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- PDB-2xcm: COMPLEX OF HSP90 N-TERMINAL, SGT1 CS AND RAR1 CHORD2 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 2xcm
TitleCOMPLEX OF HSP90 N-TERMINAL, SGT1 CS AND RAR1 CHORD2 DOMAIN
Components
  • CYTOSOLIC HEAT SHOCK PROTEIN 90
  • RAR1
  • SGT1-LIKE PROTEIN
KeywordsCHAPERONE/PROTEIN BINDING / CHAPERONE-PROTEIN BINDING COMPLEX / STRESS RESPONSE
Function / homology
Function and homology information


cellular response to auxin stimulus / regulation of defense response to fungus / plant-type hypersensitive response / embryo development ending in seed dormancy / respiratory burst involved in defense response / SCF ubiquitin ligase complex / defense response to fungus / ATP-dependent protein folding chaperone / Hsp90 protein binding / defense response ...cellular response to auxin stimulus / regulation of defense response to fungus / plant-type hypersensitive response / embryo development ending in seed dormancy / respiratory burst involved in defense response / SCF ubiquitin ligase complex / defense response to fungus / ATP-dependent protein folding chaperone / Hsp90 protein binding / defense response / unfolded protein binding / protein-folding chaperone binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / defense response to bacterium / protein stabilization / innate immune response / ATP hydrolysis activity / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Cysteine and histidine-rich domain-containing protein RAR1 / CHORD domain / CHORD / CHORD domain profile. / Protein Sgt1-like / SGS domain / SGS domain / SGS domain profile. / CS domain / CS domain ...Cysteine and histidine-rich domain-containing protein RAR1 / CHORD domain / CHORD / CHORD domain profile. / 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. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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 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 / Cysteine and histidine-rich domain-containing protein RAR1 / Cysteine and histidine-rich domain-containing protein RAR1 / Protein SGT1 homolog A
Similarity search - Component
Biological speciesHORDEUM VULGARE (barley)
ARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, M. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural Basis for Assembly of Hsp90-Sgt1-Chord Protein Complexes: Implications for Chaperoning of Nlr Innate Immunity Receptors
Authors: Zhang, M. / Kadota, Y. / Prodromou, C. / Shirasu, K. / Pearl, L.H.
History
DepositionApr 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: SGT1-LIKE PROTEIN
D: SGT1-LIKE PROTEIN
E: RAR1
F: RAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,94814
Polymers85,7836
Non-polymers1,1658
Water4,864270
1
A: CYTOSOLIC HEAT SHOCK PROTEIN 90
C: SGT1-LIKE PROTEIN
E: RAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4747
Polymers42,8923
Non-polymers5824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOSOLIC HEAT SHOCK PROTEIN 90
D: SGT1-LIKE PROTEIN
F: RAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4747
Polymers42,8923
Non-polymers5824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.890, 88.890, 117.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5008, 0.8656, 0.000464), (0.8656, 0.5008, 0.001085), (0.000707, 0.000946, -1)-0.0766, -0.06728, 253.5
2given(-0.4975, 0.8675, -0.00257), (0.8675, 0.4975, 0.003932), (0.00469, -0.000273, -1)0.5292, -0.7066, 253.5
3given(-0.4987, 0.8668, 0.000944), (0.8668, 0.4987, -0.001103), (-0.001427, 0.000268, -1)-0.07244, 0.06233, 253.5

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Components

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Protein , 3 types, 6 molecules ABCDEF

#1: Protein CYTOSOLIC HEAT SHOCK PROTEIN 90 / HSP90


Mass: 23942.936 Da / Num. of mol.: 2 / Fragment: ATPASE DOMAIN, RESIDUES 2-210
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: 10541.194 Da / Num. of mol.: 2 / Fragment: CS DOMAIN, RESIDUES 73-164
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: Protein RAR1


Mass: 8407.478 Da / Num. of mol.: 2 / Fragment: CHORD2 DOMAIN, RESIDUES 149-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9FLI9, UniProt: Q9SE33*PLUS

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Non-polymers , 4 types, 278 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.08 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5 23% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→63.37 Å / Num. obs: 52431 / % possible obs: 98.5 % / Observed criterion σ(I): 5 / Redundancy: 2.68 % / Biso Wilson estimate: 29.81 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.39
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.22 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JKL

2jkl


Resolution: 2.2→46.78 Å / SU ML: 0.34 / σ(F): 2.01 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 2676 5.1 %
Rwork0.198 --
obs0.2 52431 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.71 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3263 Å20 Å2-0 Å2
2--2.3263 Å20 Å2
3----4.6525 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 60 270 6330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086181
X-RAY DIFFRACTIONf_angle_d1.2198372
X-RAY DIFFRACTIONf_dihedral_angle_d19.0562232
X-RAY DIFFRACTIONf_chiral_restr0.09931
X-RAY DIFFRACTIONf_plane_restr0.0041065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.32672680.22734994X-RAY DIFFRACTION99
2.2786-2.36990.26272470.21444980X-RAY DIFFRACTION100
2.3699-2.47770.27752890.20594963X-RAY DIFFRACTION99
2.4777-2.60830.27042690.20985016X-RAY DIFFRACTION100
2.6083-2.77180.26112460.20935038X-RAY DIFFRACTION100
2.7718-2.98570.26062890.21784936X-RAY DIFFRACTION100
2.9857-3.28610.26992650.21715056X-RAY DIFFRACTION100
3.2861-3.76150.22382660.18894949X-RAY DIFFRACTION100
3.7615-4.73830.18272750.15845016X-RAY DIFFRACTION100
4.7383-46.79380.19822620.16964807X-RAY DIFFRACTION96

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