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- PDB-7h9p: PanDDA analysis group deposition -- Crystal structure of HSP90N i... -

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Basic information

Entry
Database: PDB / ID: 7h9p
TitlePanDDA analysis group deposition -- Crystal structure of HSP90N in complex with Fr12541
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 / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / 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 / 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 / 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 / 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 / activation of innate immune response / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / response to cold / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / neuron migration / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / tau protein binding / 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 / 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 / Aggrephagy / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint / 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
4-phenoxyphenol / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.64 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0452
Polymers26,8591
Non-polymers1861
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.900, 89.380, 100.000
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-645-

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-HX8 / 4-phenoxyphenol


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 1.64→29.74 Å / Num. obs: 36534 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 16.3 / Num. measured all: 457792 / Scaling rejects: 96
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
1.64-1.6810.71.6552858126820.5290.5281.741.6100
7.33-29.749.80.03844674580.9980.0120.0439.598.3

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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: 1.64→29.74 Å / SU ML: 0.2078 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.191 1777 4.87 %
Rwork0.17 34747 -
obs0.1711 36524 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.19 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 14 278 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371685
X-RAY DIFFRACTIONf_angle_d0.66722270
X-RAY DIFFRACTIONf_chiral_restr0.0468259
X-RAY DIFFRACTIONf_plane_restr0.0055289
X-RAY DIFFRACTIONf_dihedral_angle_d7.3525224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.3451370.31212657X-RAY DIFFRACTION100
1.68-1.730.27641200.26652646X-RAY DIFFRACTION100
1.73-1.790.25971290.22572647X-RAY DIFFRACTION100
1.79-1.850.24031380.1942625X-RAY DIFFRACTION100
1.85-1.930.211120.19222681X-RAY DIFFRACTION100
1.93-2.020.22681330.18872651X-RAY DIFFRACTION99.93
2.02-2.120.22081480.17712631X-RAY DIFFRACTION100
2.12-2.250.18881360.16622667X-RAY DIFFRACTION100
2.26-2.430.23361280.17672670X-RAY DIFFRACTION100
2.43-2.670.21291470.17922677X-RAY DIFFRACTION100
2.67-3.060.22091460.17422678X-RAY DIFFRACTION99.96
3.06-3.850.14531680.15542688X-RAY DIFFRACTION99.96
3.85-29.740.1611350.14632829X-RAY DIFFRACTION99.6
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)
12.58876200717-0.983609521933-3.001162742382.039613840150.617349302595.300979263210.160081899828-0.292879045399-0.0140355180056-0.00306961601178-0.105301791832-0.0813623902155-0.1193174346750.172872825592-0.06057851077640.1846338863140.0100942383324-0.03400053542570.254172634855-0.02994233315760.24313991167412.3263863377-17.8357660067-18.7358042352
22.38373004423-1.914158768152.531979734574.81506656509-4.232212742226.92645664769-0.1871900147320.1108204384640.2513198574650.213079166815-0.109053126782-0.098607192105-0.5867287441290.2635646589480.1616477277010.203908361482-0.0154402138403-0.005040315831230.175505589606-0.03818534687840.233857433117-5.19943232194-6.25222744143-20.881137265
31.95881259121-0.3723319506480.08464472459713.32843999963-1.524478815523.4831792770.05621389464060.103360172272-0.0905858201873-0.1944799453270.05368880671370.2740509243860.0968455897339-0.246053014582-0.1499131414030.1535477270980.0030914287783-0.03647981954370.159024760051-0.03384870723350.212769275475-10.1023000981-14.9883575834-25.1346754567
44.612518181970.591077994626-1.171277101142.586297016230.4038215299164.924345889620.177639923554-0.6038736495570.5506437967390.164482948361-0.0543256854256-0.0876274820683-0.4698377972750.848273343516-0.1686303519160.205839154059-0.03517236136990.01885190289360.27633511193-0.07129483981690.31243410028410.7030332361-7.43752228584-17.8702057693
52.80966268379-1.19673903040.2722294563082.04674994543-0.3141066584972.351853528140.1545226779540.243411859795-0.298269453089-0.214547427931-0.05815369369630.1820857047030.2012150068140.0341043729645-0.1179475191940.204419505723-0.00733880489925-0.01427960224830.178551048698-0.03497511831310.2364772512860.876501466848-19.2862747435-27.8439998671
62.74378874107-0.862667439575-0.5999470951093.66046596457-0.8192503114855.40913218653-0.128088576616-0.29234394908-0.1898505882170.302511010920.09377111233010.0183148398910.387397223640.007411736989340.02606523946810.147925269023-0.0242888296792-0.02089492517950.1944268908960.01273650986230.193987851987-5.60073043454-20.1238764464-10.3509119517
74.898371485320.5488859609830.3014066867214.75617299863-1.010698055654.256585721680.109206534485-0.236221060625-0.06578720678350.489768661853-0.03840332114160.0164232065756-0.169266533196-0.157857389062-0.01439164030690.1981154622290.01559891539220.001491785096720.221226536701-0.02870510474840.190750487444-13.9900867053-13.3719110372-14.6411904981
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 210 )183 - 210168 - 195
77chain 'A' and (resid 211 through 224 )211 - 224196 - 209

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