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- PDB-7s90: Cryogenic Human Hsp90a-NTD bound to adenine -

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Basic information

Entry
Database: PDB / ID: 7s90
TitleCryogenic Human Hsp90a-NTD bound to adenine
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 / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / 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 / 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 / protein import into mitochondrial matrix / dendritic growth cone / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / axonal growth cone / neurofibrillary tangle assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / nitric oxide metabolic process / eNOS activation / positive regulation of defense response to virus by host / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / response to salt stress / positive regulation of telomere maintenance via telomerase / Signaling by ERBB2 / cardiac muscle cell apoptotic process / 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 / Recruitment of mitotic centrosome proteins and complexes / activation of innate immune response / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of interferon-beta production / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / response to estrogen / tau protein binding / Downregulation of ERBB2 signaling / histone deacetylase binding / Chaperone Mediated Autophagy / neuron migration / Aggrephagy / positive regulation of nitric oxide biosynthetic process / positive regulation of protein catabolic process / disordered domain specific binding / MHC class II protein complex binding
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 superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENINE / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
Revision 1.2Apr 3, 2024Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details

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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)26,8752
Polymers26,7401
Non-polymers1351
Water2,774154
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)65.183, 88.451, 100.329
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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8 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: 1.79→36.26 Å / Num. obs: 26872 / % possible obs: 94.08 % / Redundancy: 2.8 % / Biso Wilson estimate: 35.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.27
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 0.833 / Num. unique obs: 2615 / CC1/2: 0.531

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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: 1.79→36.26 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 1942 7.44 %
Rwork0.1777 24159 -
obs0.1804 26101 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.4 Å2
Refinement stepCycle: LAST / Resolution: 1.79→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 10 154 1801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881710
X-RAY DIFFRACTIONf_angle_d1.05682316
X-RAY DIFFRACTIONf_chiral_restr0.0624264
X-RAY DIFFRACTIONf_plane_restr0.0082300
X-RAY DIFFRACTIONf_dihedral_angle_d5.9944231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.35371160.32661356X-RAY DIFFRACTION74.95
1.83-1.880.32921260.3131559X-RAY DIFFRACTION86.45
1.88-1.940.31231290.27041704X-RAY DIFFRACTION93.86
1.94-20.26151460.26071779X-RAY DIFFRACTION98.06
2-2.070.31861410.25821809X-RAY DIFFRACTION99.09
2.07-2.160.27831440.211778X-RAY DIFFRACTION98.87
2.16-2.260.21041440.18251798X-RAY DIFFRACTION98.28
2.26-2.370.20791430.1821765X-RAY DIFFRACTION98.66
2.37-2.520.20941390.17661738X-RAY DIFFRACTION94.42
2.52-2.720.23891380.17941721X-RAY DIFFRACTION93.79
2.72-2.990.23661450.17951798X-RAY DIFFRACTION98.33
2.99-3.420.20541460.16481814X-RAY DIFFRACTION97.85
3.42-4.310.18891440.13741790X-RAY DIFFRACTION95.74
4.31-36.260.17611410.17061750X-RAY DIFFRACTION89.54
Refinement TLS params.Method: refined / Origin x: -31.5647440412 Å / Origin y: 14.4613285858 Å / Origin z: -20.4945286589 Å
111213212223313233
T0.312742517681 Å20.0154346216948 Å20.026403426667 Å2-0.306817868416 Å20.0142888102317 Å2--0.312112995938 Å2
L0.752213827245 °20.0686942788144 °20.189755679064 °2-0.745000646932 °20.0138610439811 °2--0.807640565662 °2
S0.0109459349098 Å °-0.0606977061928 Å °0.0447525658259 Å °-0.0250784456651 Å °0.00957303400993 Å °-0.0321163334377 Å °-0.0597970262196 Å °-0.0516282434527 Å °-7.22066291392E-6 Å °
Refinement TLS groupSelection details: all

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