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- PDB-2jki: Complex of Hsp90 N-terminal and Sgt1 CS domain -

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Basic information

Entry
Database: PDB / ID: 2jki
TitleComplex of Hsp90 N-terminal and Sgt1 CS domain
Components
  • CYTOSOLIC HEAT SHOCK PROTEIN 90
  • SGT1-LIKE PROTEIN
KeywordsCHAPERONE / HSP90 SGT1 / STRESS RESPONSE
Function / homology
Function and homology information


regulation of defense response to fungus / cellular response to auxin stimulus / embryo development ending in seed dormancy / SCF ubiquitin ligase complex / ATP-dependent protein folding chaperone / defense response / unfolded protein binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / protein-folding chaperone binding ...regulation of defense response to fungus / cellular response to auxin stimulus / embryo development ending in seed dormancy / SCF ubiquitin ligase complex / ATP-dependent protein folding chaperone / defense response / unfolded protein binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / protein-folding chaperone binding / innate immune response / ATP hydrolysis activity / ATP binding / nucleus / cytosol
Similarity search - Function
Protein Sgt1-like / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Tetratricopeptide repeat ...Protein Sgt1-like / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cytosolic heat shock protein 90 / Protein SGT1 homolog A / Protein SGT1 homolog A
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
ARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhang, M. / Pearl, L.H.
CitationJournal: Embo J. / Year: 2008
Title: Structural and Functional Coupling of Hsp90- and Sgt1-Centred Multi-Protein Complexes.
Authors: Zhang, M. / Boter, M. / Li, K. / Kadota, Y. / Panaretou, B. / Prodromou, C. / Shirasu, K. / Pearl, L.H.
History
DepositionAug 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 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 / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
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: CYTOSOLIC HEAT SHOCK PROTEIN 90
B: CYTOSOLIC HEAT SHOCK PROTEIN 90
C: CYTOSOLIC HEAT SHOCK PROTEIN 90
S: SGT1-LIKE PROTEIN
T: SGT1-LIKE PROTEIN
U: SGT1-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0899
Polymers106,8076
Non-polymers1,2823
Water0
1
A: CYTOSOLIC HEAT SHOCK PROTEIN 90
S: SGT1-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0303
Polymers35,6022
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint2.4 kcal/mol
Surface area17930 Å2
MethodPQS
2
B: CYTOSOLIC HEAT SHOCK PROTEIN 90
T: SGT1-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0303
Polymers35,6022
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint1.4 kcal/mol
Surface area19070 Å2
MethodPQS
3
C: CYTOSOLIC HEAT SHOCK PROTEIN 90
U: SGT1-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0303
Polymers35,6022
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint1.4 kcal/mol
Surface area17770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.268, 129.654, 135.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 5:164 OR RESSEQ 166:212 OR RESSEQ 214:217 )
211CHAIN B AND (RESSEQ 5:164 OR RESSEQ 166:212 OR RESSEQ 214:217 )
311CHAIN C AND (RESSEQ 5:164 OR RESSEQ 166:212 OR RESSEQ 214:217 )
112CHAIN S AND (RESSEQ 151:239 )
212CHAIN T AND (RESSEQ 151:239 )
312CHAIN U AND (RESSEQ 151:239 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999606, -0.021898, -0.017565), (-0.025951, -0.482292, -0.875626), (0.010703, 0.875737, -0.482671)32.574, -59.3915, 76.7391
2given(0.999917, -0.00801, 0.010116), (-0.012767, -0.500735, 0.865507), (0.001868, -0.865564, -0.500795)65.6207, -97.2999, -14.1596
3given(0.998254, -0.030942, -0.05031), (-0.059047, -0.542806, -0.83778), (-0.001385, 0.839288, -0.543685)32.824, -63.8992, 76.6156
4given(0.999601, -0.007637, 0.027195), (-0.027701, -0.45333, 0.890912), (0.005525, -0.89131, -0.453361)65.2495, -96.8559, -16.6103

