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- PDB-7s8y: Cryogenic apo Human Hsp90a-NTD -

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Basic information

Entry
Database: PDB / ID: 7s8y
TitleCryogenic apo Human Hsp90a-NTD
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsStachowski, T.R. / Vanarotti, M. / Lopez, K. / 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 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


Theoretical massNumber of molelcules
Total (without water)26,7401
Polymers26,7401
Non-polymers00
Water4,594255
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)65.146, 88.394, 99.546
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES, pH 7 and 1.6 M sodium citrate dihydrate

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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: 1.59→44.2 Å / Num. obs: 38596 / % possible obs: 98.96 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.77
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 0.678 / Num. unique obs: 3808 / CC1/2: 0.567

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Processing

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

1yer


Resolution: 1.59→44.2 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1913 1999 5.18 %
Rwork0.1645 36597 -
obs0.1659 38596 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.28 Å2
Refinement stepCycle: LAST / Resolution: 1.59→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 0 255 1891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992025
X-RAY DIFFRACTIONf_angle_d1.04862780
X-RAY DIFFRACTIONf_chiral_restr0.0635310
X-RAY DIFFRACTIONf_plane_restr0.0099370
X-RAY DIFFRACTIONf_dihedral_angle_d5.5267310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.30221360.31012487X-RAY DIFFRACTION95.49
1.63-1.670.31021430.28022622X-RAY DIFFRACTION99.71
1.67-1.720.28181430.25352621X-RAY DIFFRACTION99.75
1.72-1.780.27161410.23172587X-RAY DIFFRACTION99.67
1.78-1.840.22621420.21092613X-RAY DIFFRACTION99.57
1.84-1.910.24361450.20012625X-RAY DIFFRACTION99.71
1.91-20.22751420.16812622X-RAY DIFFRACTION99.53
2-2.110.17931400.152548X-RAY DIFFRACTION97.22
2.11-2.240.15711440.14432637X-RAY DIFFRACTION99.96
2.24-2.410.19731440.14872636X-RAY DIFFRACTION99.86
2.41-2.650.18051450.14742653X-RAY DIFFRACTION99.82
2.65-3.040.18691440.15432626X-RAY DIFFRACTION98.61
3.04-3.830.17171440.13652651X-RAY DIFFRACTION98.24
3.83-44.20.16541460.15882669X-RAY DIFFRACTION95.36
Refinement TLS params.Method: refined / Origin x: -31.288037487 Å / Origin y: 14.6940509785 Å / Origin z: -20.2940026259 Å
111213212223313233
T0.14605158754 Å20.00241656282235 Å20.0182868918378 Å2-0.128933330022 Å20.0167671852688 Å2--0.151743361031 Å2
L1.54615841962 °2-0.239172561984 °20.0176006394608 °2-1.04543922645 °20.0428030913922 °2--1.52210728625 °2
S0.0222680960282 Å °-0.0760500953442 Å °0.0393124740468 Å °-0.018818935582 Å °-0.00502199544943 Å °-0.0104812911382 Å °-0.0349242469156 Å °-0.0620563329517 Å °-0.018613812902 Å °
Refinement TLS groupSelection details: all

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