[English] 日本語
Yorodumi
- PDB-1gml: crystal structure of the mouse CCT gamma apical domain (triclinic) -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of establishment of protein localization to telomere / binding of sperm to zona pellucida / chaperonin-containing T-complex / chaperone-mediated protein folding / 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 / positive regulation of establishment of protein localization to telomere / binding of sperm to zona pellucida / chaperonin-containing T-complex / chaperone-mediated protein folding / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / 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-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more