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(-) Description

Title :  CRYSTAL STRUCTURE OF NON-NEUTRALIZING, A32-LIKE ANTIBODY 2.2C IN COMPLEX WITH HIV-1 ENV GP120
 
Authors :  J. Mclellan, P. Acharya, C. -C. Huang, P. D. Kwong
Date :  19 Aug 14  (Deposition) - 17 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.28
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Hiv-1 Attachment Glycoprotein Gp120, Viral Protein-Immune System- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Acharya, W. D. Tolbert, N. Gohain, X. Wu, L. Yu, T. Liu, W. Huang, C. C. Huang, Y. D. Kwon, R. K. Louder, T. S. Luongo, J. S. Mclellan, M. Pancera, Y. Yang, B. Zhang, R. Flinko, J. S. Foulke, M. M. Sajadi, R. Kamin-Lewis, J. E. Robinson, L. Martin, P. D. Kwong, Y. Guan, A. L. Devico, G. K. Lewis, M. Pazgier
Structural Definition Of An Antibody-Dependent Cellular Cytotoxicity Response Implicated In Reduced Risk For Hiv-1 Infection.
J. Virol. V. 88 12895 2014
PubMed-ID: 25165110  |  Reference-DOI: 10.1128/JVI.02194-14

(-) Compounds

Molecule 1 - HIV-1 ENV GP120
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293S
    Expression System Taxid: 9606
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - T-CELL SURFACE GLYCOPROTEIN CD4
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 26-203
    Gene: CD4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: T-CELL SURFACE ANTIGEN T4/LEU-3
 
Molecule 3 - ANTIBODY 2.2C, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - ANTIBODY 2.2C, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:261 , ASN A:262 , ASN A:376 , SER A:446 , NAG A:607BINDING SITE FOR RESIDUE NAG A 601
2AC2SOFTWAREASN A:289 , GLN A:344BINDING SITE FOR RESIDUE NAG A 602
3AC3SOFTWAREASN A:295 , ASN A:332 , ILE A:333 , SER A:334BINDING SITE FOR RESIDUE NAG A 603
4AC4SOFTWAREASN A:295 , HIS A:330 , CYS A:331 , ASN A:332 , ILE A:412 , THR A:414BINDING SITE FOR RESIDUE NAG A 604
5AC5SOFTWAREARG A:335 , ALA A:336 , ASN A:339 , THR A:407BINDING SITE FOR RESIDUE NAG A 605
6AC6SOFTWAREALA A:359 , ASN A:361BINDING SITE FOR RESIDUE NAG A 606
7AC7SOFTWARESER A:291 , ASN A:447 , NAG A:601BINDING SITE FOR RESIDUE NAG A 607
8AC8SOFTWARETHR H:17 , ASN H:81BINDING SITE FOR RESIDUE NAG H 301

(-) SS Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:218 -A:247
4A:228 -A:239
5A:296 -A:331
6A:377 -A:444
7A:384 -A:417
8B:16 -B:84
9B:130 -B:159
10H:22 -H:95
11H:146 -H:202
12L:23 -L:88
13L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Thr A:77 -Asp A:78
2Asn A:80 -Pro A:81
3Ser L:7 -Pro L:8
4Tyr L:140 -Pro L:141
5Trp H:101 -Pro H:102
6Asp H:107 -Pro H:108
7Phe H:152 -Pro H:153
8Glu H:154 -Pro H:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R4H)

(-) Exons   (0, 0)

(no "Exon" information available for 4R4H)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh.........ee.....eeee...hhhhhhhhhhhhhhhhhh....eee....eee......................eeee.......eeee..eeee.............eee.........eee.........eeeeeeeeeeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhhh....eee......hhhhhheeee....eeee........ee..........eeeeeee...eee......eee........eeeeeeeeeeeeee..........eeeee....hhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r4h A  47 EATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLGNVTENFNMWKNNMVDQMHEDIISLWDESLKPCVKLTGGSVITQACPKVSFQPIPIHYCVPAGFAILKCNNKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEDIVIRSEDFTDNVKTIIVQLNESVVINCTRPNIRQAHCNISRAKWNNTLQQIVIKLREKFRNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTAQLFNSTWNVTNGTEGNDIITLQCRIKQIINMWQKVGKAMYAPPITGQIRCSSNITGLLLTRDGGNSTETETEIFRPGGGDMRDNWRSELYKYKV 488
                                    56        66        76        86        96       106       116       199       209       219       229       239       249       259       269       279       289       299||     334       344       354       364       374       384       394 ||    411       421       431       441       451       461       471       481       
                                                                                                       124|                                                                                                   300|                                                                   396|                                                                                    
                                                                                                        198                                                                                                    326                                                                    404                                                                                    


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eee............eee.....eeeee....eee....hhh.ee............eee...hhhhh.eeeeee..eeeeeeeee..eee...........eeeee........eeeee.....eeee..eeee...hhhhheeeeeeeee..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r4h B   1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..ee.....eeeeeeee.......eeeeee.......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..............eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r4h H   1 QVQLQQWGAGLLKPSETLSLTCGVYGESLSGHYWSWVRQPPGKRLEWIGEIKHNGSPNYHPSLKSRVTISLDMSKNQFSLNLTSVTAADTAVYFCARRSNWPYLPFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee.........eeeeee..........eeee........eeeee..hhhhhhhheeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee..........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r4h L   1 DIQMTQSPSFVSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLVIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQHLIGLRSFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 211
                                    10        20        30        40        50        60        70        80        90   ||  101       111       121       131       141       151       161       171       181       191       201       211
                                                                                                                        94|                                                                                                                   
                                                                                                                         96
   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 4R4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R4H)

(-) Gene Ontology  (71, 75)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD4_HUMAN | P01730: 1cdh 1cdi 1cdj 1cdu 1cdy 1g9m 1g9n 1gc1 1jl4 1opn 1opt 1opw 1q68 1rzj 1rzk 1wbr 1wio 1wip 1wiq 2b4c 2jkr 2jkt 2klu 2nxy 2nxz 2ny0 2ny1 2ny2 2ny3 2ny4 2ny5 2ny6 2qad 3b71 3cd4 3j70 3jcb 3jcc 3jwd 3jwo 3lqa 3o2d 3s4s 3s5l 3t0e 4h8w 4jm2 4p9h 4q6i 4r2g 4rqs 5a7x 5a8h 5cay 5thr 5u1f 5vn3
        ENV_HV1B9 | Q73372: 5u3k 5u3l 5u3m 5u3n 5u3o

(-) Related Entries Specified in the PDB File

4r4b 4r4f 4r4n