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- PDB-7ha1: PanDDA analysis group deposition -- Crystal structure of HSP90N i... -

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Basic information

Entry
Database: PDB / ID: 7ha1
TitlePanDDA analysis group deposition -- Crystal structure of HSP90N in complex with FL0092
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / Crystallographic Fragment Screening / Fragment-Based Drug Discovery (FBDD) / Heat shock protein 90 (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 / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / mitochondrial transport / protein insertion into mitochondrial outer membrane / 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 / TPR domain binding / non-chaperonin molecular chaperone ATPase / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / Sema3A PAK dependent Axon repulsion / skeletal muscle contraction / protein unfolding / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / regulation of protein-containing complex assembly / chaperone-mediated protein complex assembly / Attenuation phase / neurofibrillary tangle assembly / RHOBTB2 GTPase cycle / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of defense response to virus by host / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / Recruitment of NuMA to mitotic centrosomes / endocytic vesicle lumen / Anchoring of the basal body to the plasma membrane / nitric-oxide synthase regulator activity / positive regulation of cardiac muscle contraction / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / AURKA Activation by TPX2 / positive regulation of interferon-beta production / lysosomal lumen / response to cold / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / response to cocaine / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / cellular response to virus / VEGFA-VEGFR2 Pathway / Downregulation of ERBB2 signaling / histone deacetylase binding / positive regulation of protein import into nucleus / response to estrogen / Chaperone Mediated Autophagy / Aggrephagy / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / MHC class II protein complex binding / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition
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 / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsHuang, L. / Wang, W. / Zhu, Z. / Li, Q. / Li, M. / Zhou, H. / Xu, Q. / Wen, W. / Wang, Q. / Yu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YFC2301405 China
CitationJournal: Iucrj / Year: 2025
Title: Novel starting points for fragment-based drug design against human heat-shock protein 90 identified using crystallographic fragment screening.
Authors: Huang, L. / Wang, W. / Zhu, Z. / Li, Q. / Li, M. / Zhou, H. / Xu, Q. / Wen, W. / Wang, Q. / Yu, F.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0992
Polymers26,8591
Non-polymers2401
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.930, 89.480, 100.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-701-

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: 26859.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07900, non-chaperonin molecular chaperone ATPase
#2: Chemical ChemComp-A1AX6 / 5-bromo-3,3-dimethyl-1,3-dihydro-2H-indol-2-one


Mass: 240.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10BrNO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris-HCl pH 8.5, 22% PEG4000, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.46→31.3 Å / Num. obs: 51301 / % possible obs: 99.3 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 20.3 / Num. measured all: 574631 / Scaling rejects: 792
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.46-1.56.91.152397334860.6990.4591.2441.692.4
6.53-31.3100.04764676490.9980.0150.0544.298.5

