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(-) Description

Title :  STRUCTURE OF THE NEWCASTLE DISEASE VIRUS F PROTEIN IN THE POST-FUSION CONFORMATION
 
Authors :  T. S. Jardetzky, X. Wen
Date :  24 Mar 10  (Deposition) - 26 May 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Fusion Protein, Class I, Paramyxovirus, Glycoprotein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Swanson, X. Wen, G. P. Leser, R. G. Paterson, R. A. Lamb, T. S. Jardetzky
Structure Of The Newcastle Disease Virus F Protein In The Post-Fusion Conformation.
Virology V. 402 372 2010
PubMed-ID: 20439109  |  Reference-DOI: 10.1016/J.VIROL.2010.03.050

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0
    Chains: A, B
    Engineered: YES
    Fragment: UNP RESIDUE 32-499
    Gene: F
    Organism Common: NDV
    Organism Scientific: NEWCASTLE DISEASE VIRUS
    Organism Taxid: 11177
    Strain: CHICKEN/AUSTRALIA-VICTORIA/32
    Synonym: FUSION GLYCOPROTEIN F2, FUSION GLYCOPROTEIN F1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:85 , GLN A:279 , NAG A:516BINDING SITE FOR RESIDUE NAG A 515
02AC2SOFTWAREGLN A:279 , NAG A:515BINDING SITE FOR RESIDUE NAG A 516
03AC3SOFTWAREASN A:447 , NAG A:518BINDING SITE FOR RESIDUE NAG A 517
04AC4SOFTWARENAG A:517BINDING SITE FOR RESIDUE NAG A 518
05AC5SOFTWAREASN A:471BINDING SITE FOR RESIDUE NDG A 519
06AC6SOFTWAREASN B:85 , THR B:89 , GLN B:279 , NAG B:516BINDING SITE FOR RESIDUE NAG B 515
07AC7SOFTWAREGLN B:279 , NAG B:515BINDING SITE FOR RESIDUE NAG B 516
08AC8SOFTWAREASN B:68 , ASN B:447 , NAG B:518BINDING SITE FOR RESIDUE NAG B 517
09AC9SOFTWARENAG B:517BINDING SITE FOR RESIDUE NAG B 518
10BC1SOFTWAREASN B:471BINDING SITE FOR RESIDUE NDG B 519

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:76 -A:199
2A:338 -A:347
3A:362 -A:370
4A:394 -A:399
5A:401 -A:424
6B:76 -B:199
7B:338 -B:347
8B:362 -B:370
9B:394 -B:399
10B:401 -B:424

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MAW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MAW)

(-) Exons   (0, 0)

(no "Exon" information available for 3MAW)

