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- PDB-3t2s: HSP90 N-terminal domain bound to AGS -

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Basic information

Entry
Database: PDB / ID: 3t2s
TitleHSP90 N-terminal domain bound to AGS
ComponentsHeat shock protein HSP 90-alphaHeat shock response
KeywordsCHAPERONE / ATPase
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 / Uptake and function of diphtheria toxin / chaperone-mediated autophagy / 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 / Uptake and function of diphtheria toxin / chaperone-mediated autophagy / central nervous system neuron axonogenesis / mitochondrial transport / Resistance of ERBB2 KD mutants to neratinib / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Resistance of ERBB2 KD mutants to afatinib / dendritic growth cone / TPR domain binding / positive regulation of protein catabolic process => GO:0045732 / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / regulation of protein ubiquitination / protein unfolding / axon extension / chaperone-mediated protein complex assembly / Sema3A PAK dependent Axon repulsion / telomere maintenance via telomerase / positive regulation of tau-protein kinase activity / RHOBTB2 GTPase cycle / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / Attenuation phase / DNA polymerase binding / regulation of protein-containing complex assembly / eNOS activation / axonal growth cone / response to cold / positive regulation of defense response to virus by host / Loss of proteins required for interphase microtubule organization from the centrosome / Loss of Nlp from mitotic centrosomes / establishment of cell polarity / protein tyrosine kinase binding / Recruitment of mitotic centrosome proteins and complexes / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Recruitment of NuMA to mitotic centrosomes / Signaling by ERBB2 / nitric-oxide synthase regulator activity / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / protein folding chaperone / endocytic vesicle lumen / positive regulation of telomerase activity / positive regulation of interferon-beta production / lysosomal lumen / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / GTPase binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / tau protein binding / Signaling by ERBB2 TMD/JMD mutants / 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 / histone deacetylase binding / regulation of protein localization / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / protein folding / positive regulation of nitric oxide biosynthetic process / cellular response to heat / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / scaffold protein binding / disordered domain specific binding / myelin sheath / MHC class II protein complex binding / Extra-nuclear estrogen signaling / Potential therapeutics for SARS / response to heat / protein refolding / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent gene expression / secretory granule lumen / protein stabilization / Interleukin-4 and Interleukin-13 signaling
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Heat shock protein Hsp90, N-terminal / Hsp90 protein / Heat shock protein Hsp90 family / HSP90, C-terminal domain / 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 / Heat shock protein Hsp90 family / HSP90, C-terminal domain / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsLi, J.
CitationJournal: To be published
Title: HSP90 N-terminal domain bound to AGS
Authors: Li, J.
History
DepositionJul 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4096
Polymers51,3142
Non-polymers1,0954
Water7,404411
1
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2043
Polymers25,6571
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2043
Polymers25,6571
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.237, 55.939, 60.550
Angle α, β, γ (deg.)93.61, 95.60, 112.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock response / Heat shock 86 kDa / HSP 86 / HSP86 / Renal carcinoma antigen NY-REN-38


Mass: 25656.768 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 9-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90A, HSP90AA1, HSPC1, HSPCA / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P07900
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#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 / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 20~25% PEG 4000, 200mM magnesium chloride, 100mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 78308 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.268 / Rsym value: 0.268 / Net I/σ(I): 6.376

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YES
Resolution: 1.501→41.271 Å / SU ML: 0.19 / σ(F): 0.07 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1955 2.56 %
Rwork0.1848 --
obs0.1858 76450 92.4 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.153 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0496 Å21.5114 Å2-0.4802 Å2
2---0.7367 Å21.1464 Å2
3---0.6871 Å2
Refinement stepCycle: LAST / Resolution: 1.501→41.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 64 411 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133446
X-RAY DIFFRACTIONf_angle_d1.474660
X-RAY DIFFRACTIONf_dihedral_angle_d18.0651286
X-RAY DIFFRACTIONf_chiral_restr0.096532
X-RAY DIFFRACTIONf_plane_restr0.007584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5015-1.5390.30081350.2015489585
1.539-1.58060.19931350.1704507889
1.5806-1.62710.24231320.1568522790
1.6271-1.67970.23521380.1615516890
1.6797-1.73970.22761400.1589537292
1.7397-1.80940.2311400.1607534393
1.8094-1.89170.18231390.1524531893
1.8917-1.99140.21591430.1563545094
1.9914-2.11620.24691420.1706543495
2.1162-2.27960.221430.1818551195
2.2796-2.5090.21491420.1866546895
2.509-2.87190.24951400.198530892
2.8719-3.6180.22351440.1922553196
3.618-41.28630.21951420.209539294

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