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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ENDOGENOUS RETROVIRUS HERV-FRD ENVELOPE PROTEIN (SYNCITIN-2)
 
Authors :  M. Renard, P. F. Varela, C. Letzelter, S. Duquerroy, F. A. Rey, T. Heidma
Date :  01 Dec 04  (Deposition) - 15 Nov 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (4x)
Keywords :  Coat Protein, Membrane Fusion, Endogenous Retrovirus, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Renard, P. F. Varela, C. Letzelter, S. Duquerroy, F. A. Rey, T. Heidmann
Crystal Structure Of A Pivotal Domain Of Human Syncytin-2, 40 Million Years Old Endogenous Retrovirus Fusogenic Envelope Gene Captured By Primates.
J. Mol. Biol. V. 352 1029 2005
PubMed-ID: 16140326  |  Reference-DOI: 10.1016/J.JMB.2005.07.058

(-) Compounds

Molecule 1 - HERV-FRD_6P24.1 PROVIRUS ANCESTRAL ENV POLYPROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28(+)B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ECTODOMAIN OF THE TRANSMEMBRANE SUBUNIT (RESIDUES 391-443) .
    Gene: ERVFRDE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENVELOPE POLYPROTEIN, HERV-FRD, SYNCYTIN 2, UNQ6191/PRO20218

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (4x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:71 , ASN B:71 , ASN C:71BINDING SITE FOR RESIDUE CL A 136

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:86 -A:93
2B:86 -B:93
3C:86 -C:93

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y4M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y4M)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y4M)

(-) 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:53
 aligned with SYCY2_HUMAN | P60508 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:53
                                   400       410       420       430       440   
          SYCY2_HUMAN   391 NIDTMAKALTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVN 443
               SCOP domains d1y4ma1 A:46-98                                       SCOP domains
               CATH domains 1y4mA00 A:46-98  [code=1.10.287.210, no name defined] CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1y4m A  46 NIDTMAKALTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVN  98
                                    55        65        75        85        95   


Chain B from PDB  Type:PROTEIN  Length:53
 aligned with SYCY2_HUMAN | P60508 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:53
                                   400       410       420       430       440   
          SYCY2_HUMAN   391 NIDTMAKALTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVN 443
               SCOP domains d1y4mb_ B:                                            SCOP domains
               CATH domains 1y4mB00 B:46-98  [code=1.10.287.210, no name defined] CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1y4m B  46 NIDTMAKALTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVN  98
                                    55        65        75        85        95   


Chain C from PDB  Type:PROTEIN  Length:53
 aligned with SYCY2_HUMAN | P60508 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:53
                                   400       410       420       430       440   
          SYCY2_HUMAN   391 NIDTMAKALTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVN 443
               SCOP domains d1y4mc_ C:                                            SCOP domains
               CATH domains 1y4mC00 C:46-98  [code=1.10.287.210, no name defined] CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1y4m C  46 NIDTMAKALTTMQEQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVN  98
                                    55        65        75        85        95
   Legend:   → Mismatch (orange background)
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  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, 3)

Asymmetric Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y4M)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SYCY2_HUMAN | P60508)
biological process
    GO:0006949    syncytium formation    The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
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.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1mg1
1mof STRUCTURALLY AND FUNCTIONALLY RELATED PDB ENTRIES