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- PDB-9imw: Crystal structure of N-terminal domain of human Hsp90 -

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Basic information

Entry
Database: PDB / ID: 9imw
TitleCrystal structure of N-terminal domain of human Hsp90
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / Hsp90 / ATP / Hydrolase / Tumor
Function / homology
Function and homology information


sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sulfonylurea receptor binding / sperm mitochondrial sheath / 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 / 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 insertion into mitochondrial outer membrane / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / PIWI-interacting RNA (piRNA) biogenesis / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / enzyme-substrate adaptor activity / skeletal muscle contraction / HSF1 activation / regulation of protein-containing complex assembly / telomere maintenance via telomerase / regulation of postsynaptic membrane neurotransmitter receptor levels / 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 / Recruitment of mitotic centrosome proteins and complexes / nitric-oxide synthase regulator activity / activation of innate immune response / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / Anchoring of the basal body to the plasma membrane / positive regulation of interferon-beta production / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / 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 / MHC class II protein complex binding / disordered domain specific 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/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: 1.527 Å
AuthorsHuang, L.Q. / Yu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2301405 China
CitationJournal: To Be Published
Title: Novel starting points for fragment-based drug design against human heat shock protein 90 identified using crystallographic fragment screening
Authors: Huang, L.Q. / Feng, Y. / Wang, Q.S. / Wang, W.W. / Zhu, Z.M. / Li, Q.H. / Zhou, H. / Xu, Q. / Li, M.J.
History
DepositionJul 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)25,6571
Polymers25,6571
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock protein HSP 90-alpha

A: Heat shock protein HSP 90-alpha


Theoretical massNumber of molelcules
Total (without water)51,3142
Polymers51,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1580 Å2
ΔGint-12 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.849, 89.309, 99.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

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


Mass: 25656.768 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20-25% (w/v) PEG 4000, 200mM magnesium chloride, 100mM Tris-HCl, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.527→55 Å / Num. obs: 45027 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.046 / Rrim(I) all: 0.141 / Χ2: 0.88 / Net I/σ(I): 12.5
Reflection shellResolution: 1.53→1.61 Å / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 2.137 / Num. measured all: 47003 / Num. unique obs: 6487 / CC1/2: 0.461 / Rpim(I) all: 0.837 / Rrim(I) all: 2.301 / Χ2: 0.69 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.527→53 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 2227 4.96 %
Rwork0.1627 --
obs0.1636 44910 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.527→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 358 1998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141673
X-RAY DIFFRACTIONf_angle_d1.7162258
X-RAY DIFFRACTIONf_dihedral_angle_d10.2981404
X-RAY DIFFRACTIONf_chiral_restr0.076260
X-RAY DIFFRACTIONf_plane_restr0.016289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5272-1.56040.26931290.26842589X-RAY DIFFRACTION97
1.5604-1.59670.25541360.25022602X-RAY DIFFRACTION99
1.5967-1.63670.26171510.22872616X-RAY DIFFRACTION100
1.6367-1.68090.25311440.21292648X-RAY DIFFRACTION100
1.6809-1.73040.22741430.21092647X-RAY DIFFRACTION100
1.7304-1.78620.21271520.19162636X-RAY DIFFRACTION100
1.7862-1.85010.16221330.16972635X-RAY DIFFRACTION100
1.8501-1.92420.20461340.16142680X-RAY DIFFRACTION100
1.9242-2.01170.18451450.15332652X-RAY DIFFRACTION100
2.0117-2.11780.16441290.15322669X-RAY DIFFRACTION100
2.1178-2.25050.16491460.14282659X-RAY DIFFRACTION100
2.2505-2.42420.18371390.1462687X-RAY DIFFRACTION100
2.4242-2.66820.15881310.14872697X-RAY DIFFRACTION100
2.6682-3.05430.19391520.15462683X-RAY DIFFRACTION100
3.0543-3.84790.14441410.14812733X-RAY DIFFRACTION100
3.8479-530.16191220.15232850X-RAY DIFFRACTION99
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)
12.2219-0.6541-2.38731.39910.45694.80020.1212-0.2762-0.04450.0017-0.0546-0.074-0.0530.2311-0.05310.07990.0067-0.02190.1397-0.02590.120112.4068-17.8426-18.6052
21.3549-1.29521.4253.8317-3.20184.80210.0099-0.0210.12940.0509-0.09310.0175-0.19420.12570.07680.1048-0.0029-0.00380.0941-0.03170.122-5.0041-6.6597-20.3008
31.6319-0.80120.72924.3215-4.35715.9970.10640.2217-0.0276-0.16490.08830.441-0.1469-0.2304-0.31080.13130.0211-0.05340.1353-0.03070.1492-13.4846-10.0691-28.2534
41.7493-0.53590.17643.8668-2.82314.54410.0106-0.0167-0.2502-0.04860.07280.190.2011-0.1135-0.06420.0934-0.0006-0.01010.0744-0.03230.1314-6.0606-19.7562-21.828
52.37851.64623.74813.73025.69539.8185-0.00160.2420.235-0.2562-0.1357-0.0862-0.09040.00460.080.14160.01860.0180.1285-0.00850.176.9109-11.0384-29.7312
60.85180.4990.38262.85290.01624.61070.6139-1.03450.64910.2175-0.1049-0.2346-0.63151.322-0.05480.173-0.1220.02180.3928-0.14640.25112.2637-5.8304-12.6113
72.3682-1.0810.35311.5865-0.43921.79930.13960.2284-0.2291-0.1667-0.07450.12630.1450.0204-0.09540.09280.0037-0.01190.068-0.04060.10270.9213-19.2624-27.8492
82.3537-1.0028-0.82992.8422-0.57254.093-0.0946-0.2799-0.18110.22480.08920.00760.24020.02360.00020.0702-0.0256-0.02480.10370.01090.1097-5.6011-20.1345-10.3674
92.87962.63420.04646.4623-0.21010.99510.1474-0.26120.05570.3934-0.19530.1157-0.1006-0.09150.050.1153-0.00470.01790.1143-0.03090.1044-13.7838-12.6333-14.6008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 136 )
7X-RAY DIFFRACTION7chain 'A' and (resid 137 through 182 )
8X-RAY DIFFRACTION8chain 'A' and (resid 183 through 210 )
9X-RAY DIFFRACTION9chain 'A' and (resid 211 through 224 )

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