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(-) Description

Title :  SOLUTION STRUCTURES OF UBIQUITIN AT 30 BAR AND 3 KBAR
 
Authors :  R. Kitahara, S. Yokoyama, K. Akasaka, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Dec 03  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Pressure, Signaling Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Kitahara, S. Yokoyama, K. Akasaka
Nmr Snapshots Of A Fluctuating Protein Structure: Ubiquitin At 30 Bar-3 Kbar.
J. Mol. Biol. V. 347 277 2005
PubMed-ID: 15740740  |  Reference-DOI: 10.1016/J.JMB.2005.01.052
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN/60S RIBOSOMAL PROTEIN L40 FUSION
    ChainsA
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1V80)

(-) Sites  (0, 0)

(no "Site" information available for 1V80)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V80)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V80)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V80)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76  1A:1-76
RL40_BOVIN1-76  1A:1-76
UBB_BOVIN1-76
77-152
153-228
229-304
  1-
-
A:1-76
-
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
  1-
-
-
-
-
-
-
-
A:1-76
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52  1A:27-52
RL40_BOVIN27-52  1A:27-52
UBB_BOVIN27-52
103-128
179-204
255-280
  1-
-
A:27-52
-
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
  1-
-
-
-
-
-
-
-
A:27-52

(-) Exons   (0, 0)

(no "Exon" information available for 1V80)

(-) Sequences/Alignments

NMR Structure
   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:76
 aligned with RL40_BOVIN | P63048 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:76
                                    10        20        30        40        50        60        70      
           RL40_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
               SCOP domains d1v80a_ A: automated matches                                                 SCOP domains
               CATH domains 1v80A00 A:1-76                                                               CATH domains
               Pfam domains -----ubiquitin-1v80A01 A:6-74                                             -- Pfam domains
         Sec.struct. author ..eeee.....eeee......hhhhhhhhhhhhhh.hhhhheee.....................eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) UBIQUITIN_2  PDB: A:1-76 UniProt: 1-76                                       PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------------------------UBIQUITIN_1  PDB: A:27-52 ------------------------ PROSITE (6)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1v80 A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      

Chain A from PDB  Type:PROTEIN  Length:76
 aligned with RS27A_BOVIN | P62992 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:76
                                    10        20        30        40        50        60        70      
          RS27A_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
               SCOP domains d1v80a_ A: automated matches                                                 SCOP domains
               CATH domains 1v80A00 A:1-76                                                               CATH domains
               Pfam domains -----ubiquitin-1v80A01 A:6-74                                             -- Pfam domains
         Sec.struct. author ..eeee.....eeee......hhhhhhhhhhhhhh.hhhhheee.....................eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-76 UniProt: 1-76                                       PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------UBIQUITIN_1  PDB: A:27-52 ------------------------ PROSITE (4)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1v80 A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      

Chain A from PDB  Type:PROTEIN  Length:76
 aligned with UBB_BOVIN | P0CG53 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:76
                                   162       172       182       192       202       212       222      
            UBB_BOVIN   153 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 228
               SCOP domains d1v80a_ A: automated matches                                                 SCOP domains
               CATH domains 1v80A00 A:1-76                                                               CATH domains
               Pfam domains -----ubiquitin-1v80A01 A:6-74                                             -- Pfam domains
         Sec.struct. author ..eeee.....eeee......hhhhhhhhhhhhhh.hhhhheee.....................eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-76 UniProt: 153-228                                    PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------UBIQUITIN_1  PDB: A:27-52 ------------------------ PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------- PROSITE (5)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1v80 A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      

Chain A from PDB  Type:PROTEIN  Length:76
 aligned with UBC_BOVIN | P0CH28 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:76
                                   618       628       638       648       658       668       678      
            UBC_BOVIN   609 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 684
               SCOP domains d1v80a_ A: automated matches                                                 SCOP domains
               CATH domains 1v80A00 A:1-76                                                               CATH domains
               Pfam domains -----ubiquitin-1v80A01 A:6-74                                             -- Pfam domains
         Sec.struct. author ..eeee.....eeee......hhhhhhhhhhhhhh.hhhhheee.....................eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: A:27-52 ------------------------ PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-76 UniProt: 609-684                                    PROSITE (1)
                PROSITE (4) ---------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ---------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) ---------------------------------------------------------------------------- PROSITE (7)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1v80 A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (10, 21)

NMR Structure(hide GO term definitions)
Chain A   (RL40_BOVIN | P63048)
molecular function
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain A   (RS27A_BOVIN | P62992)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain A   (UBB_BOVIN | P0CG53)
molecular function
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain A   (UBC_BOVIN | P0CH28)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL40_BOVIN | P630481aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4ljo 4ljp 4s22
        RS27A_BOVIN | P629921aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4m0w 4y1h 4z9s 5bz0 5fer 5jqs 5mn9
        UBB_BOVIN | P0CG531aar 1cmx 1e0q 1gjz 1p3q 1ud7 1uzx 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 2xbb 3h1u 3m3j 4bbn
        UBC_BOVIN | P0CH281aar 1cmx 1e0q 1gjz 1p3q 1ud7 1uzx 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 2xbb 2zcc 3h1u 3m3j 4bbn 4xkh 4xyz 5ait

(-) Related Entries Specified in the PDB File

1v81 THE SAME PROTEIN AT 3 KBAR RELATED ID: MY_001000119.1 RELATED DB: TARGETDB