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- PDB-8ki4: Crystal structure of human HSP90 in intermediate state -

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Basic information

Entry
Database: PDB / ID: 8ki4
TitleCrystal structure of human HSP90 in intermediate state
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / HSP90 / ATPase / NTD
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / 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 / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / 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 / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / 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 / Regulation of necroptotic cell death / tau protein binding / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Downregulation of ERBB2 signaling / response to estrogen / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / neuron migration / Aggrephagy / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint
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: 1.55 Å
AuthorsXu, C. / Zhang, X.L. / Bai, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82003654 China
CitationJournal: Jacs Au / Year: 2024
Title: Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies.
Authors: Xu, C. / Zhang, X. / Zhao, L. / Verkhivker, G.M. / Bai, F.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)54,7994
Polymers54,6752
Non-polymers1242
Water8,395466
1
A: Heat shock protein HSP 90-alpha
hetero molecules

A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7994
Polymers54,6752
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area19670 Å2
MethodPISA
2
B: Heat shock protein HSP 90-alpha
hetero molecules

B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7994
Polymers54,6752
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1850 Å2
ΔGint-13 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.568, 88.507, 98.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 27337.559 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Bis-Tris, pH 8.5, 20% PEG 3350, 200 mM NaF / PH range: 8.2 - 8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 83031 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.036 / Rrim(I) all: 0.127 / Χ2: 0.936 / Net I/σ(I): 7.6 / Num. measured all: 1055773
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.55-1.589.91.0341010.8140.9470.3391.0850.788
1.58-1.6111.20.9340870.8780.9670.2880.9740.817
1.61-1.6412.50.80841150.9040.9740.2360.8430.859
1.64-1.6713.20.71740950.9310.9820.2040.7460.898
1.67-1.7113.10.60941080.9710.9930.1740.6340.927
1.71-1.7512.90.52141070.9560.9890.150.5430.972
1.75-1.7912.50.43141060.9640.9910.1260.4491.036
1.79-1.8413.10.37541040.9740.9930.1070.391.042
1.84-1.8912.70.31641330.9750.9940.0920.3291.079
1.89-1.9513.40.27741140.9830.9960.0780.2881.157
1.95-2.0213.20.23941300.9840.9960.0680.2491.198
2.02-2.112.70.21541310.9840.9960.0620.2241.208
2.1-2.213.10.19241250.9870.9970.0550.21.16
2.2-2.3212.80.17241630.9880.9970.050.1791.078
2.32-2.4613.50.15741600.990.9980.0440.1630.999
2.46-2.6513.10.14241470.9930.9980.0410.1480.942
2.65-2.9213.10.12641780.9930.9980.0360.1310.821
2.92-3.3413.30.10842170.9950.9990.0310.1120.658
3.34-4.2112.80.09242620.9960.9990.0270.0950.527
4.21-50120.07844480.990.9970.0240.0820.506

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-3000data scaling
PHASER1.20.1-4487phasing
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→39.21 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 4006 4.95 %
Rwork0.1854 --
obs0.1865 80904 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 8 466 3763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063361
X-RAY DIFFRACTIONf_angle_d0.8884531
X-RAY DIFFRACTIONf_dihedral_angle_d5.799451
X-RAY DIFFRACTIONf_chiral_restr0.056521
X-RAY DIFFRACTIONf_plane_restr0.006579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.3056960.23761730X-RAY DIFFRACTION64
1.57-1.590.27131050.23432138X-RAY DIFFRACTION79
1.59-1.610.30011120.22732456X-RAY DIFFRACTION92
1.61-1.630.26971470.21742617X-RAY DIFFRACTION98
1.63-1.650.28241280.20732678X-RAY DIFFRACTION99
1.65-1.670.24161490.19872669X-RAY DIFFRACTION100
1.67-1.70.23461410.19642710X-RAY DIFFRACTION100
1.7-1.720.22821470.19852633X-RAY DIFFRACTION100
1.72-1.750.22231500.18852700X-RAY DIFFRACTION100
1.75-1.780.22631220.19312706X-RAY DIFFRACTION100
1.78-1.810.19221400.19222690X-RAY DIFFRACTION100
1.81-1.850.22631530.19212708X-RAY DIFFRACTION100
1.85-1.890.22141520.19212672X-RAY DIFFRACTION100
1.89-1.930.20411280.18112699X-RAY DIFFRACTION100
1.93-1.970.18931430.17932691X-RAY DIFFRACTION100
1.97-2.020.17791480.17852697X-RAY DIFFRACTION100
2.02-2.080.20241460.17922705X-RAY DIFFRACTION100
2.08-2.140.19111410.16922690X-RAY DIFFRACTION100
2.14-2.210.21211430.17542704X-RAY DIFFRACTION100
2.21-2.290.22191400.18092738X-RAY DIFFRACTION100
2.29-2.380.21061480.1782707X-RAY DIFFRACTION100
2.38-2.490.20781520.18182719X-RAY DIFFRACTION100
2.49-2.620.23721170.19142740X-RAY DIFFRACTION100
2.62-2.780.19251470.19082716X-RAY DIFFRACTION100
2.78-30.21561330.1912760X-RAY DIFFRACTION100
3-3.30.22891360.19372770X-RAY DIFFRACTION100
3.3-3.770.17441550.17742757X-RAY DIFFRACTION99
3.77-4.750.18221210.15862811X-RAY DIFFRACTION99
4.75-39.210.18941660.19322887X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.4302 Å / Origin y: 14.1304 Å / Origin z: 24.478 Å
111213212223313233
T0.0521 Å20.0058 Å20.0133 Å2-0.0492 Å2-0.0052 Å2--0.0641 Å2
L0.0663 °20.0582 °2-0.0614 °2-0.0686 °2-0.047 °2--0.3646 °2
S0.036 Å °-0.021 Å °0.0415 Å °0.0031 Å °-0.002 Å °0.0028 Å °-0.0551 Å °0.0149 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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