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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

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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

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