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- PDB-4b2t: The crystal structures of the eukaryotic chaperonin CCT reveal it... -

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Basic information

Entry
Database: PDB / ID: 4b2t
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 / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / : / binding of sperm to zona pellucida ...Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / : / binding of sperm to zona pellucida / Neutrophil degranulation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / WD40-repeat domain binding / chaperone-mediated protein complex assembly / beta-tubulin binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / positive regulation of telomere maintenance via telomerase / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / mRNA 5'-UTR binding / response to virus / unfolded protein binding / melanosome / protein folding / G-protein beta-subunit binding / cell body / microtubule / protein stabilization / cilium / ubiquitin protein ligase binding / centrosome / ATP hydrolysis activity / ATP binding / identical protein binding
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
T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit delta / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit beta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 5.5 Å
AuthorsKalisman, N. / Schroeder, G.F. / Levitt, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Open Conformation of the Mammalian Chaperonin Cct in Complex with Tubulin.
Authors: Munoz, I.G. / Yebenes, H. / Zhou, M. / Mesa, P. / Serna, M. / Park, A.Y. / Bragado-Nilsson, E. / Beloso, A. / De Carcer, G. / Malumbres, M. / Robinson, C.V. / Valpuesta, J.M. / Montoya, G.
History
DepositionJul 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Jun 5, 2013Group: Other / Structure summary
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 4B2T REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2XSMSF) ...THIS ENTRY 4B2T REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2XSMSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2XSM: I.G.MUNOZ,H.YEBENES,M.ZHOU,P.MESA,M.SERNA,E.BRAGADO-NILSSON, A.BELOSO,C.V.ROBINSON,J.M.VALPUESTA,G.MONTOYA

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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 ALPHA
B: T-COMPLEX PROTEIN 1 SUBUNIT BETA
D: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
E: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
G: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
H: T-COMPLEX PROTEIN 1 SUBUNIT ETA
Q: T-COMPLEX PROTEIN 1 SUBUNIT THETA
Z: T-COMPLEX PROTEIN 1 SUBUNIT ZETA
a: T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
b: T-COMPLEX PROTEIN 1 SUBUNIT BETA
d: T-COMPLEX PROTEIN 1 SUBUNIT DELTA
e: T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
g: T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
h: T-COMPLEX PROTEIN 1 SUBUNIT ETA
q: T-COMPLEX PROTEIN 1 SUBUNIT THETA
z: T-COMPLEX PROTEIN 1 SUBUNIT ZETA


Theoretical massNumber of molelcules
Total (without water)947,34016
Polymers947,34016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100200 Å2
ΔGint625.6 kcal/mol
Surface area338050 Å2
MethodPQS
Unit cell
Length a, b, c (Å)272.700, 313.500, 158.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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T-COMPLEX PROTEIN 1 SUBUNIT ... , 8 types, 16 molecules AaBbDdEeGgHhQqZz

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


Mass: 60281.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q32L40
#2: Protein T-COMPLEX PROTEIN 1 SUBUNIT BETA / TCP-1-BETA / CCT-BETA


Mass: 57555.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q3ZBH0
#3: Protein T-COMPLEX PROTEIN 1 SUBUNIT DELTA / TCP-1-DELTA / CCT-DELTA


Mass: 58233.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q2T9X2
#4: Protein T-COMPLEX PROTEIN 1 SUBUNIT EPSILON / TCP-1-EPSILON / CCT-EPSILON


Mass: 59695.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: F1MWD3*PLUS
#5: Protein T-COMPLEX PROTEIN 1 SUBUNIT GAMMA / TCP-1-GAMMA / CCT-GAMMA


Mass: 60666.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q3T0K2
#6: Protein T-COMPLEX PROTEIN 1 SUBUNIT ETA / TCP-1-ETA / CCT-ETA


Mass: 59518.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q2NKZ1
#7: Protein T-COMPLEX PROTEIN 1 SUBUNIT THETA / TCP-1-THETA / CCT-THETA


Mass: 59681.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q3ZCI9
#8: Protein T-COMPLEX PROTEIN 1 SUBUNIT ZETA / TCP-1-ZETA / CCT-ZETA / CCT-ZETA-1


Mass: 58037.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / References: UniProt: Q3MHL7

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Details

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: 4.66 Å3/Da / Density % sol: 73.38 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2XSM.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.114 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.114 Å / Relative weight: 1

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Processing

SoftwareName: CNS / Version: 1.3 / Classification: refinement
RefinementResolution: 5.5→200 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.3986 2238 5 %RANDOM
Rwork0.3404 ---
obs0.3404 44462 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 228.728 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 277.1 Å2
Baniso -1Baniso -2Baniso -3
1--19.558 Å20 Å20 Å2
2--95.347 Å20 Å2
3----75.789 Å2
Refinement stepCycle: LAST / Resolution: 5.5→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51877 0 0 0 51877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00222
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_deg0.65511
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
LS refinement shellResolution: 5.5→5.7 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4954 205 -
Rwork0.457 4136 -
obs--0.984 %

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