[English] 日本語
Yorodumi
- PDB-9d9i: Human Hsp90b nucleotide binding domain in complex with BRI2312 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d9i
TitleHuman Hsp90b nucleotide binding domain in complex with BRI2312
ComponentsHeat shock protein HSP 90-beta
KeywordsCHAPERONE / HSP90 nucleotide binding domain inhibitor complex
Function / homology
Function and homology information


HSP90-CDC37 chaperone complex / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / histone methyltransferase binding / dynein axonemal particle / receptor ligand inhibitor activity / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity ...HSP90-CDC37 chaperone complex / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / histone methyltransferase binding / dynein axonemal particle / receptor ligand inhibitor activity / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity / protein folding chaperone complex / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / positive regulation of transforming growth factor beta receptor signaling pathway / Uptake and function of diphtheria toxin / dendritic growth cone / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / The NLRP3 inflammasome / protein phosphatase activator activity / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / axonal growth cone / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / : / supramolecular fiber organization / DNA polymerase binding / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / peptide binding / cellular response to interleukin-4 / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / placenta development / nitric-oxide synthase regulator activity / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / tau protein binding / histone deacetylase binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint / melanosome / unfolded protein binding / protein folding / double-stranded RNA binding / regulation of protein localization / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / regulation of cell cycle / protein dimerization activity / protein stabilization / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / negative regulation of apoptotic process / virion attachment to host cell / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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
: / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Canada Foundation for Innovation Canada
CitationJournal: To be published
Title: Human Hsp90b nucleotide binding domain in complex with BRI2312
Authors: Kuntz, D.A. / Prive, G.G.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,9154
Polymers25,1181
Non-polymers7973
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.794, 90.524, 97.451
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP 84 / HSP84 / Heat shock protein family C member 3


Mass: 25118.373 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPC3, HSPCB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08238
#2: Chemical ChemComp-A1A24 / (1P)-3-amino-6-[({1-[(2R)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]piperidin-4-yl}amino)methyl]-1-(4-phenyl-3,4-dihydro-2H-1,4-benzoxazin-6-yl)thieno[2,3-b]pyrazin-2(1H)-one


Mass: 725.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H37F2N9O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 21% PEG6000, 0.1M NaCacodylate pH 6.6, 1M Li

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54189 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54189 Å / Relative weight: 1
ReflectionResolution: 1.5→29.21 Å / Num. obs: 46661 / % possible obs: 98.2 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 15.5 / Num. measured all: 228923
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 87.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.582 / Num. measured all: 5732 / Num. unique obs: 2030 / CC1/2: 0.733 / Rpim(I) all: 0.385 / Rrim(I) all: 0.704 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0430 (refmacat 0.4.77)refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.841 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.852 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1868 2286 5.011 %
Rwork0.159 43332 -
all0.16 --
obs-45618 95.854 %
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: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.895 Å2-0 Å20 Å2
2--0.319 Å2-0 Å2
3---0.576 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 54 383 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121913
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161790
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.8712611
X-RAY DIFFRACTIONr_angle_other_deg0.8341.7994130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.397511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79310338
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2641088
X-RAY DIFFRACTIONr_chiral_restr0.0960.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022305
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02439
X-RAY DIFFRACTIONr_nbd_refined0.2170.2391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21626
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2965
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0830.218
X-RAY DIFFRACTIONr_nbd_other0.1150.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.232
X-RAY DIFFRACTIONr_mcbond_it1.8091.42930
X-RAY DIFFRACTIONr_mcbond_other1.811.419930
X-RAY DIFFRACTIONr_mcangle_it2.8222.5431187
X-RAY DIFFRACTIONr_mcangle_other2.8292.5481188
X-RAY DIFFRACTIONr_scbond_it3.1731.775983
X-RAY DIFFRACTIONr_scbond_other3.171.775983
X-RAY DIFFRACTIONr_scangle_it4.9813.0941424
X-RAY DIFFRACTIONr_scangle_other4.9793.0931425
X-RAY DIFFRACTIONr_lrange_it6.93617.4312462
X-RAY DIFFRACTIONr_lrange_other6.39214.7792307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.241470.26327310.26234460.9550.94983.51710.241
1.539-1.5810.2441570.23328270.23334070.9580.96187.58440.21
1.581-1.6270.2711370.22628130.22832840.9560.96589.82950.194
1.627-1.6760.2521470.20927850.21131880.9580.97191.96990.181
1.676-1.7310.2121540.19627920.19731290.9710.97694.15150.165
1.731-1.7920.1951350.17427530.17529910.9770.98196.55630.148
1.792-1.8590.1731450.16627400.16729180.9820.98398.86910.142
1.859-1.9350.1921460.1626290.16227840.9770.98499.67670.138
1.935-2.020.1681360.15925520.1626930.9830.98599.81430.14
2.02-2.1180.1961230.15624650.15825890.9750.98599.96140.142
2.118-2.2320.1751210.14323100.14524340.9820.98899.87670.133
2.232-2.3670.1571240.13522030.13723290.9850.98899.91410.125
2.367-2.5290.1751070.13320770.13521840.9820.9891000.122
2.529-2.730.1521010.13219520.13320550.9860.98999.90270.125
2.73-2.9880.202990.15117990.15418990.9780.98699.94730.146
2.988-3.3360.199790.14916500.15217300.9760.98699.94220.147
3.336-3.8440.187780.14514340.14715160.9790.98899.73610.146
3.844-4.6870.136630.13212480.13213210.990.98999.2430.139
4.687-6.5420.214530.189740.18210390.9790.98598.8450.186
6.542-28.8410.189340.1935980.1936430.980.97398.28930.195
Refinement TLS params.Method: refined / Origin x: 0.2976 Å / Origin y: 14.8722 Å / Origin z: 20.7238 Å
111213212223313233
T0.0128 Å2-0.0017 Å20.0105 Å2-0.0074 Å2-0.0123 Å2--0.0318 Å2
L0.5928 °20.042 °2-0.0314 °2-0.0439 °20.0458 °2--0.389 °2
S0.0065 Å °0.0261 Å °0.0171 Å °0.02 Å °0.0065 Å °0.0019 Å °0.0248 Å °0.0175 Å °-0.013 Å °
Refinement TLS groupSelection: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more