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- PDB-8z3h: Benzbromarone interferes with the interaction between Hsp90 and A... -

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Basic information

Entry
Database: PDB / ID: 8z3h
TitleBenzbromarone interferes with the interaction between Hsp90 and Aha1 by interacting with both of them
ComponentsActivator of 90 kDa heat shock protein ATPase homolog 1
KeywordsSTRUCTURAL PROTEIN / Holdase / activator of HSP90
Function / homology
Function and homology information


maintenance of unfolded protein / positive regulation of ATP-dependent activity / ATPase activator activity / protein folding chaperone / Hsp90 protein binding / unfolded protein binding / protein folding / protein-folding chaperone binding / cadherin binding / endoplasmic reticulum ...maintenance of unfolded protein / positive regulation of ATP-dependent activity / ATPase activator activity / protein folding chaperone / Hsp90 protein binding / unfolded protein binding / protein folding / protein-folding chaperone binding / cadherin binding / endoplasmic reticulum / extracellular exosome / cytosol
Similarity search - Function
Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, Aha1 / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily
Similarity search - Domain/homology
Activator of 90 kDa heat shock protein ATPase homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShi, L. / Zhong, Y. / Tang, J. / Xu, Z. / Zhang, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Benzbromarone interferes with the interaction between Hsp90 and Aha1 by interacting with both of them
Authors: Zhong, Y. / Shi, L.
History
DepositionApr 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activator of 90 kDa heat shock protein ATPase homolog 1


Theoretical massNumber of molelcules
Total (without water)15,1851
Polymers15,1851
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.200, 66.340, 68.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21A-468-

HOH

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Components

#1: Protein Activator of 90 kDa heat shock protein ATPase homolog 1 / AHA1 / p38


Mass: 15185.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: pET15b / Source: (gene. exp.) Homo sapiens (human) / Gene: AHSA1, C14orf3, HSPC322 / Production host: Eschenbachia (plant) / References: UniProt: O95433
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MIB pH 7.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979145 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979145 Å / Relative weight: 1
ReflectionResolution: 1.5→42.45 Å / Num. obs: 19683 / % possible obs: 97.92 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 17.71
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 1875 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia23.6.1data scaling
xia23.6.1data reduction
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.24 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21848 995 5.1 %RANDOM
Rwork0.17853 ---
obs0.18062 18688 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.471 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0 Å2
2--0.88 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 0 70 1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131100
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151007
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.6641488
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5762328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4965131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70221.96761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.04157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5861.367527
X-RAY DIFFRACTIONr_mcbond_other1.5591.364526
X-RAY DIFFRACTIONr_mcangle_it2.3172.044657
X-RAY DIFFRACTIONr_mcangle_other2.3182.046658
X-RAY DIFFRACTIONr_scbond_it3.1521.819573
X-RAY DIFFRACTIONr_scbond_other3.1491.82574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8662.575832
X-RAY DIFFRACTIONr_long_range_B_refined6.38418.1831243
X-RAY DIFFRACTIONr_long_range_B_other6.20917.5561215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 64 -
Rwork0.22 1299 -
obs--93.87 %

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