(-) 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:418
 aligned with FUS_NDVA | P12572 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:460
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
             FUS_NDVA    34 GRPLAAAGIVVTGDKAVNIYTSSQTGSIIVKLHPNMPKDKEACAKAPLEAYNRTLTTLLTPLGDSIRRIQESVTTSGGRRQKRFIGAIIGSVALGVATAAQITAASALIQANQNAANILRLKESITATIEAVHEVTDGLSQLAVAVGKMQQFVNDQFNNTAQELDCIKITQQVGVELNLYLTELTTVFGPQITSPALTQLTIQALYNLAGGNMDYLLTKLGVGNNQLSSLIGSGLITGNPILYDSQTQLLGIQVTLPSVGNLNNMRATYLETLSVSTTKGFASALVPKVVTQVGSVIEELDTSYCIETDLDLYCTRIVTFPMSPGIYSCLNGNTSACMYSKTEGALTTPYMTLKGSVIANCKMTTCRCADPPGIISQNYGEAVSLIDRHSCNVLSLDGITLRLSGEFDATYQKNISILDSQVIVTGNLDISTELGNVNNSISNALDKLEESNSKLDKVNV 493
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeeee....eeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhh.------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh....eeeeeeee....eeeeeeee...eeeeeeeeeeeee.ee......eee....eeeee..eeeee....eee...eeee....ee..hhhhhhhhhhhhhhh.ee.........eeee..eeee......eee.....ee........eee.......ee..................................hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3maw A  34 GRPLAAAGIVVTGDKAVNIYTSSQTGSIIVKLLPNMPKDKEACAKAPLEAYNRTLTTLLTPLGDSIRRI------------------------------------------NQNAANILRLKESITATNEAVHEVTDGLSQLAVAVGKMQQFVNDQFNNTAQELDCIKITQQVGVELNLYLTELTTVFGPQITSPALTQLTIQALYNLAGGNMDYLLTKLGVGNNQLSSLIGSGLITGNPILYDSQTQLLGIQVTLPSVGNLNNMRATYLETLSVSTTKGFASALVPKVVTQVGSVIEELDTSYCIETDLDLYCTRIVTFPMSPGIYSCLNGNTSACMYSKTEGALTTPYMTLKGSVIANCKMTTCRCADPPGIISQNYGEAVSLIDRHSCNVLSLDGITLRLSGEFDATYQKNISILDSQVIVTGNLDISTELGNVNNSISNALDKLEESNSKLDKVNV 493
                                    43        53        63        73        83        93        |-         -         -         -         - |     153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
                                                                                              102                                        145                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:418
 aligned with FUS_NDVA | P12572 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:460
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
             FUS_NDVA    34 GRPLAAAGIVVTGDKAVNIYTSSQTGSIIVKLHPNMPKDKEACAKAPLEAYNRTLTTLLTPLGDSIRRIQESVTTSGGRRQKRFIGAIIGSVALGVATAAQITAASALIQANQNAANILRLKESITATIEAVHEVTDGLSQLAVAVGKMQQFVNDQFNNTAQELDCIKITQQVGVELNLYLTELTTVFGPQITSPALTQLTIQALYNLAGGNMDYLLTKLGVGNNQLSSLIGSGLITGNPILYDSQTQLLGIQVTLPSVGNLNNMRATYLETLSVSTTKGFASALVPKVVTQVGSVIEELDTSYCIETDLDLYCTRIVTFPMSPGIYSCLNGNTSACMYSKTEGALTTPYMTLKGSVIANCKMTTCRCADPPGIISQNYGEAVSLIDRHSCNVLSLDGITLRLSGEFDATYQKNISILDSQVIVTGNLDISTELGNVNNSISNALDKLEESNSKLDKVNV 493
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Fusion_gly-3mawB01 B:34-493                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) Fusion_gly-3mawB02 B:34-493                                                                                                                                                                                                                                                                                                                                                                                                                                                  Pfam domains (2)
         Sec.struct. author .hhhhhh.eeeeeeeeeee....eeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhh.------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh....eeeeeeee....eeeeeeee...eeeeeeeeeeeee.ee......eee....eeeee..eeeee....eee...eeee....ee..hhhhhhhhhhhhhhh.ee.........eeee..eeee......eee.....ee........eee.......ee..................................hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3maw B  34 GRPLAAAGIVVTGDKAVNIYTSSQTGSIIVKLLPNMPKDKEACAKAPLEAYNRTLTTLLTPLGDSIRRI------------------------------------------NQNAANILRLKESITATNEAVHEVTDGLSQLAVAVGKMQQFVNDQFNNTAQELDCIKITQQVGVELNLYLTELTTVFGPQITSPALTQLTIQALYNLAGGNMDYLLTKLGVGNNQLSSLIGSGLITGNPILYDSQTQLLGIQVTLPSVGNLNNMRATYLETLSVSTTKGFASALVPKVVTQVGSVIEELDTSYCIETDLDLYCTRIVTFPMSPGIYSCLNGNTSACMYSKTEGALTTPYMTLKGSVIANCKMTTCRCADPPGIISQNYGEAVSLIDRHSCNVLSLDGITLRLSGEFDATYQKNISILDSQVIVTGNLDISTELGNVNNSISNALDKLEESNSKLDKVNV 493
                                    43        53        63        73        83        93        |-         -         -         -         - |     153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
                                                                                              102                                        145
   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 3MAW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Fusion_gly] (9)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FUS_NDVA | P12572)
biological process
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0006948    induction by virus of host cell-cell fusion    The process of syncytia-forming cell-cell fusion, caused by a virus.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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: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.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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