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

(-) Description

Title :  SEC61 IN THE CANINE RIBOSOME-CHANNEL COMPLEX FROM THE ENDOPLASMIC RETICULUM
 
Authors :  J. -F. Menetret, C. Akey
Date :  25 Jun 08  (Deposition) - 19 Aug 08  (Release) - 14 Apr 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  8.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ribosome-Channel Complex, Cryo-Electron Microscopy, Co- Translational Translocation, Endoplasmic Reticulum, Protein Transport/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. F. Menetret, R. S. Hegde, M. Aguiar, S. P. Gygi, E. Park, T. A. Rapoport, C. W. Akey
Single Copies Of Sec61 And Trap Associate With A Nontranslating Mammalian Ribosome.
Structure V. 16 1126 2008
PubMed-ID: 18611385  |  Reference-DOI: 10.1016/J.STR.2008.05.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PREPROTEIN TRANSLOCASE SUBUNIT SECY
    Chains: A
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Synonym: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA HOMOLOG
 
Molecule 2 - PREPROTEIN TRANSLOCASE SUBUNIT SECE
    Chains: B
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Synonym: PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT HOMOLOG
 
Molecule 3 - PREPROTEIN TRANSLOCASE SUBUNIT SECG
    Chains: C
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Synonym: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA HOMOLOG
 
Molecule 4 - RNA (5'- R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*G P*C)-3')
    Chains: D
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Other Details: HELIX 6
 
Molecule 5 - RNA (5'- R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3')
    Chains: E
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Other Details: HELIX 7
 
Molecule 6 - RNA (32-MER)
    Chains: F
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Other Details: HELIX 50

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DKN)

(-) Sites  (0, 0)

(no "Site" information available for 3DKN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DKN)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ile A:233 -Pro A:234
2His A:237 -Gly A:238
3Gly A:238 -Arg A:239
4Arg A:239 -Ile A:240
5Lys A:241 -Gly A:242
6Lys A:246 -Tyr A:247
7Glu A:336 -Thr A:337
8Ile A:356 -Lys A:357

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DKN)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SECY_1PS00755 Protein secY signature 1.SECY_METJA69-88  1A:69-88
2SECY_2PS00756 Protein secY signature 2.SECY_METJA156-173  1A:156-173

(-) Exons   (0, 0)

(no "Exon" information available for 3DKN)

(-) Sequences/Alignments

Asymmetric/Biological 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:430
 aligned with SECY_METJA | Q60175 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:432
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431  
          SECY_METJA      2 KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQTITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKVSELHPAIAKL  433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh...............hhhhhh..........hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.............--hhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------SECY_1  PDB: A:69-88-------------------------------------------------------------------SECY_2            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3dkn A    2 KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQTITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKS--AIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKVSELHPAIAKL  431
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361|  |   369       379       389       399       409       419       429  
                                                                                                                                                                                                                                                                                                                                                                                                  362  |                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                     363                                                                    


Chain B from PDB  Type:PROTEIN  Length:65
 aligned with SECE_METJA | Q57817 from UniProtKB/Swiss-Prot  Length:74

    Alignment length:65
                                    12        22        32        42        52        62     
          SECE_METJA      3 TDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILK   67
               SCOP domains d3dknb1 B:2-66 Preprotein translocase SecE subunit                SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                3dkn B    2 TDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILK   66
                                    11        21        31        41        51        61     


Chain C from PDB  Type:PROTEIN  Length:32
 aligned with SECG_METJA | P60460 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:32
                                    30        40        50  
          SECG_METJA     21 ETFSKIRVKPEHVIGVTVAFVIIEAILTYGRF   52
               SCOP domains d3dknc1 C:21-52 Sec-beta subunit SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                3dkn C   21 ETFSKIRVKPEHVIGVTVAFVIIEAILTYGRF   52
                                    30        40        50  


Chain D from PDB  Type:RNA  Length:20
                                                     
                3dkn D   53 CGUGCCAAGCUGCGAUAAGC   72
                                    62        72


Chain E from PDB  Type:RNA  Length:17
                                                  
                3dkn E   80 AGCCGCACGGAGGCGAA   96
                                    89       


Chain F from PDB  Type:RNA  Length:32
                                                                 
                3dkn F 1415 GGGUUCCUCAGCACUGCUGAUCAGCUGAGGGU 1446
                                  1424      1434      1444
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DKN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DKN)

(-) Gene Ontology  (11, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SECY_METJA | Q60175)
biological process
    GO:0065002    intracellular protein transmembrane transport    The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
    GO:0006605    protein targeting    The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain B   (SECE_METJA | Q57817)
molecular function
    GO:0015450    P-P-bond-hydrolysis-driven protein transmembrane transporter activity    Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0065002    intracellular protein transmembrane transport    The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0006605    protein targeting    The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain C   (SECG_METJA | P60460)
biological process
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 3dkn)
 
  Sites
(no "Sites" information available for 3dkn)
 
  Cis Peptide Bonds
    Arg A:239 - Ile A:240   [ RasMol ]  
    Glu A:336 - Thr A:337   [ RasMol ]  
    Gly A:238 - Arg A:239   [ RasMol ]  
    His A:237 - Gly A:238   [ RasMol ]  
    Ile A:233 - Pro A:234   [ RasMol ]  
    Ile A:356 - Lys A:357   [ RasMol ]  
    Lys A:241 - Gly A:242   [ RasMol ]  
    Lys A:246 - Tyr A:247   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dkn
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SECE_METJA | Q57817
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SECG_METJA | P60460
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SECY_METJA | Q60175
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SECE_METJA | Q57817
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SECG_METJA | P60460
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SECY_METJA | Q60175
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SECE_METJA | Q57817: 1rh5 1rhz 2yxq 2yxr 3bo0 3bo1 4v4n 4v7i
        SECG_METJA | P60460: 1rh5 1rhz 2yxq 2yxr 3bo0 3bo1 4v4n 4v7i
        SECY_METJA | Q60175: 1rh5 1rhz 2yxq 2yxr 3bo0 3bo1 4v4n 4v7i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DKN)