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- PDB-6ksq: Middle Domain of Human HSP90 Alpha -

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Basic information

Entry
Database: PDB / ID: 6ksq
TitleMiddle Domain of Human HSP90 Alpha
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / HSP90
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
Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ...Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsSu, H.X. / Zhou, C. / Zhang, N.X. / Xu, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Iscience / Year: 2020
Title: Allosteric Regulation of Hsp90 alpha's Activity by Small Molecules Targeting the Middle Domain of the Chaperone.
Authors: Zhou, C. / Zhang, C. / Zhu, H. / Liu, Z. / Su, H. / Zhang, X. / Chen, T. / Zhong, Y. / Hu, H. / Xiong, M. / Zhou, H. / Xu, Y. / Zhang, A. / Zhang, N.
History
DepositionAug 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)33,9651
Polymers33,9651
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13220 Å2
Unit cell
Length a, b, c (Å)36.072, 38.968, 108.029
Angle α, β, γ (deg.)90.000, 95.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33964.602 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 M (NH4)2SO4, 5% Glycerol, 29.5% PEG 3350, PH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14524 / % possible obs: 94.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 32.15 Å2 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.078 / Rrim(I) all: 0.201 / Χ2: 4.424 / Net I/σ(I): 8.5 / Num. measured all: 90998
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.245.80.867320.4440.3870.9451.34397.2
2.24-2.285.80.767150.6920.3320.8320.88193.8
2.28-2.3260.6877260.7220.2990.7520.95496.8
2.32-2.3760.6457370.8260.2810.7051.15197.7
2.37-2.425.60.5897370.7720.2640.6481.01694.1
2.42-2.485.90.5266680.8360.230.5761.33490.9
2.48-2.546.30.4647040.8690.1960.5051.56289.9
2.54-2.616.50.3857230.9260.1610.4191.495.1
2.61-2.696.70.3627320.9120.150.3921.62598.5
2.69-2.776.40.3087740.9450.1290.3351.49498.1
2.77-2.876.70.2617200.960.1070.2831.82897.7
2.87-2.996.30.2337720.9490.0980.2532.27997.6
2.99-3.126.50.1967290.9320.0830.2142.54897.9
3.12-3.296.20.1737500.9660.0740.1894.51795.9
3.29-3.496.30.1487180.9760.0630.1614.73395
3.49-3.766.20.1366390.980.0580.1495.81783.9
3.76-4.146.50.1157530.990.0480.1256.98595.9
4.14-4.746.50.1187640.9890.050.12810.36797.4
4.74-5.976.40.1247360.9820.0520.13412.20693.9
5.97-506.70.1536950.9770.0640.16622.13684.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HK7

1hk7


Resolution: 2.202→36.638 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2316 725 4.99 %
Rwork0.1822 --
obs0.1848 14517 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.63 Å2 / Biso mean: 45.4035 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 2.202→36.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 62 2148
Biso mean---40.27 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082136
X-RAY DIFFRACTIONf_angle_d0.8672878
X-RAY DIFFRACTIONf_chiral_restr0.053314
X-RAY DIFFRACTIONf_plane_restr0.005369
X-RAY DIFFRACTIONf_dihedral_angle_d11.3731839
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.202-2.37190.27951350.2202269493
2.3719-2.61060.27781450.2063270893
2.6106-2.98820.25791370.1924286898
2.9882-3.76420.24141620.1806270793
3.7642-36.6380.19541460.165281593
Refinement TLS params.Method: refined / Origin x: 2.3627 Å / Origin y: -38.1074 Å / Origin z: 29.6876 Å
111213212223313233
T0.1835 Å20.0153 Å2-0.0002 Å2-0.1622 Å20.0267 Å2--0.1729 Å2
L0.7067 °20.1772 °20.1709 °2-0.8662 °20.4454 °2--1.2404 °2
S-0.0222 Å °0.1006 Å °0.065 Å °-0.1518 Å °0.079 Å °-0.0225 Å °-0.0063 Å °0.0473 Å °0 Å °
Refinement TLS groupSelection details: all

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