[English] 日本語
Yorodumi
- PDB-2iae: Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iae
TitleCrystal structure of a protein phosphatase 2A (PP2A) holoenzyme.
Components
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
  • Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
  • microcystin-LR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein phosphorylation / phosphatase / PP2A / B56 / tumor suppressor / methylation / HYDROLASE / TOXIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / meiotic spindle elongation / RAF activation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin D associated events in G1 / regulation of microtubule binding / PKR-mediated signaling / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / Degradation of beta-catenin by the destruction complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / DARPP-32 events / peptidyl-serine dephosphorylation / RHO GTPases Activate Formins / peptidyl-threonine dephosphorylation / Separation of Sister Chromatids / positive regulation of microtubule binding / Platelet sensitization by LDL / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / ERK/MAPK targets / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / female meiotic nuclear division / protein antigen binding / AURKA Activation by TPX2 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase regulator activity / GABA receptor binding / Regulation of PLK1 Activity at G2/M Transition / negative regulation of epithelial to mesenchymal transition / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / protein phosphatase activator activity / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / mesoderm development / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / meiotic cell cycle / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / regulation of protein phosphorylation / Spry regulation of FGF signaling / RAF activation
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / HEAT repeat / HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / : / HEAT repeat / HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Microcystin LR / : / : / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsCho, U.S. / Xu, W.
CitationJournal: Nature / Year: 2007
Title: Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme.
Authors: Cho, U.S. / Xu, W.
History
DepositionSep 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
M: microcystin-LR
N: microcystin-LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,70512
Polymers300,4858
Non-polymers2204
Water0
1
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
M: microcystin-LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3536
Polymers150,2434
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
N: microcystin-LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3536
Polymers150,2434
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)265.301, 265.301, 265.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a heterotrimer from one A subunit, one B subunit, and one C subunit. There are two heterotrimers in one asymmetric unit. each heterotrimer has one microcystin-LR, PP2A inhibitor.

-
Components

#1: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / PP2A / subunit A / PR65-alpha isoform / PP2A / subunit A / R1-alpha isoform


Mass: 65392.367 Da / Num. of mol.: 2 / Fragment: Aalpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp2r1a / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star
References: UniProt: Q76MZ3, protein-serine/threonine phosphatase
#2: Protein Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / PP2A / B subunit / B' gamma isoform / PP2A / B subunit / B56 gamma isoform / PP2A / B subunit / ...PP2A / B subunit / B' gamma isoform / PP2A / B subunit / B56 gamma isoform / PP2A / B subunit / PR61 gamma isoform / PP2A / B subunit / R5 gamma isoform / NY-REN-29 antigen


Mass: 48186.934 Da / Num. of mol.: 2 / Fragment: B56gamma1 subunit, residues 30-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star
References: UniProt: Q13362, protein-serine/threonine phosphatase
#3: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35649.195 Da / Num. of mol.: 2 / Fragment: Calpha subunit / Mutation: D88N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P67775, protein-serine/threonine phosphatase
#4: Protein/peptide microcystin-LR / / Microcystin-LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.19 Å3/Da / Density % sol: 76.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MES, pH 7.0, 50mM NaCl, 1.4M ammonium sulfate, 0.2M LiCl, 2% 1,6-diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2006
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 8.5 % / Av σ(I) over netI: 5.9 / Number: 554144 / Rmerge(I) obs: 0.161 / Χ2: 1.4 / D res high: 3.7 Å / D res low: 50 Å / Num. obs: 65390 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.96509610.0533.0778.5
6.327.9697.710.1171.8518.6
5.536.3298.410.1871.3038.7
5.025.5398.710.2121.2048.7
4.665.0299.110.2171.1688.7
4.394.6699.310.2561.1348.7
4.174.3999.510.3331.0928.7
3.994.1799.610.4951.0468.7
3.833.9999.810.681.0158.5
3.73.8399.610.9161.0017.1
ReflectionResolution: 3.5→50 Å / Num. obs: 76332 / % possible obs: 97.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.5-3.634.10.905198.1
3.63-3.774.30.614198.5
3.77-3.944.40.438198.9
3.94-4.154.40.297198.9
4.15-4.414.40.185198.7
4.41-4.754.40.137197.9
4.75-5.234.40.118198
5.23-5.984.40.115196.8
5.98-7.534.40.094196.1
7.53-504.40.046193

