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- PDB-2cg9: Crystal structure of an Hsp90-Sba1 closed chaperone complex -

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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) / regulation of telomerase activity / The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / regulation of telomerase activity / The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / negative regulation of DNA binding / protein maturation / proteasome assembly / chaperone-mediated protein complex assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / Hsp90 protein binding / unfolded protein binding / protein folding / cellular response to heat / protein-folding chaperone binding / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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 / Adenosine 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

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Experimental details

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Experiment

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

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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.

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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

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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

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