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(-) Description

Title :  CRYSTAL STRUCTURE OF DENGUE 2 VIRUS ENVELOPE GLYCOPROTEIN IN COMPLEX WITH THE FAB FRAGMENT OF THE BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
 
Authors :  A. Rouvinski, P. Guardado-Calvo, G. Barba-Spaeth, S. Duquerroy, M. C. F. A. Rey
Date :  18 Jul 14  (Deposition) - 28 Jan 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,H,I,L,M
Biol. Unit 1:  B,I,M  (1x)
Biol. Unit 2:  A,H,L  (1x)
Keywords :  Immune System-Viral Protein Complex, Viral Protein, Membrane Fusion, Class 2 Fusion Protein, Dengue Virus, Broadly Neutralizing Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rouvinski, P. Guardado-Calvo, G. Barba-Spaeth, S. Duquerroy, M. Vaney, C. M. Kikuti, M. E. N. Sanchez, W. Dejnirattisai, W. Wongwiwat, A. Haouz, C. Girard-Blanc, S. Petres, W. E. Shepard, P. Despres, F. Arenzana-Seisdedos, P. Dussart, J. Mongkolsapaya, G. R. Screaton, F. A. Rey
Recognition Determinants Of Broadly Neutralizing Human Antibodies Against Dengue Viruses.
Nature V. 520 109 2015
PubMed-ID: 25581790  |  Reference-DOI: 10.1038/NATURE14130
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN E
    Chains: A, B
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER 2
    Expression System Common: FRUIT FLY
    Expression System Plasmid: PMT/BIP/V5-HIS
    Expression System Taxid: 7227
    Fragment: SOLUBLE ECTODOMAIN, RESIDUES 281-671
    Organism Scientific: DENGUE VIRUS 2
    Organism Taxid: 11060
    Strain: FGA-02
    Synonym: E PROTEIN
 
Molecule 2 - BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAIN
    Cell: B-LYMPHOCYTE
    Chains: H, I
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER 2
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SEE SECONDARY REFERENCE
 
Molecule 3 - BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN
    Cell: B-LYMPHOCYTE
    Chains: L, M
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER 2
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    Fragment: FAB FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SEE SECONDARY REFERENCE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHILM
Biological Unit 1 (1x):  B I M
Biological Unit 2 (1x): A H L 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MAN-1Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:64 , THR A:66 , ASN A:67 , ARG A:89 , LYS A:118 , HOH A:2006 , GLY I:66 , GLU I:82 , ASN I:84 , SER I:85BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 567 THROUGH BMA A 570 BOUND TO ASN A 67
2AC2SOFTWARETHR B:66 , ASN B:67 , ARG B:89 , LYS B:118 , GLY H:66 , ASN H:84 , SER H:85BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 567 THROUGH MAN B 572 BOUND TO ASN B 67

(-) SS Bonds  (20, 20)

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
13H:22 -H:96
14H:149 -H:205
15I:22 -I:96
16I:149 -I:205
17L:23 -L:88
18L:135 -L:195
19M:23 -M:88
20M:135 -M:195

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Ser A:331 -Pro A:332
2Ser B:331 -Pro B:332
3Glu B:383 -Pro B:384
4Phe H:155 -Pro H:156
5Glu H:157 -Pro H:158
6Phe I:155 -Pro I:156
7Glu I:157 -Pro I:158
8Ser L:7 -Pro L:8
9Pro L:95 -Pro L:96
10Tyr L:141 -Pro L:142
11Ser M:7 -Pro M:8
12Pro M:95 -Pro M:96
13Tyr M:141 -Pro M:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UTA)

