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- PDB-1gml: crystal structure of the mouse CCT gamma apical domain (triclinic) -

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Basic information

Entry
Database: PDB / ID: 1gml
Titlecrystal structure of the mouse CCT gamma apical domain (triclinic)
ComponentsT-COMPLEX PROTEIN 1 SUBUNIT 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: 2.2 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
DepositionSep 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
B: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
C: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
D: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9478
Polymers82,5794
Non-polymers3684
Water11,620645
1
A: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
D: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4744
Polymers41,2892
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-6.2 kcal/mol
Surface area15630 Å2
MethodPISA
2
B: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
C: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4744
Polymers41,2892
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-4.6 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.740, 65.020, 65.470
Angle α, β, γ (deg.)89.97, 103.95, 90.35
Int Tables number1
Space group name H-MP1
DetailsTHE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATEOF THE MOLECULE IS THE MONOMER. TOGETHER WITH THE SEVEN OTHER SUBUNITS OF CCT, IT IS PART OF A DOUBLE TOROIDAL QUATERNARY STRUCTURE OF 2X8 SUBUNITS.

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Components

#1: Protein
T-COMPLEX PROTEIN 1 SUBUNIT GAMMA / TCP-1-GAMMA / CCT-GAMMA / MATRICIN / MTRIC-P5


Mass: 20644.701 Da / Num. of mol.: 4 / Fragment: APICAL DOMAIN, RESIDUES 210-380
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS GROWN BY HANGING DROP METHOD USING A 1:1 MIXTURE OF 12MG/ML PROTEIN, 400MM NACL, 20% GLYCEROL, 8MM TRIS PH8.0, 0.4MM EDTA AND 100MM TRIS PH8.0, 200MM NACL, 10MM MG(OAC)2, pH 8.00
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
250 mMTris1droppH8.0
3300 mM1dropNaCl
45 mM1dropMg(OAc)2
50.2 mMEDTA1drop
610 %(v/v)glycerol1drop
7100 mMTris1reservoirpH8.0
8200 mM1reservoirNaCl
910 mM1reservoirMg(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 39106 / % possible obs: 93 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.2 / % possible all: 92.6
Reflection
*PLUS
Lowest resolution: 29 Å
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E0R

1e0r


Resolution: 2.2→28.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1072988.9 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
Details: NO DENSITY WAS FOUND FOR THE LOOPS A249 - A262 B249 - B261 C249 - C262 D249 - D268 NO DENSITY WAS FOUND FOR SEVERAL SIDECHAINS. THESE WERE TRUNCATED AT CB.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1859 4.8 %RANDOM
Rwork0.203 ---
obs0.203 39105 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9464 Å2 / ksol: 0.322875 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-30.5 Å20.63 Å27.12 Å2
2---13.03 Å20 Å2
3----17.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4815 0 24 645 5484
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.561.5
X-RAY DIFFRACTIONc_mcangle_it3.632
X-RAY DIFFRACTIONc_scbond_it4.32
X-RAY DIFFRACTIONc_scangle_it5.712.5
Refine LS restraints NCSRms dev Biso : 0.2 Å2 / Weight position: 2000
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 303 4.6 %
Rwork0.373 6217 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GOL.PARGOL.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor obs: 0.373

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