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- PDB-8x2r: The Crystal Structure of HSP 90-alpha from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x2r
TitleThe Crystal Structure of HSP 90-alpha from Biortus.
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / Host-virus interaction / ATP-binding
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 / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / 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 / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / 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 / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / tau protein binding / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Downregulation of ERBB2 signaling / response to estrogen / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / neuron migration / Aggrephagy / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint
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: 1.45 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Lu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of HSP 90-alpha from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Lu, Y.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,0787
Polymers26,5861
Non-polymers4936
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.712, 88.653, 99.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

21A-693-

HOH

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Components

#1: Protein Heat shock protein HSP 90-alpha


Mass: 26585.773 Da / Num. of mol.: 1 / Mutation: S52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: (Index-H6) 0.2M Sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953698 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953698 Å / Relative weight: 1
ReflectionResolution: 1.45→36.28 Å / Num. obs: 51928 / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.3
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3646

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→34.511 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.213 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1561 2640 5.084 %
Rwork0.1264 49288 -
all0.128 --
obs-51928 99.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.439 Å2
Baniso -1Baniso -2Baniso -3
1-2.845 Å20 Å20 Å2
2--0.462 Å20 Å2
3----3.307 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 32 333 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131753
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171703
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6452363
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5813945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35523.79387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.43715330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.472158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined0.1990.2356
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21550
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2868
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2225
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.28
X-RAY DIFFRACTIONr_nbd_other0.160.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.221
X-RAY DIFFRACTIONr_mcbond_it2.8822.201855
X-RAY DIFFRACTIONr_mcbond_other2.7842.195854
X-RAY DIFFRACTIONr_mcangle_it3.5123.3121071
X-RAY DIFFRACTIONr_mcangle_other3.5283.3191072
X-RAY DIFFRACTIONr_scbond_it3.5522.736898
X-RAY DIFFRACTIONr_scbond_other3.552.738899
X-RAY DIFFRACTIONr_scangle_it4.2043.891284
X-RAY DIFFRACTIONr_scangle_other4.2033.8921285
X-RAY DIFFRACTIONr_lrange_it5.23229.5862110
X-RAY DIFFRACTIONr_lrange_other4.98827.9972010
X-RAY DIFFRACTIONr_rigid_bond_restr2.31533456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.2551960.2513646X-RAY DIFFRACTION100
1.488-1.5280.2041560.2023522X-RAY DIFFRACTION100
1.528-1.5730.2051880.1763407X-RAY DIFFRACTION99.9722
1.573-1.6210.2131800.1543321X-RAY DIFFRACTION100
1.621-1.6740.2291730.1463228X-RAY DIFFRACTION100
1.674-1.7330.1651580.1233142X-RAY DIFFRACTION100
1.733-1.7980.1571720.1112976X-RAY DIFFRACTION99.9048
1.798-1.8720.1561680.112907X-RAY DIFFRACTION100
1.872-1.9550.1351410.0982794X-RAY DIFFRACTION100
1.955-2.050.151450.1072674X-RAY DIFFRACTION100
2.05-2.1610.1371350.1022545X-RAY DIFFRACTION100
2.161-2.2920.1341270.12396X-RAY DIFFRACTION99.8812
2.292-2.450.1391220.1022272X-RAY DIFFRACTION99.9582
2.45-2.6460.13960.1022156X-RAY DIFFRACTION99.9113
2.646-2.8980.1521250.1161931X-RAY DIFFRACTION99.9028
2.898-3.2390.1751100.1271779X-RAY DIFFRACTION100
3.239-3.7390.155770.1341584X-RAY DIFFRACTION99.9398
3.739-4.5750.108700.1081345X-RAY DIFFRACTION99.7181
4.575-6.4550.186620.1641058X-RAY DIFFRACTION100
6.455-34.5110.184390.173606X-RAY DIFFRACTION95.6973

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