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- PDB-4v8r: The crystal structures of the eukaryotic chaperonin CCT reveal it... -

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Basic information

Entry
Database: PDB / ID: 4v8r
TitleThe crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning
Components(T-COMPLEX PROTEIN 1 SUBUNIT ...) x 8
KeywordsCHAPERONE
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 / chaperonin-containing T-complex / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperonin-containing T-complex / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / : / Chaperonins TCP-1 signature 1. ...T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3.8 Å
AuthorsKalisman, N. / Schroder, G.F. / Levitt, M.
CitationJournal: Embo J. / Year: 2011
Title: The Crystal Structure of Yeast Cct Reveals Intrinsic Asymmetry of Eukaryotic Cytosolic Chaperonins.
Authors: Dekker, C. / Roe, S.M. / Mccormack, E.A. / Beuron, F. / Pearl, L.H. / Willison, K.R.
History
DepositionMar 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4AOL, 4APK
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Remark 0THIS ENTRY 4AOL REFLECTS AN ALTERNATIVE SOLUTION OF THE ORIGINAL STRUCTURAL DATA (R3P9DSF) ...THIS ENTRY 4AOL REFLECTS AN ALTERNATIVE SOLUTION OF THE ORIGINAL STRUCTURAL DATA (R3P9DSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3P9D: AUTHOR: C.DEKKER,S.M.ROE,E.A.MCCORMACK,F.BEURON,L.H.PEARL, K.R.WILLISON

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
AB: T-COMPLEX PROTEIN 1 SUBUNIT BETA
AD: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
AE: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
AG: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
AH: T-COMPLEX PROTEIN 1 SUBUNIT ETA
AQ: T-COMPLEX PROTEIN 1 SUBUNIT THETA
AZ: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
Aa: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
Ab: T-COMPLEX PROTEIN 1 SUBUNIT BETA
Ad: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
Ae: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
Ag: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
Ah: T-COMPLEX PROTEIN 1 SUBUNIT ETA
Aq: T-COMPLEX PROTEIN 1 SUBUNIT THETA
Az: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
BA: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
BB: T-COMPLEX PROTEIN 1 SUBUNIT BETA
BD: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
BE: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
BG: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
BH: T-COMPLEX PROTEIN 1 SUBUNIT ETA
BQ: T-COMPLEX PROTEIN 1 SUBUNIT THETA
BZ: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
Ba: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
Bb: T-COMPLEX PROTEIN 1 SUBUNIT BETA
Bd: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
Be: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
Bg: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
Bh: T-COMPLEX PROTEIN 1 SUBUNIT ETA
Bq: T-COMPLEX PROTEIN 1 SUBUNIT THETA
Bz: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,952,737128
Polymers1,936,17732
Non-polymers16,56096
Water00
1
AA: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
AB: T-COMPLEX PROTEIN 1 SUBUNIT BETA
AD: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
AE: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
AG: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
AH: T-COMPLEX PROTEIN 1 SUBUNIT ETA
AQ: T-COMPLEX PROTEIN 1 SUBUNIT THETA
AZ: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
Aa: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
Ab: T-COMPLEX PROTEIN 1 SUBUNIT BETA
Ad: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
Ae: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
Ag: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
Ah: T-COMPLEX PROTEIN 1 SUBUNIT ETA
Aq: T-COMPLEX PROTEIN 1 SUBUNIT THETA
Az: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)976,36964
Polymers968,08816
Non-polymers8,28048
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area131210 Å2
ΔGint-596 kcal/mol
Surface area281820 Å2
MethodPISA
2
BA: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
BB: T-COMPLEX PROTEIN 1 SUBUNIT BETA
BD: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
BE: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
BG: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
BH: T-COMPLEX PROTEIN 1 SUBUNIT ETA
BQ: T-COMPLEX PROTEIN 1 SUBUNIT THETA
BZ: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
Ba: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
Bb: T-COMPLEX PROTEIN 1 SUBUNIT BETA
Bd: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
Be: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
Bg: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
Bh: T-COMPLEX PROTEIN 1 SUBUNIT ETA
Bq: T-COMPLEX PROTEIN 1 SUBUNIT THETA
Bz: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)976,36964
Polymers968,08816
Non-polymers8,28048
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area131170 Å2
ΔGint-599 kcal/mol
Surface area282030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.100, 162.540, 268.100
Angle α, β, γ (deg.)85.23, 81.15, 61.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.24784, 0.92658, 0.2829), (0.94422, -0.16566, -0.28461), (-0.21685, 0.33766, -0.91595)
Vector: -115.83222, -73.76594, 139.7842)

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Components

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T-COMPLEX PROTEIN 1 SUBUNIT ... , 8 types, 32 molecules AAAaBABaABAbBBBbADAdBDBdAEAeBEBeAGAgBGBgAHAhBHBhAQAqBQBqAZAzBZBz

#1: Protein
T-COMPLEX PROTEIN 1 SUBUNIT ALPHA / TCP-1-ALPHA / CCT-ALPHA


Mass: 60557.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P12612
#2: Protein
T-COMPLEX PROTEIN 1 SUBUNIT BETA / TCP-1-BETA / CCT-BETA


Mass: 57276.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39076
#3: Protein
T-COMPLEX PROTEIN 1 SUBUNIT DELTA / TCP-1-DELTA / CCT-DELTA


Mass: 57740.449 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39078
#4: Protein
T-COMPLEX PROTEIN 1 SUBUNIT EPSILON / TCP-1-EPSILON / CCT-EPSILON


Mass: 61995.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40413
#5: Protein
T-COMPLEX PROTEIN 1 SUBUNIT GAMMA / TCP-1-GAMMA / CCT-GAMMA


Mass: 64939.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39077
#6: Protein
T-COMPLEX PROTEIN 1 SUBUNIT ETA / TCP-1-ETA / CCT-ETA


Mass: 59802.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P42943
#7: Protein
T-COMPLEX PROTEIN 1 SUBUNIT THETA / TCP-1-THETA / CCT-THETA


Mass: 61735.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P47079
#8: Protein
T-COMPLEX PROTEIN 1 SUBUNIT ZETA / TCP-1-ZETA / CCT-ZETA


Mass: 59997.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39079

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Non-polymers , 3 types, 96 molecules

#9: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical...
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: BeF3
#11: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg

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Details

Sequence detailsTHIS IS A HIS-CBP-STREP-TAG INSERTED BETWEEN PRO 374 AND LYS 375.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.32 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3P9D.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 100 Å2

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Processing

SoftwareName: CNS / Version: 1.3 / Classification: refinement
RefinementResolution: 3.8→89.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 7525914.53 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 10483 5 %RANDOM
Rwork0.248 ---
obs0.248 209671 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 114.668 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 133.3 Å2
Baniso -1Baniso -2Baniso -3
1-25.53 Å217.43 Å236.26 Å2
2---3.53 Å21.28 Å2
3----21.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a1.18 Å1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→89.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63878 0 512 0 64390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 1773 5 %
Rwork0.396 33675 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION6ADP.PARAMADP.TOP
X-RAY DIFFRACTION7BEF.PARAMBEF.TOP

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