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- PDB-7ry0: human Hsp90_MC domain structure -

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Basic information

Entry
Database: PDB / ID: 7ry0
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 / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / 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 / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / 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 / enzyme-substrate adaptor activity / response to unfolded protein / regulation of protein-containing complex assembly / skeletal muscle contraction / HSF1 activation / Attenuation phase / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / telomere maintenance via telomerase / axonal growth cone / positive regulation of lamellipodium assembly / nitric oxide metabolic process / eNOS activation / DNA polymerase binding / response to salt stress / positive regulation of defense response to virus by host / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of telomere maintenance via telomerase / Signaling by ERBB2 / 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 / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / ESR-mediated signaling / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / response to cold / Constitutive Signaling by Overexpressed ERBB2 / 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 / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / positive regulation of protein import into nucleus / Regulation of necroptotic cell death / VEGFA-VEGFR2 Pathway / response to estrogen / tau protein binding / histone deacetylase binding / Downregulation of ERBB2 signaling / neuron migration / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Aggrephagy / MHC class II protein complex binding / 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 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: 2.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5467
Polymers99,1272
Non-polymers4195
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-20 kcal/mol
Surface area38280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.898, 154.260, 156.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 295:297 or (resid 298 and (name...
21(chain B and (resseq 295:297 or (resid 298 and (name...

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
11PROPROTRPTRP(chain A and (resseq 295:297 or (resid 298 and (name...AA295 - 2976 - 8
12THRTHRTHRTHR(chain A and (resseq 295:297 or (resid 298 and (name...AA2989
13LYSLYSASPASP(chain A and (resseq 295:297 or (resid 298 and (name...AA294 - 6995 - 410
14LYSLYSASPASP(chain A and (resseq 295:297 or (resid 298 and (name...AA294 - 6995 - 410
15LYSLYSASPASP(chain A and (resseq 295:297 or (resid 298 and (name...AA294 - 6995 - 410
16LYSLYSASPASP(chain A and (resseq 295:297 or (resid 298 and (name...AA294 - 6995 - 410
17LYSLYSASPASP(chain A and (resseq 295:297 or (resid 298 and (name...AA294 - 6995 - 410
21PROPROTRPTRP(chain B and (resseq 295:297 or (resid 298 and (name...BB295 - 2976 - 8
22THRTHRTHRTHR(chain B and (resseq 295:297 or (resid 298 and (name...BB2989
23THRTHRGLUGLU(chain B and (resseq 295:297 or (resid 298 and (name...BB293 - 7004 - 411
24THRTHRGLUGLU(chain B and (resseq 295:297 or (resid 298 and (name...BB293 - 7004 - 411
25THRTHRGLUGLU(chain B and (resseq 295:297 or (resid 298 and (name...BB293 - 7004 - 411
26THRTHRGLUGLU(chain B and (resseq 295:297 or (resid 298 and (name...BB293 - 7004 - 411
27THRTHRGLUGLU(chain B and (resseq 295:297 or (resid 298 and (name...BB293 - 7004 - 411

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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: 49563.648 Da / Num. of mol.: 2 / Mutation: W320A
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes PH 7.5, 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49628 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Χ2: 0.831 / Net I/σ(I): 4.8 / Num. measured all: 317128
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.91.01548880.7540.4351.1060.63599.7
2.28-2.376.40.76848350.8850.3230.8350.65599.9
2.37-2.486.40.61148950.9040.2570.6640.661100
2.48-2.616.30.44549190.940.1920.4850.69799.8
2.61-2.776.40.32448980.9610.1380.3530.742100
2.77-2.996.80.22449390.9820.0930.2430.848100
2.99-3.296.60.1549360.9890.0630.1630.93899.9
3.29-3.766.40.09749550.9920.0420.1061.119100
3.76-4.746.60.07150590.9950.030.0771.06799.9
4.74-506.10.0553040.9990.0220.0550.90399.7

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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: 2.2→49.488 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1985 4.05 %
Rwork0.2051 47033 -
obs0.2071 49018 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.43 Å2 / Biso mean: 57.5044 Å2 / Biso min: 21.46 Å2
Refinement stepCycle: final / Resolution: 2.2→49.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 24 138 6474
Biso mean--83.81 51.01 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016430
X-RAY DIFFRACTIONf_angle_d1.3028626
X-RAY DIFFRACTIONf_chiral_restr0.069961
X-RAY DIFFRACTIONf_plane_restr0.0071096
X-RAY DIFFRACTIONf_dihedral_angle_d21.2214006
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3288X-RAY DIFFRACTION9.423TORSIONAL
12B3288X-RAY DIFFRACTION9.423TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.34291440.28723283100
2.255-2.3160.26771330.25623301100
2.316-2.38410.28111360.2423312100
2.3841-2.46110.27971440.23123322100
2.4611-2.54910.30261390.23013295100
2.5491-2.65110.27121380.22553347100
2.6511-2.77180.29031450.22963333100
2.7718-2.91790.3091380.23193320100
2.9179-3.10070.27971410.22433341100
3.1007-3.340.28871430.2313346100
3.34-3.6760.24781400.20383391100
3.676-4.20770.20931440.17283404100
4.2077-5.30030.20841480.16353443100
5.3003-49.4880.24911520.2004359599
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)
11.72341.2204-1.08251.6316-1.1610.96590.33420.31630.29260.07910.04140.2895-0.2755-0.5906-0.35760.705-0.36510.44561.5801-0.23180.575712.1052127.439269.5497
21.210.6462-2.3021.3506-0.51059.0058-0.1044-0.10840.01170.0363-0.03490.08670.4456-0.29260.09990.3653-0.04380.07680.3922-0.06830.343529.6054129.173951.0089
31.7413-1.22980.24875.35470.28721.694-0.1835-0.06180.12930.31490.2273-0.4911-0.04870.1758-0.01020.3244-0.12060.03060.3358-0.08670.326947.768143.022318.4409
43.7180.6917-0.20093.0460.79456.23850.2235-0.1581-0.09450.20180.113-0.64090.05620.6692-0.32050.2084-0.0162-0.06910.28110.00620.460.1729182.488469.0581
52.36240.5916-0.40172.47881.52456.84620.1681-0.1541-0.30560.23-0.00340.13580.5042-0.3845-0.08220.2029-0.061-0.07760.26260.05120.336147.7701179.684468.0955
63.1280.29232.74111.74960.73118.7343-0.20990.09130.2007-0.35540.1601-0.0849-0.37020.15780.02210.3738-0.0575-0.01520.204-0.00580.27947.0909178.295737.1921
72.4265-0.27580.21316.52120.10723.0298-0.18450.03450.00560.26540.18870.3118-0.0554-0.2324-0.00320.2481-0.0645-0.02710.28580.0140.243631.9318164.543117.7261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 294 through 316 )A294 - 316
2X-RAY DIFFRACTION2chain 'A' and (resid 317 through 554 )A317 - 554
3X-RAY DIFFRACTION3chain 'A' and (resid 555 through 699 )A555 - 699
4X-RAY DIFFRACTION4chain 'B' and (resid 293 through 343 )B293 - 343
5X-RAY DIFFRACTION5chain 'B' and (resid 344 through 429 )B344 - 429
6X-RAY DIFFRACTION6chain 'B' and (resid 430 through 554 )B430 - 554
7X-RAY DIFFRACTION7chain 'B' and (resid 555 through 700 )B555 - 700

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