Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOUSE CCT GAMMA APICAL DOMAIN (TRICLINIC)
 
Authors :  G. Pappenberger, J. A. Wilsher, S. M. Roe, K. R. Willison, L. H. Pearl
Date :  17 Sep 01  (Deposition) - 18 Jun 02  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Chaperone, Chaperonin, Actin, Tubulin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Pappenberger, J. A. Wilsher, S. M. Roe, D. J. Counsell, K. R. Willison, L. H. Pearl
Crystal Structure Of The Cct Gamma Apical Domain:: Implications For Substrate Binding To The Eukaryotic Cytosolic Chaperonin
J. Mol. Biol. V. 318 1367 2002
PubMed-ID: 12083524  |  Reference-DOI: 10.1016/S0022-2836(02)00190-0

(-) Compounds

Molecule 1 - T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11C
    Expression System Taxid562
    FragmentAPICAL DOMAIN, RESIDUES 210-380
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTCP-1-GAMMA, CCT-GAMMA, MATRICIN, MTRIC-P5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:351 , LYS A:353 , PHE A:362 , HOH A:2158 , HOH A:2173 , LEU D:375BINDING SITE FOR RESIDUE GOL A1379
2AC2SOFTWAREGLU B:351 , LYS B:353 , PHE B:362 , HOH B:2164 , HOH B:2180 , HOH B:2181 , LEU C:375BINDING SITE FOR RESIDUE GOL B1379
3AC3SOFTWARELEU B:376 , ARG B:377 , LEU C:215 , LEU C:349 , GLU C:351 , LYS C:353 , HOH C:2138 , HOH C:2148BINDING SITE FOR RESIDUE GOL C1379
4AC4SOFTWARELEU A:376 , ARG A:377 , LEU D:215 , LEU D:349 , GLU D:351 , LYS D:353 , HOH D:2136BINDING SITE FOR RESIDUE GOL D1379

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:366 -A:372
2B:366 -B:372
3C:366 -C:372
4D:366 -D:372

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GML)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GML)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GML)

(-) Exons   (0, 0)

(no "Exon" information available for 1GML)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:155
 aligned with TCPG_MOUSE | P80318 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:169
                                   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370         
           TCPG_MOUSE   211 DSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
               SCOP domains d1gmla_ A: Thermosome, A-domain                                                                                                                                           SCOP domains
               CATH domains 1gmlA00 A:211-378 GroEL                                                                                                                                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...........eee...eeee.......--------------hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh..eee...hhhhhhhhhhhhh..ee.hhhhhhhhhh...eeeeeeeee..eeeeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gml A 211 DSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYK--------------DFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
                                   220       230       240       | -         -  |    270       280       290       300       310       320       330       340       350       360       370         
                                                               248            263                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with TCPG_MOUSE | P80318 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:166
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373      
           TCPG_MOUSE   214 VLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
               SCOP domains d1gmlb_ B: Thermosome, A-domain                                                                                                                                        SCOP domains
               CATH domains 1gmlB00 B:214-378 GroEL                                                                                                                                              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........eee...eeee.......-------------.hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh..eee...hhhhhhhhhhhhh..ee.hhhhhhhhhh...eeeeeeeee..eeeeeeeee......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gml B 214 VLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYK-------------EDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
                                   223       233       243    |    -       263       273       283       293       303       313       323       333       343       353       363       373      
                                                            248           262                                                                                                                     

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with TCPG_MOUSE | P80318 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:169
                                   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370         
           TCPG_MOUSE   211 DSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
               SCOP domains d1gmlc_ C: Thermosome, A-domain                                                                                                                                           SCOP domains
               CATH domains 1gmlC00 C:211-378 GroEL                                                                                                                                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...........eee...eeee.......--------------hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh..eee...hhhhhhhhhhhhh.....hhhhhhhhhh...eeeeeeeee..eeeeeeeee.hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gml C 211 DSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYK--------------DFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
                                   220       230       240       | -         -  |    270       280       290       300       310       320       330       340       350       360       370         
                                                               248            263                                                                                                                    

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with TCPG_MOUSE | P80318 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:168
                                   221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371        
           TCPG_MOUSE   212 SCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
               SCOP domains d1gmld_ D: Thermosome, A-domain                                                                                                                                          SCOP domains
               CATH domains 1gmlD00 D:212-378 GroEL                                                                                                                                                - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...........eee...eeee.......-------------------hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh..eee...hhhhhhhhhhhhh.....hhhhhhhhhh...eeeeeeeee..eeeeeeeee.hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gml D 212 SCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYK-------------------LQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA 379
                                   221       231       241      |  -         -      |271       281       291       301       311       321       331       341       351       361       371        
                                                              248                 268                                                                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GML)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TCPG_MOUSE | P80318)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0044183    protein binding involved in protein folding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0007339    binding of sperm to zona pellucida    The process in which the sperm binds to the zona pellucida glycoprotein layer of the egg. The process begins with the attachment of the sperm plasma membrane to the zona pellucida and includes attachment of the acrosome inner membrane to the zona pellucida after the acrosomal reaction takes place.
    GO:0046931    pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a pore complex. A pore complex is a small opening in a membrane that allows the passage of liquids and/or gases.
    GO:1904871    positive regulation of protein localization to Cajal body    Any process that activates or increases the frequency, rate or extent of protein localization to Cajal body.
    GO:1904874    positive regulation of telomerase RNA localization to Cajal body    Any process that activates or increases the frequency, rate or extent of telomerase RNA localization to Cajal body.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0005832    chaperonin-containing T-complex    A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0002199    zona pellucida receptor complex    A multisubunit complex comprising the chaperonin-containing T-complex and several other components involved in mediating sperm-oocyte Interaction.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gml)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1gml
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TCPG_MOUSE | P80318
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TCPG_MOUSE | P80318
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TCPG_MOUSE | P803181gn1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1GML)