(-) 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:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee......eeeeee....eeeeee..eeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeeehhhhh....eeeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee.........eeeee.....eeeeee...eeeeeeeeee.......eeeeee..eeeeeehhhhhh....eee..........hhhh.eeee.......eeee...hhhhhhhhh...eeeeee..eee...eeeeeee..................eeeeeeee.....eeeeee...ee...eee....ee.....ee......eeeeee...eeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uta A   1 MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFICKHSMVDRGWGNGCGLFGKGGIVTCAKFTCKKNMEGKIVQPENLEYTIVITPHSGEEHKHGKEIKITPQSSTTEAELTGYGTVTMECSPRTGLDFNEMVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKIVKEIAETQHGTIVIRVQGSPCKIPFEITDVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIVLKLNWLRPL 395
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       331       341|      356       366       376   ||  392   
                                                                                                                                                                              149|                                                                                                                                                                     325|        341|                              380|        
                                                                                                                                                                               157                                                                                                                                                                      330         347                               387        


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee......eeeeeee...eeeeee..eeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeeehhhhh....eeeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee........eeeee.....eeeeee...eeeeeee..........eeeeee..eeeeeehhhhhh....eee..........hhhh.eeee.......eeee...hhhhhhhhh...eee.ee..ee....eeeeeee.................eeeeeeeee.....eeeeeee......ee..ee.......ee.....ee......eeeeee...eeeeeee......eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uta B   1 MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFICKHSMVDRGWGNGCGLFGKGGIVTCAKFTCKKNMEGKIVQPENLEYTIVITPHSGEEHHGKEIKITPQSSTTEAELTGYGTVTMECSPRTGLDFNEMVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKIVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIVGVEPGQLKLNWLRPLESR 398
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338||     352       362       372       382       392      
                                                                                                                                                                              149|                                                                                                                                                                                  339|                                                      
                                                                                                                                                                               158                                                                                                                                                                                   344                                                      


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uta H   2 VQLVESGGGLVQPGGSLRLSCSASGFTFSTYSMHWVRQAPGKGLEYVSAITGEGDSAFYADSVKGRFTISRDNSKNTLYFEMNSLRPEDTAVYYCVGGYSNFYYYYTMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 


Chain I from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..........ee...eeeee........eeeee..eeeeeeeeee.....eeee........eee...ee.....eeeeeeeeehhhhhh....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uta I   2 VQLVESGGGLVQPGGSLRLSCSASGFTFSTYSMHWVRQAPGKGLEYVSAITGEGDSAFYADSVKGRFTISRDNSKNTLYFEMNSLRPEDTAVYYCVGGYSNFYYYYTMDVWGQGTTVTVSSASTKGPSVFPLATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVE 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  ||   150       160       170       180       190       200       210       220 
                                                                                                                                                              134|                                                                             
                                                                                                                                                               144                                                                             


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uta L   0 SEIVLTQSPATLSLSPGERATLSCRASQSISTFLAWYQHKPGQAPRLLIYDASTRATGVPARFSGSRSGTDFTLTISTLEPEDFAVYYCQQRYNWPPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee..eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uta M   0 SEIVLTQSPATLSLSPGERATLSCRASQSISTFLAWYQHKPGQAPRLLIYDASTRATGVPARFSGSRSGTDFTLTISTLEPEDFAVYYCQQRYNWPPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      |161       171       181       191       201       211   
                                                                                                                                                                                      156|                                                       
                                                                                                                                                                                       159
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

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  A0A0B4SHY9_9 | A0A0B4SHY9
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  Q68Y26_9FLAV | Q68Y26
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 Related Entries

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

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        Q68Y26_9FLAV | Q68Y26: 5n0a
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        A0A0B4SHY9_9 | A0A0B4SHY9: 4ut6 4utb 4utc
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(-) Related Entries Specified in the PDB File

4utb CRYSTAL STRUCTURE OF DENGUE 2 VIRUS ENVELOPE GLYCOPROTEIN IN COMPLEX WITH THE FAB FRAGMENT OF THE BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
4utc CRYSTAL STRUCTURE OF DENGUE 2 VIRUS ENVELOPE GLYCOPROTEIN