-
Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 76221
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
18.19-10078.20.643518
13.13-18.1966.20.816886
10.8-13.1365.40.8581140
9.38-10.866.10.8811318
8.41-9.38650.8921529
7.69-8.4163.30.8751679
7.13-7.6965.30.8551835
6.67-7.1367.30.851946
6.29-6.6767.20.8432076
5.97-6.2968.40.8522227
5.7-5.9771.70.8542311
5.46-5.772.20.8612456
5.24-5.4671.50.8692529
5.05-5.24750.8762674
4.88-5.0576.20.8832731
4.73-4.8877.10.8882871
4.59-4.7379.70.9012937
4.46-4.5986.10.8943007
4.34-4.4690.70.8963108
4.23-4.3491.20.9023203
4.13-4.2390.40.9023288
4.04-4.1389.60.9013294
3.95-4.0491.20.9013486
3.87-3.9588.70.9043516
3.79-3.87900.9073599
3.71-3.7989.20.9073603
3.65-3.7188.70.9083751
3.58-3.6589.70.8923761
3.5-3.5890.60.7754942

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.854 / SU B: 59.364 / SU ML: 0.455 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31552 3832 5.1 %RANDOM
Rwork0.25681 ---
obs0.2598 72008 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.538 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19951 0 4 0 19955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02220389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.381.97127690
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26952511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35124.376914
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.445153435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.51315114
X-RAY DIFFRACTIONr_chiral_restr0.10.23190
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215326
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.211543
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.214144
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2719
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3631.512916
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.671220428
X-RAY DIFFRACTIONr_scbond_it0.76538308
X-RAY DIFFRACTIONr_scangle_it1.3564.57262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 253 -
Rwork0.278 5195 -
obs--97.92 %
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)
11.7024-0.7702-0.0611.4094-0.19570.21010.07320.4694-0.4192-0.6148-0.17860.53730.0092-0.17730.10540.05290.0904-0.22810.1069-0.269-0.3051118.0312220.992698.3446
20.89-0.1591-0.37091.26060.44581.8055-0.2379-0.1023-0.50660.12250.00410.26320.0921-0.38550.2338-0.5581-0.1220.2423-0.6365-0.005-0.2814166.6063168.5954107.2622
33.7098-0.0788-0.29961.7602-0.24023.266-0.07450.3330.054-0.32040.03910.0380.0248-0.14420.0354-0.06670.2689-0.2171-0.1745-0.1242-0.1876114.428249.235116.203
45.46330.6814-0.07194.1511-0.50676.0579-0.0386-0.1262-0.47620.3322-0.1080.01710.42330.04980.1467-1.0146-0.04770.2552-1.5077-0.3204-1.2523194.8149165.295786.1918
52.9339-1.8352-0.10223.48230.22170.85550.1333-0.06020.28180.0602-0.0688-0.3129-0.01340.2509-0.06440.0643-0.06440.13240.0599-0.0421-0.1589195.4888194.3911116.4937
61.47180.1804-0.20165.4423-1.63282.0073-0.177-0.15610.2922-0.18480.1289-0.2331-0.1295-0.15220.0481-0.05080.12950.0906-0.2863-0.0521-0.2816148.4674227.0913122.9527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 5897 - 589
2X-RAY DIFFRACTION2DD7 - 5897 - 589
3X-RAY DIFFRACTION3CC4 - 3094 - 309
4X-RAY DIFFRACTION4FF4 - 2944 - 294
5X-RAY DIFFRACTION5EE30 - 4061 - 377
6X-RAY DIFFRACTION6BB31 - 4062 - 377

+
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