[English] 日本語
Yorodumi
- PDB-1us7: Complex of Hsp90 and P50 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1us7
TitleComplex of Hsp90 and P50
Components
  • HEAT SHOCK PROTEIN HSP82
  • HSP90 CO-CHAPERONE CDC37
KeywordsCHAPERONE / CHAPERONE CO-CHAPERONE REGULATION / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / The NLRP3 inflammasome / HSP90-CDC37 chaperone complex / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation ...regulation of type II interferon-mediated signaling pathway / The NLRP3 inflammasome / HSP90-CDC37 chaperone complex / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / positive regulation of type 2 mitophagy / regulation of cyclin-dependent protein serine/threonine kinase activity / protein kinase regulator activity / box C/D snoRNP assembly / protein folding chaperone complex / regulation of telomere maintenance / protein targeting to mitochondrion / response to osmotic stress / 'de novo' protein folding / post-transcriptional regulation of gene expression / 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 / regulation of type I interferon-mediated signaling pathway / proteasome assembly / protein targeting / RHOBTB2 GTPase cycle / heat shock protein binding / Signaling by ERBB2 / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / Constitutive Signaling by Overexpressed ERBB2 / protein maturation / Hsp90 protein binding / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / kinase binding / Downregulation of ERBB2 signaling / unfolded protein binding / protein folding / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / protein-folding chaperone binding / cellular response to heat / protein refolding / scaffold protein binding / protein stabilization / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / ATP hydrolysis activity / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #250 / Cdc37, Hsp90 binding domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding ...Helix Hairpins - #250 / Cdc37, Hsp90 binding domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / Helix Hairpins / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histidine kinase-like ATPases / Special / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82 / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoe, S.M. / Ali, M.M.U. / Pearl, L.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: The Mechanism of Hsp90 Regulation by the Protein Kinase-Specific Cochaperone p50(Cdc37)
Authors: Roe, S.M. / Ali, M.M.U. / Meyer, P. / Vaughan, C.K. / Panaretou, B. / Piper, P.W. / Prodromou, C. / Pearl, L.H.
History
DepositionNov 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP82
B: HSP90 CO-CHAPERONE CDC37


Theoretical massNumber of molelcules
Total (without water)55,0782
Polymers55,0782
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.759, 83.759, 148.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2059-

HOH

-
Components

#1: Protein HEAT SHOCK PROTEIN HSP82 / HSP82 / HSP90 / YPL240C


Mass: 24208.582 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829
#2: Protein HSP90 CO-CHAPERONE CDC37 / P50 / HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT / P50CDC37 / CDC37


Mass: 30869.100 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 125-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q16543
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: HSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS IN HIGHER CONCENTRATIONS FOR ...FUNCTION: HSP82 IS AN ESSENTIAL PROTEIN THAT IS REQUIRED BY CELLS IN HIGHER CONCENTRATIONS FOR GROWTH AT HIGHER TEMPERATURES. CDC37 CO-CHAPERONE BINDS TO NUMEROUS KINASES AND PROMOTES THEIR INTERACTION WITH THE HSP90 COMPLEX, RESULTING IN STABILIZATION AND PROMOTION OF THEIR ACTIVITY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: CRYSTALS OF THE COMPLEX WERE GROWN FROM A MIXTURE OF N-HSP90 AND C-P50 AT A FINAL CONCENTRATION OF 0.5MM AND 0.4MM RESPECTIVELY, IN A SOLUTION CONTAINING 12% POLYETHYLENE GLYCOL 4000, 16% ...Details: CRYSTALS OF THE COMPLEX WERE GROWN FROM A MIXTURE OF N-HSP90 AND C-P50 AT A FINAL CONCENTRATION OF 0.5MM AND 0.4MM RESPECTIVELY, IN A SOLUTION CONTAINING 12% POLYETHYLENE GLYCOL 4000, 16% ISOPROPANOL AND 100MM SODIUM CITRATE, PH 6.0. CRYSTAL DROPS WERE SET UP USING THE HANGING-DROP VAPOUR DIFFUSION METHOD, INITIALLY AT 4 DEGREES C FOR 48 HOURS AND THEN TRANSFERRED TO 14 DEGREES C.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 mMN-Hsp901drop
20.4 mMC-p501drop
312 %PEG40001reservoir
416 %isopropanol1reservoir
5100 mMsodium citrate1reservoirpH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9202
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.3→36.3 Å / Num. obs: 26462 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMW

1amw


Resolution: 2.3→72.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.996 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1333 5 %RANDOM
Rwork0.185 ---
obs0.188 25125 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 0 176 3414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.9664423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1570.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21479
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3791.51986
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52323205
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.25931306
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.884.51218
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 91
Rwork0.216 1839
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7418-0.01620.25650.68470.1640.7169-0.0234-0.1178-0.0287-0.03190.01530.0217-0.04230.10850.00810.10190.03220.01140.1941-0.00590.113753.728258.48124.9341
20.42190.22550.15760.4698-0.43460.4419-0.059-0.05690.0316-0.27760.0513-0.00160.16020.11510.00760.19440.0477-0.00690.1355-0.02920.14152.430853.0334-25.4091
32.6199-0.86120.21993.4618-1.1045.21610.0392-0.09950.40230.01270.05820.4613-0.4912-0.4311-0.09740.1963-0.0716-0.01490.0266-0.0070.34011.333742.5906-45.4927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 207
2X-RAY DIFFRACTION2B148 - 286
3X-RAY DIFFRACTION3B287 - 347
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 72.5 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.075

+
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