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- PDB-7rxz: human Hsp90_MC domain structure -

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Basic information

Entry
Database: PDB / ID: 7rxz
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 / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / dATP binding / sperm plasma membrane / chaperone-mediated autophagy / mitochondrial transport / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / 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 / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / protein folding chaperone complex / response to unfolded protein / regulation of protein-containing complex assembly / Attenuation phase / enzyme-substrate adaptor activity / HSF1 activation / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / axonal growth cone / RHOBTB2 GTPase cycle / telomere maintenance via telomerase / regulation of postsynaptic membrane neurotransmitter receptor levels / nitric oxide metabolic process / positive regulation of lamellipodium assembly / skeletal muscle contraction / positive regulation of defense response to virus by host / Signaling by ERBB2 / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of telomere maintenance via telomerase / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / DNA polymerase binding / 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 / lysosomal lumen / Anchoring of the basal body to the plasma membrane / ESR-mediated signaling / activation of innate immune response / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / protein tyrosine kinase binding / response to cold / Constitutive Signaling by Overexpressed ERBB2 / 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 / cellular response to virus / positive regulation of protein import into nucleus / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to estrogen / VEGFA-VEGFR2 Pathway / Regulation of necroptotic cell death / tau protein binding / neuron migration / histone deacetylase binding / Downregulation of ERBB2 signaling / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Aggrephagy / positive regulation of protein catabolic process
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-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.152 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: J.Biomol.Struct.Dyn. / Year: 2022
Title: Structural basis of the key residue W320 responsible for Hsp90 conformational change.
Authors: Peng, S. / Matts, R.L. / Deng, J.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
D: Heat shock protein HSP 90-alpha
E: Heat shock protein HSP 90-alpha
F: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)298,0736
Polymers298,0736
Non-polymers00
Water00
1
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)99,3582
Polymers99,3582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-27 kcal/mol
Surface area40390 Å2
MethodPISA
2
C: Heat shock protein HSP 90-alpha
D: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)99,3582
Polymers99,3582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-29 kcal/mol
Surface area39620 Å2
MethodPISA
3
E: Heat shock protein HSP 90-alpha
F: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)99,3582
Polymers99,3582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-29 kcal/mol
Surface area40070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.830, 87.987, 166.178
Angle α, β, γ (deg.)90.000, 114.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and ((resid 293 and (name O or name...
21(chain B and ((resid 293 and (name O or name...
31(chain C and ((resid 293 and (name O or name...
41(chain D and ((resid 293 and (name N or name...
51(chain E and ((resid 293 and (name O or name...
61(chain F and ((resid 293 and (name N or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR(chain A and ((resid 293 and (name O or name...AA2934
12ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
13ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
14ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
15ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
16ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
21THRTHR(chain B and ((resid 293 and (name O or name...BB2934
22ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
23ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
24ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
25ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
26ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
31THRTHR(chain C and ((resid 293 and (name O or name...CC2934
32ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
33ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
34ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
35ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
36ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
41THRTHR(chain D and ((resid 293 and (name N or name...DD2934
42ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
43ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
44ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
45ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
46ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
51THRTHR(chain E and ((resid 293 and (name O or name...EE2934
52ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
53ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
54ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
55ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
56ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
61THRTHR(chain F and ((resid 293 and (name N or name...FF2934
62ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
63ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
64ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
65ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
66ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409

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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.: 6
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

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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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaAc PH 6.0, 12 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 70092 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 76.89 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.086 / Rrim(I) all: 0.158 / Χ2: 1.625 / Net I/σ(I): 8.4 / Num. measured all: 231203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.263.20.81169370.620.5310.9731.32499.7
3.26-3.393.20.62569740.7320.4090.751.42799.8
3.39-3.553.20.4269620.8560.2750.5041.66199.4
3.55-3.733.20.30569090.9110.1990.3661.74699.5
3.73-3.973.20.22570030.9470.1470.2691.85899.7
3.97-4.273.30.14969880.9730.0960.1771.74799.8
4.27-4.73.30.11470160.9820.0730.1361.72199.8
4.7-5.383.40.09970400.9850.0630.1171.679100
5.38-6.783.60.09670770.9860.0590.1131.456100
6.78-503.40.07371860.9850.0490.0881.64199.2

