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

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Basic information

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


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 ...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 / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / 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
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / 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 ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.3Dec 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82


Theoretical massNumber of molelcules
Total (without water)140,5273
Polymers140,5273
Non-polymers00
Water0
1
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82


Theoretical massNumber of molelcules
Total (without water)281,0546
Polymers281,0546
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)105.555, 105.555, 289.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
12A
22B
32D
13A
23B
33D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLEULEUAA274 - 4432 - 171
211LYSLYSLEULEUBB274 - 4432 - 171
311LYSLYSLEULEUDC274 - 4432 - 171
112ARGARGGLUGLUAA444 - 529172 - 257
212ARGARGGLUGLUBB444 - 529172 - 257
312ARGARGGLUGLUDC444 - 529172 - 257
113ASPASPARGARGAA534 - 599262 - 327
213ASPASPARGARGBB534 - 599262 - 327
313ASPASPARGARGDC534 - 599262 - 327
123LYSLYSARGARGAA610 - 670338 - 398
223LYSLYSARGARGBB610 - 670338 - 398
323LYSLYSARGARGDC610 - 670338 - 398

NCS ensembles :
ID
1
2
3

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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: 46842.391 Da / Num. of mol.: 3 / Fragment: MIDDLE AND C-TERMINAL DOMAINS, RESIDUES 273-677
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

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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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 41369 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

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

1hk7


Resolution: 3→288.67 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.896 / SU B: 51.113 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1688 5 %RANDOM
Rwork0.257 ---
obs0.258 32118 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å20 Å20 Å2
2---4.61 Å20 Å2
3---9.23 Å2
Refinement stepCycle: LAST / Resolution: 3→288.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9882 0 0 0 9882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02210065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.98113560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09851212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.81425.096471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.764151965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2191551
X-RAY DIFFRACTIONr_chiral_restr0.1140.21515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027431
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.25216
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.27162
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.2207
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4871.56199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81229870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16734292
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9164.53690
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1419tight positional0.070.05
12B1419tight positional0.070.05
13D1419tight positional0.070.05
21A707tight positional0.080.05
22B707tight positional0.080.05
23D707tight positional0.110.05
31A1007tight positional0.050.05
32B1007tight positional0.050.05
33D1007tight positional0.060.05
11A1419tight thermal0.150.5
12B1419tight thermal0.150.5
13D1419tight thermal0.150.5
21A707tight thermal0.190.5
22B707tight thermal0.220.5
23D707tight thermal0.370.5
31A1007tight thermal0.080.5
32B1007tight thermal0.070.5
33D1007tight thermal0.10.5
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 114
Rwork0.331 2325
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)
13.0657-1.1890.50852.8433-1.46122.46860.03820.0082-0.0269-0.25250.1262-0.14320.22110.1065-0.1645-0.4261-0.0106-0.1031-0.5003-0.0725-0.357-50.08538.8814-13.2738
24.1781-1.63250.295211.14270.05386.0554-0.0429-0.2622-0.27150.3486-0.1338-0.28580.7589-0.08470.1767-0.288-0.0448-0.0898-0.47130.10890.0057-51.430915.16558.077
33.7998-0.36320.26154.1269-3.1697.6363-0.1536-0.25360.20980.67720.05880.3195-0.2342-0.00320.0947-0.21680.0263-0.02250.15310.18940.4144-55.303815.753831.2736
43.1551.5501-1.36062.2288-0.95111.7103-0.01980.1697-0.2503-0.00850.0052-0.3985-0.02960.16770.0147-0.50010.0922-0.0815-0.359-0.0119-0.3549-21.988548.48571.7145
511.648-0.5820.28339.53741.9110.3967-0.03310.07570.8658-0.06940.0886-0.5997-0.36490.1724-0.0555-0.5039-0.0304-0.0553-0.26390.04550.00230.180171.14185.775
68.9758-0.66023.07358.6059-0.72014.7376-0.1136-0.3020.38280.3732-0.09950.1135-0.68520.1710.21310.0118-0.0651-0.0435-0.0281-0.13240.3365-2.588593.547812.1722
72.2342-0.35651.96032.85891.12782.96430.06320.0920.1-0.2305-0.1086-0.28730.18780.26540.0454-0.41890.01340.0542-0.40840.0869-0.2969-34.71266.6994-23.2547
811.86282.29432.03537.3231-0.837112.49810.15771.0284-0.4013-0.94560.1047-0.0262-0.3323-0.648-0.2624-0.04950.1659-0.0419-0.0948-0.0444-0.9247-59.501771.4011-42.994
95.2970.26094.62574.0095-1.46785.84550.0246-0.05790.218-0.1090.02080.28150.1671-0.1872-0.0454-0.10520.0794-0.1794-0.1744-0.0456-0.104-81.952376.3841-37.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A273 - 443
2X-RAY DIFFRACTION2A444 - 529
3X-RAY DIFFRACTION3A534 - 670
4X-RAY DIFFRACTION4B273 - 443
5X-RAY DIFFRACTION5B444 - 529
6X-RAY DIFFRACTION6B534 - 670
7X-RAY DIFFRACTION7D273 - 443
8X-RAY DIFFRACTION8D444 - 529
9X-RAY DIFFRACTION9D534 - 670

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