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
DIMPLEphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→24.8 Å / SU ML: 0.177 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196 2531 4.94 %
Rwork0.1743 48748 -
obs0.1754 51279 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.55 Å2
Refinement stepCycle: LAST / Resolution: 1.46→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 13 348 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041684
X-RAY DIFFRACTIONf_angle_d0.72552273
X-RAY DIFFRACTIONf_chiral_restr0.0689260
X-RAY DIFFRACTIONf_plane_restr0.0065289
X-RAY DIFFRACTIONf_dihedral_angle_d5.4069226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.36091240.33282426X-RAY DIFFRACTION91.1
1.49-1.520.281340.25992642X-RAY DIFFRACTION97.27
1.52-1.550.2441350.22442702X-RAY DIFFRACTION99.93
1.55-1.590.22731550.21922693X-RAY DIFFRACTION99.96
1.59-1.630.22131540.21472700X-RAY DIFFRACTION100
1.63-1.670.24821420.21392676X-RAY DIFFRACTION100
1.67-1.720.27411570.21762683X-RAY DIFFRACTION100
1.72-1.780.25271520.20662710X-RAY DIFFRACTION99.97
1.78-1.840.22121250.19872728X-RAY DIFFRACTION100
1.84-1.910.19791220.19542734X-RAY DIFFRACTION99.72
1.91-20.20121350.19552720X-RAY DIFFRACTION99.72
2-2.110.21211320.18332726X-RAY DIFFRACTION99.97
2.11-2.240.2031370.16772726X-RAY DIFFRACTION99.9
2.24-2.410.21131400.17812743X-RAY DIFFRACTION99.52
2.41-2.650.18931540.17392722X-RAY DIFFRACTION99.69
2.65-3.040.16241370.16982747X-RAY DIFFRACTION99.62
3.04-3.820.16821450.1532784X-RAY DIFFRACTION99.76
3.82-24.80.18871510.15252886X-RAY DIFFRACTION99.35
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)
12.50712820899-0.697300381643-2.809054782370.8810587640090.4734013223934.730135710760.118124706809-0.303328984311-0.01659290834560.0126136201287-0.0601589473071-0.0496780754055-0.04887299175390.214977670465-0.09360034816240.1768059830810.00226223696923-0.02545403560620.206441044588-0.02592873844210.2091457565812.3607669217-17.9231763668-18.7384871289
21.56985553264-1.487685608972.218987031343.90337048766-4.028174572546.3712343437-0.07883596264550.08832304441720.1240025443860.207602201751-0.1082864901470.00538010964821-0.4942992514170.2812277924020.1349604168280.184397549568-0.00723137662386-0.003872119522760.159072255347-0.03481981440140.19902025687-5.21244798572-6.2670199564-20.9027289615
31.65754213743-0.291204472755-0.07665300208792.93362836675-1.582362301123.622260431890.04886558353270.0890516527446-0.124311664722-0.1211513316420.05588471200840.2556176937330.0619896689446-0.198167446082-0.1403827098230.149762771366-0.000154295932928-0.03716966851660.135090782907-0.04122887719170.197368806405-10.1243919534-14.979459374-25.1866012667
43.404939770740.265580272412-1.765380402892.384187672320.4206316289034.668886902510.193502662817-0.5500834738860.4043669765470.167005914951-0.0488139852986-0.133943760815-0.4128731585330.854393413931-0.1358306758070.178698509232-0.04112477711140.01709979006360.245217783329-0.05720066335190.26226804179510.7098430675-7.50651162656-17.9062879358
52.41853021602-1.104146620420.1459109442161.78300911985-0.4111089930171.566607606590.156221242820.215825938495-0.251772225648-0.176349449339-0.06985712862040.1501314262650.1592083370770.0587877355354-0.1066425576130.157968442020.00127777679417-0.01489021244260.127356033476-0.03393747418750.183940837760.886330698851-19.2972349464-27.8929813355
62.69181271237-0.517272081310.07164538300773.30339416026-1.689282038254.613557811280.0134675160233-0.241973871478-0.262033893210.192901354865-0.0178176923719-0.006786857452220.2368935756870.110169656224-0.01461131019670.1801603698020.00429898506432-0.01003171589110.1548200741750.01069719258740.197166149403-2.57556683895-23.6786975777-13.7218857911
73.02325534882-0.6743153473120.6586928543011.98169783918-0.8677943919584.415408057870.0319230717716-0.26924418358-0.1012439060320.185500866102-0.01214962489680.0726681852805-0.0814932717746-0.0771458355759-0.003884275454940.1507629854850.002866887837640.01062273279740.197994413732-0.01704891171690.169210326266-12.1016821652-14.2323086012-10.4826782659
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 40 )16 - 401 - 25
22chain 'A' and (resid 41 through 65 )41 - 6526 - 50
33chain 'A' and (resid 66 through 99 )66 - 9951 - 84
44chain 'A' and (resid 100 through 136 )100 - 13685 - 121
55chain 'A' and (resid 137 through 182 )137 - 182122 - 167
66chain 'A' and (resid 183 through 199 )183 - 199168 - 184
77chain 'A' and (resid 200 through 224 )200 - 224185 - 209

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