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- PDB-7hb7: PanDDA analysis group deposition -- Crystal structure of HSP90N i... -

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Basic information

Entry
Database: PDB / ID: 7hb7
TitlePanDDA analysis group deposition -- Crystal structure of HSP90N in complex with Fr12696
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
Chem-WP1 / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 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)27,0502
Polymers26,8591
Non-polymers1911
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.280, 88.230, 96.750
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

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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-WP1 / 2,2-dimethyl-2,3-dihydro-1-benzofuran-7-carboxamide


Mass: 191.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO2 / Feature type: SUBJECT OF INVESTIGATION
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: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.98→30.29 Å / Num. obs: 6399 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.059 / Rrim(I) all: 0.206 / Net I/σ(I): 10.1 / Num. measured all: 78659 / Scaling rejects: 7
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
2.98-3.06131.19558544520.7870.3431.2442.5100
13.33-30.296.50.096534820.9890.0360.10315.190.3

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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: MOLECULAR REPLACEMENT / Resolution: 2.98→30.29 Å / SU ML: 0.3568 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.52
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2795 300 4.69 %
Rwork0.2273 6096 -
obs0.2296 6396 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.76 Å2
Refinement stepCycle: LAST / Resolution: 2.98→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 14 0 1658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151685
X-RAY DIFFRACTIONf_angle_d0.38952274
X-RAY DIFFRACTIONf_chiral_restr0.0384260
X-RAY DIFFRACTIONf_plane_restr0.0021289
X-RAY DIFFRACTIONf_dihedral_angle_d6.4497227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.750.31151480.27022990X-RAY DIFFRACTION99.97
3.75-30.290.26521520.20943106X-RAY DIFFRACTION99.88
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)
13.39478704059-0.559212597423-3.627242339143.563375889190.3965200841154.82402057608-0.2220760284-0.216119655128-0.3745065528060.3581639967880.00955431658466-0.3300422750290.003337107291140.5446026867840.2677425093080.54205419310.1056658598-0.1395091882470.6643627442990.02629585631520.69704038191113.824236646127.388549722531.0493971739
24.73249257375-2.370525184533.359560440166.58514446711-5.003199904577.26500352111-0.5316226262360.317551760130.6624751694580.7976273030750.2182119560210.252289492419-1.70527623580.2122043626920.3292731725080.508431092884-0.118910929929-0.03369268418220.390391008985-0.0641439510710.54344302176-4.1321162173237.031799600427.3399913318
34.62738900572-2.22565745272.430444216558.47651095860.05991294500849.1770209174-0.006170418417341.63485521349-0.604521279927-2.04624734149-0.2752226719320.9494737220950.443065066821-0.703812288567-0.2646335537160.572504166106-0.0657959077731-0.0723213509550.7342378817620.07827348582070.767562214901-12.262735324937.507476650212.2874488979
43.65827649427-2.47172997742-1.369601293813.15201377901-1.692884639766.386090715140.223442680826-0.420231989805-0.09567366172620.0473212152662-0.260086746967-0.2370853782750.1781703188830.140553414327-0.0687454303830.4211090015560.067906422343-0.1225532774960.31198561247-0.04231804606590.448232000148-2.2269491164825.992446557424.4911212195
58.88206685717-0.6214862288640.9059864232667.81035641388-4.19350863228.4159140574-0.2931431251040.4037001478721.021521830060.7338701339420.00670617593925-1.52687655795-0.3629685311692.435073753440.3597892483370.4423779798040.0105890087976-0.1116174169260.4236526534110.01184083096370.83851633106814.812692927239.304151873531.9787100439
68.211439504850.267841715972-2.983634474679.53524591397-2.784320356476.626641218960.381365762596-1.861955011091.782908768670.745218039625-0.133739000291.11194038822-0.5253126239630.7377829744440.04330608052720.847482326418-0.02316360126390.04880182762280.864434728801-0.1541405109240.6301248041618.2082412286739.092479892638.6819241396
74.99868391509-1.596462321330.7491275497932.35348252864-1.619053501864.977947458160.398150976871-0.131094621434-0.617877430130.0952141394502-0.1149232700520.1578712504870.5938376946070.957149945125-0.1030396292640.441950054527-0.0739591559571-0.0423959803850.487260093521-0.009688471452520.5395756203334.488069784925.392626945628.4520073761
84.70065297308-1.895204935240.7433844329083.44459650393-3.467899979833.61624634614-0.05362341100410.244595372757-0.232586713293-0.2453999210780.1003244407650.06415772340860.118773699753-0.0532272003362-0.2433130420440.568634775781-0.00626994435598-0.02186299019530.394565047431-0.1031690327560.5415017516222.1673760153524.093421609618.6287123368
98.04514081926-1.77387785516-0.07482474950177.471195338150.7242938647218.924638701720.050310033926-1.65487489581-0.5561316651421.04153210117-0.229378302846-0.04457943280260.121444122442-0.1607050291240.08388585253010.560282642473-0.002476585290390.01232093428890.6778854115390.1205520803840.440583776774-5.7789632301524.037199710241.2975369383
107.773275630790.630449915428-0.8144319207417.04568070356-5.815692633637.80102071433-0.257056172321-0.0674932685531-0.144846035611.54689085362-0.0298589915032-1.97025139913-1.2529078525-0.5705529748670.2146862473270.527472084831-0.00855617341807-0.05947843738240.4471862851780.03768130599010.483304199294-13.064582293329.948507272532.3658328796
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 64 )41 - 6426 - 49
33chain 'A' and (resid 65 through 76 )65 - 7650 - 61
44chain 'A' and (resid 77 through 106 )77 - 10662 - 91
55chain 'A' and (resid 107 through 123 )107 - 12392 - 108
66chain 'A' and (resid 124 through 136 )124 - 136109 - 121
77chain 'A' and (resid 137 through 153 )137 - 153122 - 138
88chain 'A' and (resid 154 through 190 )154 - 190139 - 175
99chain 'A' and (resid 191 through 210 )191 - 210176 - 195
1010chain 'A' and (resid 211 through 224 )211 - 224196 - 209

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