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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ADCC-POTENT ANTIBODY N60-I3 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND M48U1
 
Authors :  W. D. Tolbert, N. Gohain, M. Pazgier
Date :  26 Sep 14  (Deposition) - 15 Jul 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  G,H,L,N
Keywords :  Hiv-1 Gp120, Clade A/E 93Th057, Viral Protein, Viral Protein-Immune System-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Gohain, W. D. Tolbert, P. Acharya, L. Yu, T. Liu, P. Zhao, C. Orlandi, M. L. Visciano, R. Kamin-Lewis, M. M. Sajadi, L. Martin, J. E. Robinson P. D. Kwong, A. L. Devico, K. Ray, G. K. Lewis, M. Pazgier
Cocrystal Structures Of Antibody N60-I3 And Antibody Jr4 In Complex With Gp120 Define More Cluster A Epitopes Involved In Effective Antibody-Dependent Effector Function Against Hiv-1.
J. Virol. V. 89 8840 2015
PubMed-ID: 26085162  |  Reference-DOI: 10.1128/JVI.01232-15

(-) Compounds

Molecule 1 - HIV-1 CLADE A/E GP120
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK 293 GNT1- CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: HIV-1 ENV
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - M48U1 CD4 MIMETIC PEPTIDE
    Chains: N
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: M48U1 IS AN ENGINEERED CD4 MIMETIC
    Synthetic: YES
 
Molecule 3 - N60-I3 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK 293 CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - N60-I3 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK 293 CELLS
    Expression System Taxid: 9606
    Gene: FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : GHLN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1DPR1Mod. Amino AcidD-PROLINE
2MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NH21Mod. Amino AcidAMINO GROUP
5U2X1Mod. Amino AcidO-(CYCLOHEXYLMETHYL)-L-TYROSINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMPT N:1 , CYS N:19 , ALA N:20 , THR N:22 , U2X N:23BINDING SITE FOR RESIDUE DPR N 21
02AC2SOFTWAREASN G:234 , THR G:236 , PRO G:238 , LEU G:277BINDING SITE FOR RESIDUE NAG G 501
03AC3SOFTWAREASN G:229 , LYS G:231 , ASN G:241 , NAG G:506BINDING SITE FOR RESIDUE NAG G 502
04AC4SOFTWAREPRO G:212 , LYS G:252 , VAL G:254 , LEU G:261 , ASN G:262 , CYS G:445 , SER G:447BINDING SITE FOR RESIDUE NAG G 503
05AC5SOFTWAREASN G:276 , THR G:278 , ASN G:279BINDING SITE FOR RESIDUE NAG G 504
06AC6SOFTWAREGLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS G:348BINDING SITE FOR RESIDUE NAG G 505
07AC7SOFTWAREASN G:295 , GLU G:332 , NAG G:502BINDING SITE FOR RESIDUE NAG G 506
08AC8SOFTWARELYS G:231 , GLU G:268 , ASN G:334 , THR G:336BINDING SITE FOR RESIDUE NAG G 507
09AC9SOFTWAREMET G:373 , ASN G:386BINDING SITE FOR RESIDUE NAG G 508
10BC1SOFTWAREGLN G:389 , ASN G:392 , THR G:394BINDING SITE FOR RESIDUE NAG G 509

(-) SS Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1G:54 -G:74
2G:119 -G:205
3G:218 -G:247
4G:228 -G:239
5G:296 -G:331
6G:378 -G:445
7G:385 -G:418
8G:395 -G:410
9H:22 -H:92
10H:140 -H:196
11L:23 -L:88
12L:134 -L:193
13N:1 -N:19
14N:6 -N:24
15N:10 -N:26

(-) Cis Peptide Bonds  (17, 17)

Asymmetric/Biological Unit
No.Residues
1Ala G:460 -Asn G:461
2Asn G:461 -Asn G:462
3Ser H:30 -Ser H:31
4Ser H:31 -Gly H:32
5Gly H:32 -Gly H:33
6Val H:95 -Pro H:96
7Phe H:146 -Pro H:147
8Glu H:148 -Pro H:149
9Gly L:28 -Gly L:29
10Pro L:40 -Asp L:41
11Ser L:94 -Ser L:95
12Tyr L:140 -Pro L:141
13Gly L:142 -Ala L:143
14Ser L:152 -Ser L:153
15Lys L:156 -Ala L:157
16Ala L:157 -Gly L:158
17Gly L:158 -Val L:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RFO)

