[English] 日本語
Yorodumi
- PDB-2cg9: Crystal structure of an Hsp90-Sba1 closed chaperone complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cg9
TitleCrystal structure of an Hsp90-Sba1 closed chaperone complex
Components
  • ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
  • CO-CHAPERONE PROTEIN SBA1
KeywordsCHAPERONE / CHAPERONE COMPLEX / HSP90 / HEAT SHOCK PROTEIN / CO-CHAPERONE / ATP-BINDING / HEAT SHOCK / NUCLEOTIDE-BINDING / ACETYLATION
Function / homology
Function and homology information


Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / The NLRP3 inflammasome / 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 ...Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / The NLRP3 inflammasome / 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 / box C/D snoRNP assembly / regulation of telomere maintenance / protein targeting to mitochondrion / response to osmotic stress / 'de novo' protein folding / proteasome assembly / chaperone-mediated protein complex assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / protein maturation / Hsp90 protein binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / protein-containing complex / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Co-chaperone protein p23-like / Ribosomal Protein S5; domain 2 - #80 / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain ...Co-chaperone protein p23-like / Ribosomal Protein S5; domain 2 - #80 / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Ribosomal Protein S5; domain 2 / 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 / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent molecular chaperone HSP82 / Co-chaperone protein SBA1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAli, M.M.U. / Roe, S.M. / Prodromou, C. / Pearl, L.H.
CitationJournal: Nature / Year: 2006
Title: Crystal Structure of an Hsp90-Nucleotide-P23/Sba1 Closed Chaperone Complex
Authors: Ali, M.M.U. / Roe, S.M. / Vaughan, C. / Meyer, P. / Panaretou, B. / Piper, P.W. / Prodromou, C. / Pearl, L.H.
History
DepositionMar 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
X: CO-CHAPERONE PROTEIN SBA1
Y: CO-CHAPERONE PROTEIN SBA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,7256
Polymers187,7114
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.729, 126.729, 279.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15X
25Y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 210
2111B2 - 210
1121A240 - 327
2121B240 - 327
1131A342 - 520
2131B342 - 520
1141A526 - 677
2141B526 - 677
1151X12 - 130
2151Y12 - 130

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / 82 KDA HEAT SHOCK PROTEIN


Mass: 78082.758 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-677
Source method: isolated from a genetically manipulated source
Details: CHARGED LINKER REMOVED BETWEEN 221 AND 255 AND REPLACE BY LQHMASVD
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02829
#2: Protein CO-CHAPERONE PROTEIN SBA1


Mass: 15772.727 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-134 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28707
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Compound detailsENGINEERED RESIDUE IN CHAIN X, GLU 126 TO ALA ENGINEERED RESIDUE IN CHAIN Y, GLU 126 TO ALA
Sequence detailsCHARGED LINKER 221-255 REMOVED AND REPLACED BY LQHMASVD

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN WAS CRYSTALLISED BY THE HANGING DROP METHOD WITH 1:1 DROPS. PROTEIN AT 15MG/ML MIXED WITH 100MM HEPES PH 7.5, 20% PEG4K, 10% ISOPROPANOL, 10% GLYCEROL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.1→100 Å / Num. obs: 28878 / % possible obs: 67.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.7
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.3 / % possible all: 20.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HK7 AND 1AMW

1hk7

1amw


Resolution: 3.1→115.47 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.789 / SU B: 81.183 / SU ML: 0.68 / Cross valid method: THROUGHOUT / ESU R Free: 0.833 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.353 1451 5 %RANDOM
Rwork0.312 ---
obs0.314 27364 68.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2--1.6 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11844 0 62 0 11906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.98316365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77851444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.62625.269577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.633152309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1541558
X-RAY DIFFRACTIONr_chiral_restr0.0930.21838
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.26652
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.28313
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2061.57475
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.36211808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.50735246
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8664.54557
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
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1659tight positional0.030.05
2A553tight positional0.030.05
3A1470tight positional0.020.05
4A1100tight positional0.030.05
5X924tight positional0.020.05
1A1659tight thermal0.050.5
2A553tight thermal0.050.5
3A1470tight thermal0.040.5
4A1100tight thermal0.020.5
5X924tight thermal0.030.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.431 27
Rwork0.437 381

+
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