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Processing

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

3q6m


Resolution: 3.152→48.09 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1848 2.86 %
Rwork0.1911 62701 -
obs0.1927 64549 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.87 Å2 / Biso mean: 88.8291 Å2 / Biso min: 40.24 Å2
Refinement stepCycle: final / Resolution: 3.152→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19425 0 0 0 19425
Num. residues----2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01219744
X-RAY DIFFRACTIONf_angle_d1.40526515
X-RAY DIFFRACTIONf_chiral_restr0.0732946
X-RAY DIFFRACTIONf_plane_restr0.0083370
X-RAY DIFFRACTIONf_dihedral_angle_d13.11412291
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8708X-RAY DIFFRACTION12.152TORSIONAL
12B8708X-RAY DIFFRACTION12.152TORSIONAL
13C8708X-RAY DIFFRACTION12.152TORSIONAL
14D8708X-RAY DIFFRACTION12.152TORSIONAL
15E8708X-RAY DIFFRACTION12.152TORSIONAL
16F8708X-RAY DIFFRACTION12.152TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.152-3.2370.37361120.3259407578
3.237-3.33220.32491330.3043425482
3.3322-3.43970.4191410.2978431683
3.4397-3.56260.30731290.2617459088
3.5626-3.70520.3261380.256471790
3.7052-3.87380.31361450.2317474391
3.8738-4.07790.28161340.2103487993
4.0779-4.33320.24551470.1763505596
4.3332-4.66750.2281480.1579507497
4.6675-5.13680.18581510.1525514498
5.1368-5.87890.24541510.1688523799
5.8789-7.40250.24371630.1786525199
7.4025-48.090.17041560.1421536699
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)
16.4464-0.9146-0.30124.89571.99016.12680.13010.6938-0.0448-0.2553-0.10090.0136-0.4434-0.1868-0.15090.4783-0.07920.05840.5593-0.00010.466544.252423.1929139.4531
21.1579-1.35190.56184.91380.72470.81260.3167-0.30370.8407-0.3353-0.4074-0.85140.1989-0.54970.13980.71120.0885-0.00160.6572-0.04470.750532.515835.9968141.4844
34.95971.16733.41920.72960.28912.98050.1791-0.386-0.08270.6389-0.1818-0.20190.0865-0.23650.02040.7425-0.1147-0.02750.5474-0.02260.642462.938931.4761158.1157
43.9660.928-1.03992.5688-0.4273.80860.1308-0.44320.40640.4502-0.06640.34170.03170.0309-0.03950.69720.0086-0.16470.4519-0.07820.710785.595450.9232163.4777
54.527-0.79151.22032.984-0.22494.05480.0590.16260.12470.17680.0153-0.03870.2879-0.113-0.06350.61780.0427-0.04290.51870.11870.51963.57163.4968112.6753
63.2464-1.28892.42461.5716-1.37693.68230.04940.27310.1976-0.124-0.2524-0.2120.13450.17380.17830.5680.096-0.10660.60220.00560.712196.254347.457135.107
75.3058-0.3236-1.20965.01080.70343.5044-0.1948-0.0889-0.13940.34560.2262-0.11770.23530.501-0.01590.620.0336-0.01370.6067-0.00310.435934.242921.2762112.7267
83.78550.9591-2.47624.3668-2.8266.1368-0.02160.19780.40020.42070.0511-0.061-0.41710.3401-0.05810.80970.062-0.12320.5385-0.04930.577229.912533.1097108.0682
93.9816-1.5452-1.66521.2551.00792.7847-0.1490.2021-0.40290.1154-0.14960.57880.3689-0.26790.34170.66450.05560.15750.524-0.09080.87735.919729.7781124.6403
102.1021-1.6722-1.36571.390.79192.03810.1750.4817-0.2102-0.4521-0.34010.2223-0.3546-0.43710.2060.66510.13510.02190.7677-0.060.8714-6.713843.1084129.5983
