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(-) Description

Title :  STRUCTURAL BASIS OF EBOLA VIRUS ENTRY: VIRAL GLYCOPROTEIN BOUND TO ITS ENDOSOMAL RECEPTOR NIEMANN-PICK C1
 
Authors :  H. Wang, Y. Shi, J. Song, J. Qi, G. Lu, J. Yan, G. F. Gao
Date :  30 Nov 15  (Deposition) - 20 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ebola Virus, Glycoprotein, Npc1-C, Viral Protein-Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, Y. Shi, J. Song, J. Qi, G. Lu, J. Yan, G. F. Gao
Ebola Viral Glycoprotein Bound To Its Endosomal Receptor Niemann-Pick C1.
Cell V. 164 258 2016
PubMed-ID: 26771495  |  Reference-DOI: 10.1016/J.CELL.2015.12.044

(-) Compounds

Molecule 1 - GP1
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS
    Expression System Taxid: 7111
    Expression System Vector: PFASTBAC1
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 32-188
    Gene: GP
    Organism Common: ZEBOV
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 128951
    Strain: KIKWIT-95
    Synonym: GP1,2,GP
 
Molecule 2 - GP2
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS
    Expression System Taxid: 7111
    Expression System Vector: PFASTBAC1
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 509-598
    Gene: GP
    Organism Common: ZEBOV
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 128951
    Strain: KIKWIT-95
    Synonym: GP1,2,GP
 
Molecule 3 - NIEMANN-PICK C1 PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 374-620
    Gene: NPC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:70 , VAL A:180 , LYS B:510 , ASN B:563 , THR B:566binding site for Poly-Saccharide residues NAG B 701 through NAG B 702 bound to ASN B 563

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:108 -A:135
2A:121 -A:147
3B:511 -B:556
4C:96 -C:107
5C:144 -C:161

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly C:28 -Pro C:29
2Tyr C:51 -Pro C:52
3Ser C:101 -Pro C:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F1B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1B)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1B)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee............hhh.eeeeeee........hhhhhh..eeee......eee..eee.eeeeeeeeee....................eeeeeeeeee......eeee....eee...eee.........eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1b A  31 RSIPLGVIHNSVLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQ 188
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain B from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..............hhhh.eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 5f1b B 509 PKCNPNLHYWTTQAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWG 598
                                   518  ||   531       541       551       561       571       581       591       
                                      521|                                                                         
                                       525                                                                         


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeeeeee......eee........eeehhhhhhhhhhhhhhhhhhhhh..eee..eeehhhhhh..............hhhhhhh.hhhhhh..ee....eeehhhhhhhhhh........................hhhhhee.....hhhhh.eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f1b C  18 LEKEYFDQHFGPFFRTEQLIIRAPLTDKHIYQPYPSGADVPFGPPLDIQILHQVLDLQIAIENITASYDNETVTLQDICLAPLSPYNTNCTILSVLNYFQNSHSVLDHKKGDDFFVYADYHTHFLYCVRAPASLNDTSLLHDPCLGTFGGPVFPWLVLGGYDDQNYNNATALVITFPVNNYYNDTEKLQRAQAWEKEFINFVKNYKNPNLTISFT 232
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227
   Legend:   → Mismatch (orange background)
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  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 5F1B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1B)

(-) Gene Ontology  (61, 66)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  VGP_EBOZ5 | P87666
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 Related Entries

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

UniProtKB/Swiss-Prot
        NPC1_HUMAN | O15118: 3gkh 3gki 3gkj 3jd8 5f18 5hns 5i31 5jnx 5kwy
        VGP_EBOZ5 | P87666: 2y6s 3csy 5hj3 5jnx

(-) Related Entries Specified in the PDB File

5f18