[English] 日本語
Yorodumi
- PDB-7ry1: human Hsp90_MC domain structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ry1
Titlehuman Hsp90_MC domain structure
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / Hsp90 / hexamer
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / chaperone-mediated autophagy / sperm plasma membrane ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / chaperone-mediated autophagy / sperm plasma membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Uptake and function of diphtheria toxin / protein import into mitochondrial matrix / TPR domain binding / dendritic growth cone / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / protein folding chaperone complex / enzyme-substrate adaptor activity / response to unfolded protein / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / RHOBTB2 GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / axonal growth cone / telomere maintenance via telomerase / skeletal muscle contraction / positive regulation of lamellipodium assembly / nitric oxide metabolic process / positive regulation of defense response to virus by host / response to salt stress / eNOS activation / positive regulation of telomere maintenance via telomerase / DNA polymerase binding / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / cardiac muscle cell apoptotic process / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / lysosomal lumen / activation of innate immune response / ESR-mediated signaling / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / response to cold / AURKA Activation by TPX2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of protein import into nucleus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / response to estrogen / Regulation of necroptotic cell death / VEGFA-VEGFR2 Pathway / extracellular matrix / tau protein binding / Downregulation of ERBB2 signaling / neuron migration / histone deacetylase binding / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Aggrephagy
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-MDC / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.523 Å
AuthorsPeng, S. / Deng, J. / Matts, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA219907-01 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystal structure of the middle and C-terminal domains of Hsp90 alpha labeled with a coumarin derivative reveals a potential allosteric binding site as a drug target.
Authors: Peng, S. / Woodruff, J. / Pathak, P.K. / Matts, R.L. / Deng, J.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1876
Polymers149,0363
Non-polymers1,1503
Water00
1
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1244
Polymers99,3582
Non-polymers7672
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-26 kcal/mol
Surface area42350 Å2
MethodPISA
2
C: Heat shock protein HSP 90-alpha
hetero molecules

C: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1244
Polymers99,3582
Non-polymers7672
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5440 Å2
ΔGint-29 kcal/mol
Surface area43280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.850, 311.964, 88.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 293 or resseq 295:296 or (resid...
21(chain B and (resseq 293 or resseq 295:296 or (resid...
31(chain C and (resseq 293 or resseq 295:296 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and (resseq 293 or resseq 295:296 or (resid...AA2934
12PROPROILEILE(chain A and (resseq 293 or resseq 295:296 or (resid...AA295 - 2966 - 7
13TRPTRPTRPTRP(chain A and (resseq 293 or resseq 295:296 or (resid...AA2978
14THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
15THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
16THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
17THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
18THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
19THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
110THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
21THRTHRTHRTHR(chain B and (resseq 293 or resseq 295:296 or (resid...BB2934
22PROPROILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB295 - 2966 - 7
23TRPTRPTRPTRP(chain B and (resseq 293 or resseq 295:296 or (resid...BB2978
24THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
25THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
26THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
27THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
28THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
29THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
210THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
31THRTHRTHRTHR(chain C and (resseq 293 or resseq 295:296 or (resid...CC2934
32PROPROILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC295 - 2966 - 7
33TRPTRPTRPTRP(chain C and (resseq 293 or resseq 295:296 or (resid...CC2978
34THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
35THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
36THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
37THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
38THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
39THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
310THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409

-
Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS- ...Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 49678.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli)
References: UniProt: P07900, non-chaperonin molecular chaperone ATPase
#2: Chemical ChemComp-MDC / N-[2-(1-MALEIMIDYL)ETHYL]-7-DIETHYLAMINOCOUMARIN-3-CARBOXAMIDE


Mass: 383.398 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H21N3O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Succinic acid PH 6.5, 12% PEG3350, 20mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 27438 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 127.52 Å2 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.063 / Rrim(I) all: 0.161 / Χ2: 0.688 / Net I/σ(I): 3.9 / Num. measured all: 176259
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.636.41.36627080.5360.5811.4870.466100
3.63-3.776.30.84426860.7090.3620.920.484100
3.77-3.946.10.64527160.8120.2830.7060.511100
3.94-4.156.30.44527090.9220.1920.4850.55799.9
4.15-4.416.70.29127220.9550.1210.3160.647100
4.41-4.756.60.22427210.9780.0930.2430.695100
4.75-5.236.30.18127260.9830.0780.1980.77499.9
5.23-5.986.80.17727590.9870.0730.1920.716100
5.98-7.536.60.11627890.9940.0480.1250.757100
7.53-506.10.05529020.9980.0230.061.24699.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6M

