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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF DENGUE VIRUS SEROTYPE 1 SE CONTAINING STEM
 
Authors :  D. E. Klein, J. L. Choi, S. C. Harrison
Date :  28 Aug 12  (Deposition) - 19 Dec 12  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Viral Fusion Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Klein, J. L. Choi, S. C. Harrison
Structure Of A Dengue Virus Envelope Protein Late-Stage Fusion Intermediate.
J. Virol. V. 87 2287 2013
PubMed-ID: 23236058  |  Reference-DOI: 10.1128/JVI.02957-12

(-) Compounds

Molecule 1 - ENVELOPE PROTEIN E
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 281-691
    Gene: ENVELOPE PROTEIN
    Mutation: YES
    Organism Common: DENV-1
    Organism Scientific: DENGUE VIRUS 1
    Organism Taxid: 11059
    Strain: WP74

 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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION
2CL1Ligand/IonCHLORIDE ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:67 , HOH A:733 , HOH A:896BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWARETHR A:76 , ASP A:98 , HOH A:710 , GLU B:311BINDING SITE FOR RESIDUE CD A 502
3AC3SOFTWAREASP A:10 , HOH A:623 , HOH A:777 , HOH A:932BINDING SITE FOR RESIDUE CD A 503
4AC4SOFTWAREGLY A:102 , HOH A:628 , GLU B:311BINDING SITE FOR RESIDUE CL A 504
5AC5SOFTWAREASN B:67 , LYS B:118 , HOH B:775BINDING SITE FOR RESIDUE NAG B 501
6AC6SOFTWAREASP B:10 , HOH B:849BINDING SITE FOR RESIDUE CD B 502
7AC7SOFTWAREHIS B:27 , HIS B:282 , GLU B:368 , HOH B:789 , HOH B:806BINDING SITE FOR RESIDUE CD B 503

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:3 -A:30
2A:60 -A:121
3A:74 -A:105
4A:92 -A:116
5A:185 -A:285
6A:302 -A:333
7B:3 -B:30
8B:60 -B:121
9B:74 -B:105
10B:92 -B:116
11B:185 -B:285
12B:302 -B:333

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:331 -Pro A:332
2Ala B:331 -Pro B:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GSX)

(-) Exons   (0, 0)

(no "Exon" information available for 4GSX)

(-) 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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4gsxa1 A:2-297 automated matches                                                                                                                                                                                                                                                           d4gsxa2 A:298-403 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhh.eee....eeeeeeeee....eee.......eeeeeeeeeee..eeeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeeehhhhh....eeeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee....eeeee.....eeeeee...eeeeeeeee........eeeeee..eeeeeehhhhhh....eee..........hhhh.eee.........eee...hhhhhhhhh...eeeeee..eeee..eeeeeeeee...............eee....ee.....eeeeeee......ee..eeeee...............ee......eeeee....eeeeeee.hhhhheeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gsx A   2 RCVGIGNRDFVEGLSGATWVDVVLEHGSCVTTMAKDKPTLDIELLKTEVTNPAVLRKLCIEAKISNTTTDSRCPTQGEATLVEEQDTNFVCRRTFVDRGHGNGCGLFGKGSLITCAKFKCVTKLEGKIVQYENLKYSVIVTVHTGGTIATITPQAPTSEIQLTDYGALTLDCSPRTGLDFNEMVLLTMEKKSWLVHKQWFLDLPLPWTSGASTSQETWNRQDLLVTFKTAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGTTTIFAGHLKCRLKMDKLTLKGMSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKGSSIGKMFE 403
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    || 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
                                                                                                                                                                          146|                                                                                                                                                                                                                                                    
                                                                                                                                                                           159                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4gsxb1 B:2-297 automated matches                                                                                                                                                                                                                                                          d4gsxb2 B:298-404 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.hhh.eee....eeeeeeeee...eeeee.....eeeeeeeeeeee..eeeeeeeeeeeeeeeeeee.........hhhhh...eeeeeeeee..........eeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee....eeeee.....eeeeee...eeeeeeeee........eeeeee..eeeeeehhhhhh....eee..........hhhh.eee.........eee...hhhhhhhhhh...ee.ee..eeee..eeeeeeeee...............eee....ee.....eeeeeee......ee..eeeee...............ee......eeeee....eeeeeee......eeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gsx B   2 RCVGIGNRDFVEGLSGATWVDVVLEHGSCVTTMAKDKPTLDIELLKTEVTNPAVLRKLCIEAKISNTTTDSRCPTQGEATLVEEQDTNFVCRRTFVDRGGNGCGLFGKGSLITCAKFKCVTKLEGKIVQYENLKYSVIVTVHTHGTIATITPQAPTSEIQLTDYGALTLDCSPRTGLDFNEMVLLTMEKKSWLVHKQWFLDLPLPWTSGASTSQETWNRQDLLVTFKTAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGTTTIFAGHLKCRLKMDKLTLKGMSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKGSSIGKMFEA 404
                                    11        21        31        41        51        61        71        81        91       102       112       122       132       142  ||   164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404
                                                                                                                            100|                                        145|                                                                                                                                                                                                                                                      
                                                                                                                             102                                         158
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        POLG_DEN1W | P17763: 3l6p 3lkw 4al8 4ffz 4gt0 4lcy 4oig 5vic

(-) Related Entries Specified in the PDB File

1ok8 1urz 3g7t 4gt0