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- PDB-1gn1: crystal structure of the mouse CCT gamma apical domain (monoclinic) -

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Basic information

Entry
Database: PDB / ID: 1gn1
Titlecrystal structure of the mouse CCT gamma apical domain (monoclinic)
ComponentsCCT-GAMMA
KeywordsCHAPERONE / CHAPERONIN / ACTIN / TUBULIN
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / zona pellucida receptor complex / chaperonin-containing T-complex / : / binding of sperm to zona pellucida / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / zona pellucida receptor complex / chaperonin-containing T-complex / : / binding of sperm to zona pellucida / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / myelin sheath / cell body / microtubule / protein stabilization / ATP hydrolysis activity / ATP binding
Similarity search - Function
GroEL / GroEL / T-complex protein 1, gamma subunit / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) ...GroEL / GroEL / T-complex protein 1, gamma subunit / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
T-complex protein 1 subunit gamma
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPappenberger, G. / Wilsher, J.A. / Roe, S.M. / Willison, K.R. / Pearl, L.H.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of the Cct Gamma Apical Domain:: Implications for Substrate Binding to the Eukaryotic Cytosolic Chaperonin
Authors: Pappenberger, G. / Wilsher, J.A. / Roe, S.M. / Counsell, D.J. / Willison, K.R. / Pearl, L.H.
History
DepositionOct 1, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2002Provider: 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 / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 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
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCT-GAMMA
B: CCT-GAMMA
C: CCT-GAMMA
D: CCT-GAMMA
E: CCT-GAMMA
F: CCT-GAMMA
G: CCT-GAMMA
H: CCT-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,23810
Polymers165,1588
Non-polymers802
Water81145
1
A: CCT-GAMMA
B: CCT-GAMMA


Theoretical massNumber of molelcules
Total (without water)41,2892
Polymers41,2892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CCT-GAMMA
D: CCT-GAMMA


Theoretical massNumber of molelcules
Total (without water)41,2892
Polymers41,2892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: CCT-GAMMA
F: CCT-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3293
Polymers41,2892
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: CCT-GAMMA
H: CCT-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3293
Polymers41,2892
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.244, 234.229, 62.703
Angle α, β, γ (deg.)90.00, 114.70, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATEOF THE MOLECULE IS THE MONOMER . TOGETHER WITH THE SEVENOTHER SUBUNITS OF CCT, IT IS PART OF A DOUBLE TOROIDALQUATERNARY STRUCTURE OF 2X8 SUBUNITS.

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Components

#1: Protein
CCT-GAMMA / GAMMA SUBUNIT (TCP-1-GAMMA) / (MATRICIN)


Mass: 20644.701 Da / Num. of mol.: 8 / Fragment: APICAL DOMAIN, RESIDUES 209-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80318
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49 %
Crystal growMethod: microbatch / pH: 6.5
Details: CRYSTALS GROWN BY MICROBATCH METHOD (UNDER OIL) USING A 1:1 MIXTURE OF 30MG/ML PROTEIN, 400MM NACL, 20% GLYCEROL, 8MM TRIS PH8.0, 0.4MM EDTA AND 14% PEG 8K, 100MM NA-CACODYLATE PH6.5, 40MM ...Details: CRYSTALS GROWN BY MICROBATCH METHOD (UNDER OIL) USING A 1:1 MIXTURE OF 30MG/ML PROTEIN, 400MM NACL, 20% GLYCEROL, 8MM TRIS PH8.0, 0.4MM EDTA AND 14% PEG 8K, 100MM NA-CACODYLATE PH6.5, 40MM CA(OAC)2, 40% GLYCEROL, pH 6.50
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein11
28 mMTris11pH8.0
3400 mM11NaCl
40.4 mMEDTA11
520 %glycerol11
6100 mMsodium cacodylate11pH6.5
714 %(w/v)PEG800011
840 mM11Ca(OAc)2
940 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 32855 / % possible obs: 85.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 100.6 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4.7 / % possible all: 74.1
Reflection
*PLUS
Lowest resolution: 29 Å / Num. obs: 33738
Reflection shell
*PLUS
% possible obs: 74.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GML

1gml


Resolution: 2.8→29.11 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1054377.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
Details: NO INTERPRETABLE DENSITY WAS FOUND FOR THE LOOPS A250 - A260, B249 - B270, C248 - C272, D248 - D266, E248 - E272, F250 - F262, G249 - G261, H248 - H264 NO INTERPRETABLE DENSITY WAS FOUND FOR ...Details: NO INTERPRETABLE DENSITY WAS FOUND FOR THE LOOPS A250 - A260, B249 - B270, C248 - C272, D248 - D266, E248 - E272, F250 - F262, G249 - G261, H248 - H264 NO INTERPRETABLE DENSITY WAS FOUND FOR SEVERAL SIDECHAINS THESE WERE TRUNCATED AT CB
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1632 5 %RANDOM
Rwork0.238 ---
obs0.238 32815 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4219 Å2 / ksol: 0.288995 e/Å3
Displacement parametersBiso mean: 83.5 Å2
Baniso -1Baniso -2Baniso -3
1-11.48 Å20 Å229.12 Å2
2---24.03 Å20 Å2
3---12.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8971 0 2 45 9018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.761.5
X-RAY DIFFRACTIONc_mcangle_it4.462
X-RAY DIFFRACTIONc_scbond_it3.922
X-RAY DIFFRACTIONc_scangle_it5.622.5
Refine LS restraints NCSRms dev Biso : 5 Å2 / Weight position: 2000
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.464 231 4.8 %
Rwork0.433 4540 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Rfactor obs: 0.433

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