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(-) Description

Title :  CRYSTAL STRUCTURE OF NON-NEUTRALIZING, A32-LIKE ANTIBODY 2.2C IN COMPLEX WITH HIV-1 YU2 GP120
 
Authors :  P. Acharya, P. D. Kwong
Date :  19 Aug 14  (Deposition) - 17 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
Chains :  Asym./Biol. Unit :  A,H,L,R
Keywords :  Hiv-1 Attachment Protein, Membrane, 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: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - ANTIBODY 2.2C LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY 2.2C HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - M48U1 PEPTIDE
    Chains: R
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : AHLR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 18)

Asymmetric/Biological Unit (8, 18)
No.NameCountTypeFull Name
1BU33Ligand/Ion(R,R)-2,3-BUTANEDIOL
2DPR1Mod. Amino AcidD-PROLINE
3MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NH21Mod. Amino AcidAMINO GROUP
6OAS1Mod. Amino AcidO-ACETYLSERINE
7SO42Ligand/IonSULFATE ION
8U2X1Mod. Amino AcidO-(CYCLOHEXYLMETHYL)-L-TYROSINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS R:19 , ALA R:20 , THR R:22 , U2X R:23BINDING SITE FOR RESIDUE DPR R 21
02AC2SOFTWARETHR A:278 , ASN A:280 , ARG A:456 , GLY A:458 , GLY A:459BINDING SITE FOR RESIDUE BU3 A 508
03AC3SOFTWAREPRO L:59 , SER L:60BINDING SITE FOR RESIDUE BU3 L 301
04AC4SOFTWARELYS H:43 , ARG H:44BINDING SITE FOR RESIDUE SO4 A 510
05AC5SOFTWAREARG H:94BINDING SITE FOR RESIDUE SO4 H 301
06AC6SOFTWAREASN A:234 , THR A:236 , SER A:274BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 234
07AC7SOFTWAREGLU A:211 , PRO A:212 , VAL A:254 , LEU A:261 , ASN A:262 , CYS A:445 , SER A:446 , SER A:447BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 262
08AC8SOFTWAREASN A:276 , THR A:278 , ASN A:279BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 276
09AC9SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLN A:344BINDING SITE FOR MONO-SACCHARIDE NAG A 507 BOUND TO ASN A 289
10BC1SOFTWAREASN A:295 , ASN A:413BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 295
11BC2SOFTWAREASN A:386 , THR A:388BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 386
12BC3SOFTWAREASN A:448BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 448
13BC4SOFTWARESER H:19 , SER H:70 , SER H:79 , ASN H:81BINDING SITE FOR MONO-SACCHARIDE NAG H 302 BOUND TO ASN H 81

(-) SS Bonds  (14, 14)

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:378 -A:445
7A:385 -A:418
8H:22 -H:92
9H:140 -H:196
10L:23 -L:88
11L:134 -L:194
12R:1 -R:19
13R:6 -R:24
14R:10 -R:26

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Thr A:77 -Asp A:78
2Asp A:78 -Pro A:79
3Pro A:81 -Gln A:82
4Gly A:459 -Lys A:460
5Lys A:460 -Asp A:461
6Tyr L:140 -Pro L:141
7Trp H:98 -Pro H:99
8Leu H:100A-Pro H:100B
9Asp H:101 -Pro H:102
10Phe H:146 -Pro H:147
11Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R4F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R4F)

(-) Exons   (0, 0)

(no "Exon" information available for 4R4F)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee........hhhhhhhhhhh................eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eee..............eee.........eeee.........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee...............eeeeeeee..eee......eee........eeeeeeeeeeeeee........eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r4f A   45 WKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    54        64        74        84        94       104       114       124|      207       217       227       237       247       257       267       277       287       297   ||  330       340       350       360       370       380       390     ||412       422       432       442       452       462       472       482       492
                                                                                                         124|                                                                                                    301|                                                                    396|                                                                                   
                                                                                                          198                                                                                                     325                                                                     409                                                                                   


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..ee.....eeeeeeee.......eeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r4f H    2 VQLQQWGAGLLKPSETLSLTCGVYGESLSGHYWSWVRQPPGKRLEWIGEIKHNGSPNYHPSLKSRVTISLDMSKNQFSLNLTSVTAADTAVYFCARRSNWPYLPFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    11        21        31        41        51        61        71        81 |||    88        98  |||  105       115       125       135       145       155       165       175       185       195       205         
                                                                                                           82A||               100A||                                                                                                                  
                                                                                                            82B|                100B|                                                                                                                  
                                                                                                             82C                 100C                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....ee.....eeeeeeeeeee...eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeee..........ee.ee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee.....eeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4r4f L    2 IQMTQSPSFVSASVGDRVTITCRASQGIsSYLAWYQQKPGKAPKLVIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQHLIGLRSFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    11        21        31        41        51        61        71        81        91  ||   102       112       122       132       142       152       162       172       182       192       202         
                                                       30-OAS                                                          94|                                                                                                                   
                                                                                                                        96                                                                                                                   


Chain R from PDB  Type:PROTEIN  Length:28
                                                             
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                4r4f R    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 4R4F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R4F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R4F)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly A:459 - Lys A:460   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1Y2 | P35961: 1g9n 1rzk 1yyl 1yym 2i5y 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jo3 4jzw 4jzz 4k0a 4ka2 4laj 4rqs 4rwy 5a7x 5a8h

(-) Related Entries Specified in the PDB File

4r4b 4r4h 4r4n