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- PDB-1byq: HSP90 N-TERMINAL DOMAIN BOUND TO ADP-MG -

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Basic information

Entry
Database: PDB / ID: 1byq
TitleHSP90 N-TERMINAL DOMAIN BOUND TO ADP-MG
ComponentsPROTEIN (HEAT SHOCK PROTEIN 90)
KeywordsCHAPERONE / CHAPERONE PROTEIN / ATP BINDING
Function / homology
Function and homology information


Scavenging by Class F Receptors / positive regulation of protein polymerization / vRNP Assembly / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Uptake and function of diphtheria toxin / central nervous system neuron axonogenesis / mitochondrial transport / Resistance of ERBB2 KD mutants to neratinib ...Scavenging by Class F Receptors / positive regulation of protein polymerization / vRNP Assembly / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Uptake and function of diphtheria toxin / central nervous system neuron axonogenesis / mitochondrial transport / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to tesevatinib / Drug-mediated inhibition of ERBB2 signaling / Drug resistance in ERBB2 TMD/JMD mutants / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / 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 / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / positive regulation of cellular protein catabolic process / dendritic growth cone / non-chaperonin molecular chaperone ATPase / regulation of protein ubiquitination / axon extension / protein unfolding / chaperone-mediated protein complex assembly / telomere maintenance via telomerase / Sema3A PAK dependent Axon repulsion / regulation of protein localization => GO:0032880 / RHOBTB2 GTPase cycle / positive regulation of tau-protein kinase activity / HSF1-dependent transactivation / HSF1 activation / response to unfolded protein / Attenuation phase / DNA polymerase binding / regulation of protein-containing complex assembly / eNOS activation / MHC class II protein complex binding / response to cold / axonal growth cone / 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 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / establishment of cell polarity / Recruitment of NuMA to mitotic centrosomes / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / activation of innate immune response / Signaling by ERBB2 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / endocytic vesicle lumen / positive regulation of telomerase activity / AURKA Activation by TPX2 / lysosomal lumen / positive regulation of interferon-beta production / Constitutive Signaling by Overexpressed ERBB2 / VEGFR2 mediated vascular permeability / ESR-mediated signaling / GTPase binding / nitric-oxide synthase regulator activity / cellular response to virus / myelin sheath / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 TMD/JMD mutants / tau protein binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Regulation of necroptotic cell death / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / Aggrephagy / VEGFA-VEGFR2 Pathway / Regulation of actin dynamics for phagocytic cup formation / Chaperone Mediated Autophagy / melanosome / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / histone deacetylase binding / unfolded protein binding / protein folding / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / positive regulation of nitric oxide biosynthetic process / cellular response to heat / scaffold protein binding / Extra-nuclear estrogen signaling / Potential therapeutics for SARS / disordered domain specific binding / response to heat / protein refolding / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / Estrogen-dependent gene expression / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / protein stabilization
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Heat shock protein Hsp90, N-terminal / Hsp90 protein / HSP90, C-terminal domain / Heat shock protein Hsp90 family / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-like ATPases / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Heat shock protein Hsp90, N-terminal / Hsp90 protein / HSP90, C-terminal domain / Heat shock protein Hsp90 family / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-like ATPases / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRusso, A.A. / Pavletich, N.P.
CitationJournal: J.Cell Biol. / Year: 1998
Title: In vivo function of Hsp90 is dependent on ATP binding and ATP hydrolysis.
Authors: Obermann, W.M. / Sondermann, H. / Russo, A.A. / Pavletich, N.P. / Hartl, F.U.
History
DepositionOct 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HEAT SHOCK PROTEIN 90)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1223
Polymers25,6711
Non-polymers4522
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)53.140, 42.500, 53.960
Angle α, β, γ (deg.)90.00, 115.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (HEAT SHOCK PROTEIN 90) / HSP90


Mass: 25670.795 Da / Num. of mol.: 1 / Fragment: RESIDUES 9 - 236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMATPgammaS11
20.2 Mmagnesium chloride11
30.1 MTris-HCl11
430 %PEG400011

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorDate: Jul 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 33303 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.059

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YES

1yes


Resolution: 1.5→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1600 4.6 %RANDOM
Rwork0.189 ---
obs0.189 31430 90.1 %-
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 28 384 2090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.6
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it6.5
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO

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