3q6m


Resolution: 3.523→47.421 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 1995 7.28 %
Rwork0.2164 25399 -
obs0.2204 27394 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 319.62 Å2 / Biso mean: 141.4972 Å2 / Biso min: 72.89 Å2
Refinement stepCycle: final / Resolution: 3.523→47.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9949 0 84 0 10033
Biso mean--180.8 --
Num. residues----1207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410205
X-RAY DIFFRACTIONf_angle_d0.80613701
X-RAY DIFFRACTIONf_chiral_restr0.0471504
X-RAY DIFFRACTIONf_plane_restr0.0041743
X-RAY DIFFRACTIONf_dihedral_angle_d14.8996323
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5296X-RAY DIFFRACTION8.528TORSIONAL
12B5296X-RAY DIFFRACTION8.528TORSIONAL
13C5296X-RAY DIFFRACTION8.528TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.523-3.61080.38911180.3429149884
3.6108-3.70840.34111430.32621819100
3.7084-3.81740.33861440.30981829100
3.8174-3.94060.33221400.30291784100
3.9406-4.08140.32841420.29561816100
4.0814-4.24470.32931420.26141812100
4.2447-4.43770.29251450.24211828100
4.4377-4.67150.25231440.23511835100
4.6715-4.96390.28681420.22511815100
4.9639-5.34670.25791450.20321826100
5.3467-5.88380.25951460.21851861100
5.8838-6.73320.29031460.21851857100
6.7332-8.47520.26081470.18991861100
8.4752-47.420.21211510.142195899
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)
18.24581.44432.90412.4932-1.97439.3351-0.17321.55980.3043-3.2550.0777-0.55160.157-0.5309-0.0051.56740.1301-0.04281.39090.20071.12-11.4122-39.2473-7.6209
28.57382.31292.02352.44553.73839.7126-0.57340.5710.3546-2.14970.4276-0.5722-0.6730.27420.28241.0334-0.05460.14581.10140.13451.0015-16.6525-37.7801-0.537
39.24252.7445-1.98654.60513.8759.43210.5341-1.8296-0.39152.1534-0.79740.18551.95431.16170.26841.67830.1032-0.12581.11910.0421.2189-11.8231-43.441710.5408
46.17774.2925-1.87048.8379-0.33747.59780.7244-0.98041.18160.9001-0.48390.31730.10380.3436-0.1991.2537-0.0213-0.14831.0595-0.12350.9407-18.0828-33.685410.1674
59.39742.7957-2.7075.9321-0.58126.2202-0.22860.56090.0296-0.26420.08840.6558-0.2104-1.53510.18091.11720.0567-0.07741.4284-0.00181.0704-42.2292-51.63077.8703
62.4317-0.7195-2.05246.6608-0.44613.0531-0.0379-1.26880.57720.14640.66641.2331-0.8737-1.5379-0.47621.43390.39010.10322.07720.24921.3088-48.6351-49.209917.2611
76.55121.70775.98466.9501-0.18885.9011-1.5487-3.74771.1165-1.53980.23692.41430.308-0.31531.29321.49530.16450.71233.54210.74522.212-66.3199-62.335528.6932
88.4913.2317-0.18975.8115-4.07862.9536-0.351-1.3552-0.2905-0.61520.4654-0.53560.4285-1.0438-0.07951.2823-0.00660.11081.76820.36131.5282-47.8834-62.11326.3735
90.2219-1.170.90276.1623-2.47749.0856-0.4576-0.571-0.30980.51911.1933-0.2432-0.0665-1.3414-0.95331.5689-0.21340.03552.20910.25691.4388-53.4395-68.980629.486
104.4302-1.40541.13482.2934-1.03247.80991.00010.0467-0.33220.36380.36840.53491.5541-0.8609-1.31221.4086-0.2943-0.10611.68810.43451.813-50.9043-79.845728.0664
117.535.08450.49535.16090.27453.25410.124-1.53370.23571.486-0.3571-0.7420.19310.20160.22551.31420.0624-0.1591.09480.05391.05663.9861-66.799148.5569
124.19510.8976-2.64439.4813.58858.50320.1740.89180.2609-1.3578-0.2618-0.0385-1.6243-0.65080.07721.40950.08540.01620.89840.06711.21912.0828-62.952435.5788
135.6002-0.61623.71128.85381.19765.4095-0.36810.5286-0.306-0.30810.5801-0.9717-0.24870.1891-0.08881.0108-0.00630.03221-0.01310.85575.6948-72.83634.3449
148.07543.14762.66489.31720.78135.80680.3088-0.5091-0.99730.68120.20750.43611.4113-1.3436-0.4561.2921-0.2830.04791.18370.24461.1675-21.2165-85.52337.318
156.0433-0.52483.32333.98640.19024.53070.23370.778-1.592-1.27580.19620.52692.3882-0.5235-0.32972.1863-0.58290.00681.5395-0.12481.6008-31.7964-95.637421.7012
