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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING HIV-1 FUSION PEPTIDE-TARGETING 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 :  2.66
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C
    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, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1ZN10Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:50binding site for residue ZN A 301
02AC2SOFTWAREHIS A:53 , HOH A:414 , HOH C:414binding site for residue ZN A 302
03AC3SOFTWAREGLU A:100A , ARG B:24 , GLU B:32 , HIS B:70binding site for residue ZN A 303
04AC4SOFTWAREHIS A:164 , ASN B:137 , ASN B:138binding site for residue ZN A 304
05AC5SOFTWAREILE B:2 , HOH B:420 , ZN D:301binding site for residue ZN B 301
06AC6SOFTWARETRP C:50binding site for residue ZN C 301
07AC7SOFTWAREHOH A:403 , HOH A:412 , HIS C:53 , HOH C:424binding site for residue ZN C 302
08AC8SOFTWAREGLU C:100A , HOH C:411 , GLU D:32 , HIS D:70binding site for residue ZN C 303
09AC9SOFTWAREHIS C:164 , ASN D:137 , ASN D:138 , HOH D:419binding site for residue ZN C 304
10AD1SOFTWAREILE B:2 , ZN B:301 , ILE D:2binding site for residue ZN D 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:194
5C:22 -C:92
6C:140 -C:196
7D:23 -D:88
8D:134 -D:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:128 -Lys A:129
2Phe A:146 -Pro A:147
3Glu A:148 -Pro A:149
4Ser B:7 -Pro B:8
5Tyr B:94 -Pro B:95
6Tyr B:140 -Pro B:141
7Pro C:126 -Ser C:127
8Phe C:146 -Pro C:147
9Glu C:148 -Pro C:149
10Ser D:7 -Pro D:8
11Tyr D:94 -Pro D:95
12Tyr D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I8E)

(-) Exons   (0, 0)

(no "Exon" information available for 5I8E)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.hhhhh...eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee..........eeeeehhhheeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5i8e A    2 EVLVQSGAEVKKPGASVKVSCRAFGYTFTGNALHWVRQAPGQGLEWLGWINPHSGDTTTSQKFQGRVYMTRDKSINTAFLDVTRLTSDDTGIYYCARDKYYGNEAVGMDVWGQGTSVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||102       112       122      |136       146       156       166       176       186       196       206       
                                                                             52A                            82A||               100A||||                          129|                                                                               
                                                                                                             82B|                100B|||                           134                                                                               
                                                                                                              82C                 100C||                                                                                                             
                                                                                                                                   100D|                                                                                                             
                                                                                                                                    100E                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               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...eeeeeeeeee.....eeee....eeeee.........eeeeeeeee...........eeeee.......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5i8e B    2 IQLTQSPSFLSASVGDKVTITCRASQGVRNELAWYQQKPGKAPNLLIYYASTLQSGVPSRFSATGSGTHFTLTVSSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFN  210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       157       167       177       187       197       207   
                                                                                                                                                                              150|                                                     
                                                                                                                                                                               157                                                     


Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.hhhhh...eeee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeee..hhhhhh..eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5i8e C    1 QEVLVQSGAEVKKPGASVKVSCRAFGYTFTGNALHWVRQAPGQGLEWLGWINPHSGDTTTSQKFQGRVYMTRDKSINTAFLDVTRLTSDDTGIYYCARDKYYGNEAVGMDVWGQGTSVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121     ||137       147       157       167       177       187       197       207      
                                                                              52A                            82A||               100A||||                        127|                                                                               
                                                                                                              82B|                100B|||                         134                                                                               
                                                                                                               82C                 100C||                                                                                                           
                                                                                                                                    100D|                                                                                                           
                                                                                                                                     100E                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               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.....eeeee.........eeeee.........eeeeeeeeeehhhhh....eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5i8e D    2 IQLTQSPSFLSASVGDKVTITCRASQGVRNELAWYQQKPGKAPNLLIYYASTLQSGVPSRFSATGSGTHFTLTVSSLQPEDFATYFCQHMSSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNA  211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (0, 0)

(no "SCOP Domain" information available for 5I8E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I8E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I8E)

(-) Gene Ontology  (0, 0)

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5i8c RELATED STRUCTURE, SAME MANUSCRIPT.
5i8h