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(-) Description

Title :  THE UBAP1 SUBUNIT OF ESCRT-I INTERACTS WITH UBIQUITIN VIA A NOVEL SOUBA DOMAIN
 
Authors :  M. Agromayor, N. Soler, A. Caballe, T. Kueck, S. M. Freund, M. D. Allen, M O. Perisic, Y. Ye, B. Mcdonald, H. Scheel, K. Hofmann, S. J. D. Neil, J. Martin-Serrano, R. L. Williams
Date :  06 Jan 12  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport, Endosomal Sorting, Tetherin, Vpu, Hiv-1, Monoubiquitin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Agromayor, N. Soler, A. Caballe, T. Kueck, S. M. Freund, M. D. Allen, M. Bycroft, O. Perisic, Y. Ye, B. Mcdonald, H. Scheel, K. Hofmann, S. J. D. Neil, J. Martin-Serrano, R. L. Williams
The Ubap1 Subunit Of Escrt-I Interacts With Ubiquitin Via A Souba Domain.
Structure V. 20 414 2012
PubMed-ID: 22405001  |  Reference-DOI: 10.1016/J.STR.2011.12.013

(-) Compounds

Molecule 1 - UBIQUITIN-ASSOCIATED PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPTH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41 RIPL
    Expression System Vector Type: PLASMID
    Fragment: SOUBA DOMAIN, RESIDUES 389-502
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBAP-1, UBAP1, NASOPHARYNGEAL CARCINOMA-ASSOCIATED GENE 20 PROTEIN
 
Molecule 2 - UBIQUITIN-ASSOCIATED PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPTH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41 RIPL
    Expression System Vector Type: PLASMID
    Fragment: SOUBA DOMAIN, RESIDUES 389-502
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: 2 OXIDIZED SELENOMETHIONINES, B 402 AND B 449
    Synonym: UBAP-1, UBAP1, NASOPHARYNGEAL CARCINOMA-ASSOCIATED GENE 20 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 26)

Asymmetric/Biological Unit (6, 26)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K4Ligand/IonPOTASSIUM ION
3MSE16Mod. Amino AcidSELENOMETHIONINE
4MSO2Mod. Amino AcidSELENOMETHIONINE SELENOXIDE
5NA1Ligand/IonSODIUM ION
6NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:408 , ARG A:411 , LEU A:427 , HOH A:2075BINDING SITE FOR RESIDUE NHE A1500
2AC2SOFTWAREHIS A:450 , CYS A:452 , LYS A:456BINDING SITE FOR RESIDUE K A1501
3AC3SOFTWARELYS A:436 , GLY A:437BINDING SITE FOR RESIDUE GOL A1502
4AC4SOFTWAREMSE A:449BINDING SITE FOR RESIDUE K A1503
5AC5SOFTWARECYS B:408 , ARG B:411 , LEU B:427 , HOH B:2064BINDING SITE FOR RESIDUE NHE B1501
6AC6SOFTWAREHIS B:450 , CYS B:452BINDING SITE FOR RESIDUE K B1502
7AC7SOFTWAREMSO B:449 , HOH B:2073BINDING SITE FOR RESIDUE NA B1504

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:452 -B:452

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AE4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AE4)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBAP1_HUMAN389-430
 
451-498
 		  4A:389-430
B:389-430
A:451-498
B:451-498

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003595442ENSE00001694558chr9:34220437-3422046529UBAP1_HUMAN-00--
1.3ENST000003595443ENSE00001383696chr9:34220906-3422094641UBAP1_HUMAN1-12120--
1.4ENST000003595444ENSE00001089270chr9:34234214-34234338125UBAP1_HUMAN12-53420--
1.5ENST000003595445ENSE00001089268chr9:34241183-34242106924UBAP1_HUMAN54-3613080--
1.6ENST000003595446ENSE00001089271chr9:34249777-34249959183UBAP1_HUMAN362-422612A:386-422
B:386-422		37
37
1.7ENST000003595447ENSE00001089269chr9:34250656-34250757102UBAP1_HUMAN423-456342A:423-456
B:423-456		34
34
1.8aENST000003595448aENSE00001089272chr9:34251390-342525201131UBAP1_HUMAN457-502462A:457-499
B:457-500		43
44

(-) 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:114
 aligned with UBAP1_HUMAN | Q9NZ09 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:114
                                   395       405       415       425       435       445       455       465       475       485       495    
          UBAP1_HUMAN   386 QMLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEVLLLHNNDQDNALEDLMARA 499
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---UBA  PDB: A:389-430 UniProt: 389-430      --------------------UBA  PDB: A:451-498 UniProt: 451-498            - PROSITE
               Transcript 1 Exon 1.6  PDB: A:386-422 [INCOMPLETE]Exon 1.7  PDB: A:423-456          Exon 1.8a  PDB: A:457-499 UniProt: 457-502  Transcript 1
                 4ae4 A 386 SHmSPSERQCVETVVNmGYSYECVLRAmKAAGANIEQILDYLFAHGQLCEKGFDPLLVEEALEmHQCSEEKmmEFLQLmSKFKEmGFELKDIKEVLLLHNNDQDNALEDLmARA 499
                              |    395      |405       415       425       435       445   |   455 ||    465    |  475       485       495|   
                              |           402-MSE    413-MSE                             449-MSE 457-MSE  |     |                       496-MSE
                            388-MSE                                                               458-MSE |     |                             
                                                                                                        464-MSE |                             
                                                                                                              470-MSE                         


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with UBAP1_HUMAN | Q9NZ09 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:115
                                   395       405       415       425       435       445       455       465       475       485       495     
          UBAP1_HUMAN   386 QMLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEVLLLHNNDQDNALEDLMARAG 500
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBA  PDB: B:389-430 UniProt: 389-430      --------------------UBA  PDB: B:451-498 UniProt: 451-498            -- PROSITE
               Transcript 1 Exon 1.6  PDB: B:386-422 [INCOMPLETE]Exon 1.7  PDB: B:423-456          Exon 1.8a  PDB: B:457-500 UniProt: 457-502   Transcript 1
                 4ae4 B 386 SHmSPSERQCVETVVNmGYSYECVLRAmKAAGANIEQILDYLFAHGQLCEKGFDPLLVEEALEmHQCSEEKmmEFLQLmSKFKEmGFELKDIKEVLLLHNNDQDNALEDLmARAG 500
                              |    395      |405       415       425       435       445   |   455 ||    465    |  475       485       495|    
                              |           402-MSO    413-MSE                             449-MSO 457-MSE  |     |                       496-MSE
                            388-MSE                                                               458-MSE |     |                              
                                                                                                        464-MSE |                              
                                                                                                              470-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 4AE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AE4)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UBAP1_HUMAN | Q9NZ09)
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).
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
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.
    GO:0043162    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
cellular component
    GO:0000813    ESCRT I complex    An endosomal sorting complex required for transport. It consists of the class E vacuolar protein sorting (Vps) proteins and interacts with ubiquitinated cargoes.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBAP1_HUMAN | Q9NZ09: 1wgn 5lm1

(-) Related Entries Specified in the PDB File

1wgn SOLUTION STRUCTURE OF UBA DOMAIN OF HUMAN UBIQUITINASSOCIATED PROTEIN 1 (UBAP1)