163.468-3.37251.32223.7205-2.17516.5053-0.08550.90570.8317-0.9097-0.4939-1.69760.06570.24640.58921.5667-0.3398-0.21781.77920.34041.9524-27.898-80.434619.2727
176.3831-4.83441.04325.70933.18697.7856-0.24810.0463-0.5981-1.1031-0.5219-1.19190.9129-1.38330.9881.5171-0.3852-0.33421.7173-0.07121.3122-33.5798-82.410817.1537
186.2041-6.56620.83817.14650.22845.10820.19460.9604-0.7411-0.72330.0630.96450.6467-0.7906-0.17231.5018-0.7659-0.20792.14980.19511.5464-50.3907-85.744815.9042
198.9833-0.9231.80216.1737-1.26753.991-0.1657-1.3802-0.74031.3389-0.018-0.09590.2207-0.4890.41481.44210.15690.15291.18350.00631.1103-15.1872-44.157649.1903
208.088-2.28164.66539.09162.18438.4915-0.09521.2938-0.9566-1.03290.4111-0.46330.22351.00250.0441.2410.05630.10791.1243-0.1321.2004-14.1867-45.016833.67
219.49122.85690.43853.4608-0.02983.1149-0.56680.47580.0912-0.0996-0.06191.96670.1603-0.3120.60211.4358-0.0227-0.11920.9350.02981.0224-24.9274-38.786937.8057
224.77250.10020.958510.0721-3.72553.8757-0.3574-0.23730.34130.32720.03340.1251-0.5473-0.19640.37631.140.124-0.15970.9112-0.1711.0599-18.9096-13.623136.9987
232.973-0.4636-1.71146.8311-1.31552.08340.2370.61971.2617-0.0210.07791.5732-0.9783-0.8906-0.08361.64190.3087-0.59971.5508-0.13152.0272-26.32143.720923.4961
246.8750.4441-0.73468.7199-0.6265.0416-0.30890.60310.3736-0.9663-0.47061.1132-0.5238-0.91370.51451.50670.0562-0.11841.05550.13531.5705-17.04890.897118.4434
254.52742.8375-1.01453.83622.45025.8061-0.8130.4383-0.6157-0.3185-0.11290.36960.27130.67731.20871.9551-0.1053-0.11461.21690.07381.4211-10.0349-8.762117.3676
266.95613.0648-3.25352.34150.26066.91430.63450.49671.5869-0.3222-0.0738-0.1513-1.2781-0.1727-0.48312.37720.0879-0.38961.05640.00652.0749-4.980411.819415.9325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 317 )A293 - 317
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 343 )A318 - 343
3X-RAY DIFFRACTION3chain 'A' and (resid 344 through 377 )A344 - 377
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 429 )A378 - 429
5X-RAY DIFFRACTION5chain 'A' and (resid 430 through 523 )A430 - 523
6X-RAY DIFFRACTION6chain 'A' and (resid 524 through 556 )A524 - 556
7X-RAY DIFFRACTION7chain 'A' and (resid 557 through 578 )A557 - 578
8X-RAY DIFFRACTION8chain 'A' and (resid 579 through 617 )A579 - 617
9X-RAY DIFFRACTION9chain 'A' and (resid 618 through 656 )A618 - 656
10X-RAY DIFFRACTION10chain 'A' and (resid 657 through 699 )A657 - 699
11X-RAY DIFFRACTION11chain 'B' and (resid 293 through 343 )B293 - 343
12X-RAY DIFFRACTION12chain 'B' and (resid 344 through 377 )B344 - 377
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 429 )B378 - 429
14X-RAY DIFFRACTION14chain 'B' and (resid 430 through 523 )B430 - 523
15X-RAY DIFFRACTION15chain 'B' and (resid 524 through 596 )B524 - 596
16X-RAY DIFFRACTION16chain 'B' and (resid 597 through 618 )B597 - 618
17X-RAY DIFFRACTION17chain 'B' and (resid 619 through 640 )B619 - 640
18X-RAY DIFFRACTION18chain 'B' and (resid 641 through 698 )B641 - 698
19X-RAY DIFFRACTION19chain 'C' and (resid 293 through 343 )C293 - 343
20X-RAY DIFFRACTION20chain 'C' and (resid 344 through 402 )C344 - 402
21X-RAY DIFFRACTION21chain 'C' and (resid 403 through 429 )C403 - 429
22X-RAY DIFFRACTION22chain 'C' and (resid 430 through 532 )C430 - 532
23X-RAY DIFFRACTION23chain 'C' and (resid 533 through 578 )C533 - 578
24X-RAY DIFFRACTION24chain 'C' and (resid 579 through 607 )C579 - 607
25X-RAY DIFFRACTION25chain 'C' and (resid 608 through 640 )C608 - 640
26X-RAY DIFFRACTION26chain 'C' and (resid 641 through 698 )C641 - 698

+
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