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- PDB-7s9f: Cryogenic Human Hsp90a-NTD bound to BIIB021 -

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Basic information

Entry
Database: PDB / ID: 7s9f
TitleCryogenic Human Hsp90a-NTD bound to BIIB021
ComponentsHeat shock protein HSP 90-alpha
KeywordsChaperone / Hydrolase / CHAPERONE PROTEIN / SIGNAL TRANSDUCTION / HEAT SHOCK
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
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-94M / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStachowski, T.R. / Vanarotti, M. / Seetharaman, J. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142772-01 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Water Networks Repopulate Protein-Ligand Interfaces with Temperature.
Authors: Stachowski, T.R. / Vanarotti, M. / Seetharaman, J. / Lopez, K. / Fischer, M.
History
DepositionSep 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)27,1074
Polymers26,7401
Non-polymers3673
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.280, 89.668, 97.948
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 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS- ...Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 26739.922 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: Chemical ChemComp-94M / 6-chloro-9-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-9H-purin-2-amine / BIIB021


Mass: 318.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Malic acid, pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→57.1 Å / Num. obs: 14114 / % possible obs: 99.96 % / Redundancy: 8.2 % / Biso Wilson estimate: 40.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.29
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1386 / CC1/2: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
Cootmodel building
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YER

1yer


Resolution: 2.3→57.1 Å / SU ML: 0.3236 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.6308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2461 1411 10 %
Rwork0.2158 12703 -
obs0.2188 14114 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 24 100 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181944
X-RAY DIFFRACTIONf_angle_d0.43582642
X-RAY DIFFRACTIONf_chiral_restr0.0383290
X-RAY DIFFRACTIONf_plane_restr0.0031346
X-RAY DIFFRACTIONf_dihedral_angle_d5.2746272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.38671390.34121247X-RAY DIFFRACTION100
2.38-2.480.33621380.27781246X-RAY DIFFRACTION100
2.48-2.590.29381410.24241272X-RAY DIFFRACTION100
2.59-2.730.29411380.251236X-RAY DIFFRACTION100
2.73-2.90.31271400.27571262X-RAY DIFFRACTION100
2.9-3.120.29691390.25781252X-RAY DIFFRACTION100
3.12-3.440.26421410.21751270X-RAY DIFFRACTION100
3.44-3.930.21251420.1961275X-RAY DIFFRACTION100
3.93-4.950.18061430.15181286X-RAY DIFFRACTION100
4.95-57.10.21831500.2081357X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -0.578 Å / Origin y: -29.991 Å / Origin z: 28.253 Å
111213212223313233
T0.272800182793 Å20.00248869666003 Å20.0283290906977 Å2-0.194987309511 Å20.0129139675931 Å2--0.220073701758 Å2
L1.89424993623 °2-0.188661851016 °2-0.355042486713 °2-1.4848507174 °20.356269097714 °2--1.68626556817 °2
S0.0522835186739 Å °-0.0558443551083 Å °0.0831534191082 Å °-0.0279027077005 Å °-0.0388511172766 Å °-0.008413896709 Å °-0.176108378001 Å °-0.0544969928206 Å °-0.003211468954 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:224 OR RESID 301:301 OR RESID 302:303 OR RESID 401:500 ) )A11 - 224
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:224 OR RESID 301:301 OR RESID 302:303 OR RESID 401:500 ) )A301
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:224 OR RESID 301:301 OR RESID 302:303 OR RESID 401:500 ) )A302 - 303
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 11:224 OR RESID 301:301 OR RESID 302:303 OR RESID 401:500 ) )A401 - 500

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