111.9439-0.51081.22462.10930.17433.6686-0.2430.11620.09450.00150.07040.0093-0.03560.23680.15740.54190.07410.13930.5273-0.03820.6589-2.540449.5742144.0319
124.34240.3224-2.54885.1766-0.95544.8941-0.02230.73350.3928-0.00610.068-0.0412-0.18560.2517-0.08390.4705-0.0644-0.08580.61990.02670.4750.031869.5242139.2372
133.094-2.9106-1.82422.93611.79991.07670.02490.4068-0.31520.11610.04480.21220.69320.00320.22240.8528-0.0916-0.10840.6186-0.02170.642555.210354.8857141.5426
144.31042.1352-2.59930.5679-0.92021.40120.2906-0.47110.11840.6672-0.22740.1147-0.38480.0866-0.05110.7954-0.10480.13090.54630.04210.656530.809758.8676158.3263
153.2018-0.18450.59213.0334-0.0082.95060.174-0.1609-0.22170.5133-0.03940.010.02680.0333-0.13460.5534-0.01090.17560.58360.09830.70447.4739.5681164.1466
162.03740.6340.77962.15070.74836.0355-0.2518-0.2713-0.1164-0.1406-0.0050.01810.20440.17830.34630.48430.1113-0.03830.56760.10250.598864.826726.9569117.4465
171.84170.5927-0.033.9334-3.18696.7398-0.03270.4394-0.1515-0.82-0.2064-0.39260.4320.46970.21320.76480.11840.04380.580.03030.54867.520332.675185.8353
184.5562-1.0284-0.63973.4887-0.92913.8243-0.0854-0.09050.2627-0.04610.0371-0.1386-0.19480.12170.00340.91130.0019-0.09290.6380.04930.494557.40550.246668.2828
192.92751.4019-0.09563.6479-0.59316.5657-0.1947-0.55510.12410.0047-0.20310.32560.07750.05430.37560.34120.09530.01650.6073-0.08720.612229.000663.0865118.0242
201.2918-0.7016-0.99331.47111.94774.8202-0.0480.2274-0.0282-0.383-0.25190.40980.0235-0.45740.37120.8146-0.0462-0.13530.5357-0.02170.591529.549248.378277.2295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 385 )A293 - 385
2X-RAY DIFFRACTION2chain 'A' and (resid 386 through 407 )A386 - 407
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 543 )A408 - 543
4X-RAY DIFFRACTION4chain 'A' and (resid 544 through 698 )A544 - 698
5X-RAY DIFFRACTION5chain 'B' and (resid 293 through 451 )B293 - 451
6X-RAY DIFFRACTION6chain 'B' and (resid 452 through 698 )B452 - 698
7X-RAY DIFFRACTION7chain 'C' and (resid 293 through 371 )C293 - 371
8X-RAY DIFFRACTION8chain 'C' and (resid 372 through 429 )C372 - 429
9X-RAY DIFFRACTION9chain 'C' and (resid 430 through 513 )C430 - 513
10X-RAY DIFFRACTION10chain 'C' and (resid 514 through 582 )C514 - 582
11X-RAY DIFFRACTION11chain 'C' and (resid 583 through 698 )C583 - 698
12X-RAY DIFFRACTION12chain 'D' and (resid 293 through 371 )D293 - 371
13X-RAY DIFFRACTION13chain 'D' and (resid 372 through 407 )D372 - 407
14X-RAY DIFFRACTION14chain 'D' and (resid 408 through 543 )D408 - 543
15X-RAY DIFFRACTION15chain 'D' and (resid 544 through 698 )D544 - 698
16X-RAY DIFFRACTION16chain 'E' and (resid 293 through 429 )E293 - 429
17X-RAY DIFFRACTION17chain 'E' and (resid 430 through 555 )E430 - 555
18X-RAY DIFFRACTION18chain 'E' and (resid 556 through 698 )E556 - 698
19X-RAY DIFFRACTION19chain 'F' and (resid 293 through 427 )F293 - 427
20X-RAY DIFFRACTION20chain 'F' and (resid 428 through 698 )F428 - 698

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Major update of PDB

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  • 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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