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Components

#1: Protein CYTOSOLIC HEAT SHOCK PROTEIN 90 / HSP90


Mass: 25261.396 Da / Num. of mol.: 3 / Fragment: ATPASE DOMAIN, RESIDUES 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HORDEUM VULGARE (barley) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7XJ80
#2: Protein SGT1-LIKE PROTEIN


Mass: 10340.937 Da / Num. of mol.: 3 / Fragment: CS DOMAIN, RESIDUES 74-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q84LL4, UniProt: Q9SUR9*PLUS
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsN-TERMINAL 6XHIS TAG

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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: 4 Å3/Da / Density % sol: 69.26 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: INITIAL MULTIPLE CRYSTALS WERE GROWN BY VAPOR DIFFUSION AT 4 C AGAINST 26% W/V PEG4000, 100 MM TRIS (PH 8.5), AND 200 MM MAGNESIUM SULPHATE. SUBSEQUENT STREAK SEEDING INTO SOLUTIONS OF 16% ...Details: INITIAL MULTIPLE CRYSTALS WERE GROWN BY VAPOR DIFFUSION AT 4 C AGAINST 26% W/V PEG4000, 100 MM TRIS (PH 8.5), AND 200 MM MAGNESIUM SULPHATE. SUBSEQUENT STREAK SEEDING INTO SOLUTIONS OF 16% W/V PEG4000, 100 MM TRIS (PH 8.5), AND 200 MM MAGNESIUM SULFATE PRODUCED SINGLE THIN PLATES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 29660 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 59.73 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AMW, 1RL1

1amw

1rl1


Resolution: 3.3→38.072 Å / SU ML: 0.39 / σ(F): 1.14 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 2615 5.17 %
Rwork0.1988 --
obs0.2009 50605 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.372 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 53.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.07 Å2-0 Å20 Å2
2---6.7518 Å2-0 Å2
3---0.6818 Å2
Refinement stepCycle: LAST / Resolution: 3.3→38.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7323 0 81 0 7404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017541
X-RAY DIFFRACTIONf_angle_d1.4810210
X-RAY DIFFRACTIONf_dihedral_angle_d20.122741
X-RAY DIFFRACTIONf_chiral_restr0.081162
X-RAY DIFFRACTIONf_plane_restr01283
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1662X-RAY DIFFRACTIONPOSITIONAL
12B1662X-RAY DIFFRACTIONPOSITIONAL0.047
13C1662X-RAY DIFFRACTIONPOSITIONAL0.057
21S725X-RAY DIFFRACTIONPOSITIONAL
22T725X-RAY DIFFRACTIONPOSITIONAL0.055
23U725X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.360.33531330.29772573X-RAY DIFFRACTION99
3.36-3.42460.34411330.31562533X-RAY DIFFRACTION99
3.4246-3.49450.32161520.29522563X-RAY DIFFRACTION99
3.4945-3.57040.29381570.26082530X-RAY DIFFRACTION99
3.5704-3.65340.27981270.24962533X-RAY DIFFRACTION99
3.6534-3.74470.27251430.2392544X-RAY DIFFRACTION99
3.7447-3.84580.24611360.22652562X-RAY DIFFRACTION99
3.8458-3.95890.28241260.21312530X-RAY DIFFRACTION99
3.9589-4.08650.21081260.18862559X-RAY DIFFRACTION99
4.0865-4.23240.2351380.18252539X-RAY DIFFRACTION99
4.2324-4.40160.18021380.15422518X-RAY DIFFRACTION98
4.4016-4.60160.1781340.14582533X-RAY DIFFRACTION98
4.6016-4.84380.16111820.13142499X-RAY DIFFRACTION98
4.8438-5.14660.18281360.13412505X-RAY DIFFRACTION98
5.1466-5.54280.191510.14692491X-RAY DIFFRACTION98
5.5428-6.09860.231380.1582526X-RAY DIFFRACTION98
6.0986-6.97640.24341320.18152516X-RAY DIFFRACTION98
6.9764-8.77170.21891160.16032501X-RAY DIFFRACTION97
8.7717-38.0750.20871170.19862435X-RAY DIFFRACTION94

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