(-) 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 G from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhh.eee...............eee...hhhhhhhhhhhhhhhhhhh.....................eee....eeeeee.......eee...ee...............ee..........eeee.........eeee.....eeeeee........eeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeeehhhhh............eee..eee.eee......eee........eeeeee..eeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4rfo G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123|      211       221       231       241       251       261       271       281       291       301|      334       344       354||     365       375       385       395||     416       426       436       446       456       466       476       486      
                                                                                                         123|                                                                                                301|                           355|                                    396|                                                                                    
                                                                                                          202                                                                                                 325                            357                                     408                                                                                    


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...ee.....eeeee.............eeeeee......eeeeee.....eee........eeeee..eeeeeeee........eeeeeee................eeeee........eeeee.....eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee...........eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rfo H    1 EVQLVESGPGLVKPSQTLSLTCTVSGASISSGGYFWSWIRQHPGKGLEWIGNIYYIGNTYYNPSLKSRLTISVDTTQNQFSLKLTSVTAADTAVYYCARVPRLRGGNYFDSWGQGTLVTVSSASTKGPSVFPLAPSSAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVE  212
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||101       111       121      |138       148       158       168       178       188       198       208    
                                                             35A|                                             82A||               100A|||                         128|                                                                            
                                                              35B                                              82B|                100B||                          136                                                                            
                                                                                                                82C                 100C|                                                                                                         
                                                                                                                                     100D                                                                                                         


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeee.......eeee..............eeeee..eeeeee...hhhhh.eeeeeeee...eeee...eeeee..........eee..hhhhhh.....eeeeeeee.....eeeeee.........ee...ee.....eeeeeee..hhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rfo L    1 QSVLTQPASVSGSPGQSITISCTGTSSDVGGYKYVSWYQQHPDKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    11        21      ||28        38        48        58        68        78        88       |97      106A       116       126       136       146       156       166       176       186       196       206  
                                    9|              27A||                                                                  95A        106A                                                                                                      
                                    11               27B|                                                                                                                                                                                       
                                                      27C                                                                                                                                                                                       


Chain N from PDB  Type:PROTEIN  Length:28
                                                             
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeee....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                4rfo N    1 xNLHFCQLRCKSLGLLGRCAxTyCACVx   28
                            |       10        20| |    |
                            1-MPT              21-DPR  |
                                                 23-U2X|
                                                      28-NH2
   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 4RFO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala G:460 - Asn G:461   [ RasMol ]  
    Ala L:157 - Gly L:158   [ RasMol ]  
    Asn G:461 - Asn G:462   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:32 - Gly H:33   [ RasMol ]  
    Gly L:142 - Ala L:143   [ RasMol ]  
    Gly L:158 - Val L:159   [ RasMol ]  
    Gly L:28 - Gly L:29   [ RasMol ]  
    Lys L:156 - Ala L:157   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Pro L:40 - Asp L:41   [ RasMol ]  
    Ser H:30 - Ser H:31   [ RasMol ]  
    Ser H:31 - Gly H:32   [ RasMol ]  
    Ser L:152 - Ser L:153   [ RasMol ]  
    Ser L:94 - Ser L:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Val H:95 - Pro H:96   [ RasMol ]  
 

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  4rfo
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  Q0ED31_9HIV1 | Q0ED31
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 Related Entries

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

UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED31: 3ngb 3se8 3se9 3tgt 3u7y 4dko 4dkp 4dkq 4dkr 4dku 4dkv 4dvs 4dvt 4dvv 4dvw 4dvx 4h8w 4i54 4jb9 4jdt 4jkp 4jpv 4jpw 4lsp 4lsq 4lsr 4lsu 4olu 4olv 4olw 4olx 4oly 4olz 4om0 4om1 4p9h 4rfn 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

4h8w CRYSTAL STRUCTURE OF THE ADCC POTENT ANTIBODY N5-I5 FAB, HIV-1 GP120, AND SOLUBLE TWO DOMAIN CD4
4jzw CRYSTAL STRUCTURE OF THE YU2 GP120 AND THE M48U1 CD4 MIMETIC
4rfe
4rfn CRYSTAL STRUCTURE OF THE ADCC POTENT RHESUS MACAQUE ANTIBODY JR4, HIV-1 GP120, AND THE M48 CD4 MIMETIC