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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 CLADE A BG505 FUSION PEPTIDE (RESIDUE 512-520) IN COMPLEX WITH BROADLY NEUTRALIZING ANTIBODY VRC34.01 FAB
 
Authors :  K. Xu, T. Zhou, K. Liu, P. D. Kwong
Date :  18 Feb 16  (Deposition) - 25 May 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hiv-1, Envelope, Trimer, Fusion Peptide, Antibody, Neutralizing, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kong, K. Xu, T. Zhou, P. Acharya, T. Lemmin, K. Liu, G. Ozorowski, C. Soto, J. D. Taft, R. T. Bailer, E. M. Cale, L. Chen, C. W. Choi, G. Y. Chuang, N. A. Doria-Rose, A. Druz, I. S. Georgiev, J. Gorman, J. Huang, M. G. Joyce, M. K. Louder, X. Ma, K. Mckee, S. O'Dell, M. Pancera, Y. Yang, S. C. Blanchard, W. Mothes, D. R. Burton, W. C. Koff M. Connors, A. B. Ward, P. D. Kwong, J. R. Mascola
Fusion Peptide Of Hiv-1 As A Site Of Vulnerability To Neutralizing Antibody.
Science V. 352 828 2016
PubMed-ID: 27174988  |  Reference-DOI: 10.1126/SCIENCE.AAE0474

(-) Compounds

Molecule 1 - VRC34.01 FAB HEAVY CHAIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Gene: IGHG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - VRC34.01 FAB LIGHT CHAIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HIV-1 CLADE A BG505 FUSION PEPTIDE (RESIDUE 512-520)
    Chains: C
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5I8C)

(-) Sites  (0, 0)

(no "Site" information available for 5I8C)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Ser B:7 -Pro B:8
4Tyr B:94 -Pro B:95
5Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I8C)

(-) Exons   (0, 0)

(no "Exon" information available for 5I8C)

(-) 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:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.hhhhh...eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5i8c A    1 QEVLVQSGAEVKKPGASVKVSCRAFGYTFTGNALHWVRQAPGQGLEWLGWINPHSGDTTTSQKFQGRVYMTRDKSINTAFLDVTRLTSDDTGIYYCARDKYYGNEAVGMDVWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       131       141       151       161       171       181       191       201       211   
                                                                              52A                            82A||               100A||||                                                                                                                  
                                                                                                              82B|                100B|||                                                                                                                  
                                                                                                               82C                 100C||                                                                                                                  
                                                                                                                                    100D|                                                                                                                  
                                                                                                                                     100E                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               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......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5i8c B    1 DIQLTQSPSFLSASVGDKVTITCRASQGVRNELAWYQQKPGKAPNLLIYYASTLQSGVPSRFSATGSGTHFTLTVSSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain C from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                5i8c C  512 AVGIGAVF  519
   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 5I8C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I8C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I8C)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:148 - Pro A:149   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr B:94 - Pro B:95   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

5i8e 5i8h