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- PDB-7s9i: Room-temperature Human Hsp90a-NTD bound to EC144 -

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Basic information

Entry
Database: PDB / ID: 7s9i
TitleRoom-temperature Human Hsp90a-NTD bound to EC144
ComponentsHeat shock protein HSP 90-alphaHeat shock response
KeywordsChaperone / Hydrolase / heat shock / signaling
Function / homology
Function and homology information


sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity ...sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / 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 / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / skeletal muscle contraction / regulation of protein ubiquitination / positive regulation of cell size / protein unfolding / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / DNA polymerase binding / axonal growth cone / 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 cardiac muscle contraction / Signaling by ERBB2 / cardiac muscle cell apoptotic process / Recruitment of mitotic centrosome proteins and complexes / positive regulation of telomerase activity / response to salt stress / positive regulation of defense response to virus by host / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / response to cold / activation of innate immune response / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / cellular response to virus / VEGFA-VEGFR2 Pathway / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / histone deacetylase binding / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / melanosome
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-7PP / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStachowski, T.R. / Vanarotti, M. / 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 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1542
Polymers26,7401
Non-polymers4141
Water1,65792
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)68.315, 91.151, 99.586
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 response / 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-7PP / 5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2 -ol / EC44


Mass: 413.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
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: 278 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: 1.75→36.81 Å / Num. obs: 30975 / % possible obs: 94.25 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.29 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.35
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.743 / Num. unique obs: 3036 / CC1/2: 0.395

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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: 1.75→36.81 Å / SU ML: 0.2492 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1914 1944 6.5 %
Rwork0.1665 27945 -
obs0.1681 29889 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 29 92 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761906
X-RAY DIFFRACTIONf_angle_d1.11752605
X-RAY DIFFRACTIONf_chiral_restr0.0585289
X-RAY DIFFRACTIONf_plane_restr0.0091339
X-RAY DIFFRACTIONf_dihedral_angle_d8.7153275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.3351240.31751657X-RAY DIFFRACTION79.65
1.79-1.840.29681240.3031781X-RAY DIFFRACTION85.31
1.84-1.90.35791350.31911875X-RAY DIFFRACTION90.22
1.9-1.960.36391330.31221921X-RAY DIFFRACTION92.31
1.96-2.030.27791370.2411986X-RAY DIFFRACTION94.86
2.03-2.110.2191440.19012085X-RAY DIFFRACTION98.85
2.11-2.20.20421430.17112075X-RAY DIFFRACTION99.06
2.2-2.320.20581430.17892085X-RAY DIFFRACTION98.89
2.32-2.470.23781440.17332083X-RAY DIFFRACTION98.89
2.47-2.660.19451440.16792079X-RAY DIFFRACTION98.36
2.66-2.920.19991440.16922087X-RAY DIFFRACTION97.47
2.92-3.350.1811400.15832022X-RAY DIFFRACTION94.95
3.35-4.220.13511430.13062079X-RAY DIFFRACTION95.94
4.22-36.810.17631460.15322130X-RAY DIFFRACTION94.75
Refinement TLS params.Method: refined / Origin x: 33.061993215 Å / Origin y: 14.745990686 Å / Origin z: -20.297855447 Å
111213212223313233
T0.262925824135 Å20.0024722647851 Å20.0161003058234 Å2-0.222031132209 Å20.0241116050844 Å2--0.265339940911 Å2
L2.86601050199 °2-0.208496292085 °20.124953102939 °2-1.7612062897 °20.0671872812528 °2--2.45305346016 °2
S0.0157531993984 Å °-0.0673439182269 Å °0.0199671765582 Å °0.0299011869688 Å °-0.0296977026057 Å °0.0169009928185 Å °-0.0741206104314 Å °-0.0599384743833 Å °0.0197223781883 Å °
Refinement TLS groupSelection details: all

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