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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC-CH31 IN COMPLEX WITH HIV-1 CLADE A/E STRAN 93TH057 GP120 WITH LOOP D AND LOOP V5 FROM CLADE A STRAIN KER_2018_11
 
Authors :  T. Zhou, S. Moquin, P. D. Kwong
Date :  23 Jul 13  (Deposition) - 21 Aug 13  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Neutralizing Antibody Vrc-Ch31, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zhou, J. Zhu, X. Wu, S. Moquin, B. Zhang, P. Acharya, I. S. Georgiev, H. R. Altae-Tran, G. Y. Chuang, M. G. Joyce, Y. Do Kwon, N. S. Longo, M. K. Louder, T. Luongo, K. Mckee, C. A. Schramm, J. Skinner, Y. Yang, Z. Yang, Z. Zhang, A. Zheng, M. Bonsignori, B. F. Haynes, J. F. Scheid, M. C. Nussenzweig, M. Simek, D. R. Burton, W. C. Koff, J. C. Mullikin, M. Connors, L. Shapiro, G. J. Nabel, J. R. Mascola, P. D. Kwong
Multidonor Analysis Reveals Structural Elements, Genetic Determinants, And Maturation Pathway For Hiv-1 Neutralization By Vrc01-Class Antibodies.
Immunity V. 39 245 2013
PubMed-ID: 23911655  |  Reference-DOI: 10.1016/J.IMMUNI.2013.04.012

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN KER_2018_11
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: 93TH057
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC-CH31
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY VRC-CH31 (N70D MUTATION)
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:80 , LYS G:340 , GLN G:344 , NAG G:504BINDING SITE FOR RESIDUE SO4 G 510
02AC2SOFTWARELYS G:59 , ALA G:60 , HIS G:61 , HOH G:685 , ASP H:72 , ARG H:73BINDING SITE FOR RESIDUE SO4 G 511
03AC3SOFTWARETRP G:69 , SER G:110 , GLN G:114 , ARG G:327 , LYS G:419 , HOH G:698BINDING SITE FOR RESIDUE SO4 G 512
04AC4SOFTWAREASN G:80 , GLN G:82 , LYS G:290 , LYS G:337 , NAG G:506BINDING SITE FOR RESIDUE SO4 G 513
05AC5SOFTWAREALA H:10 , ARG H:12 , HOH H:436BINDING SITE FOR RESIDUE SO4 H 301
06AC6SOFTWAREASN G:234 , SER G:274 , HIS G:352 , HOH G:717BINDING SITE FOR MONO-SACCHARIDE NAG G 501 BOUND TO ASN G 234
07AC7SOFTWARELYS G:252 , LEU G:261 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:618 , HOH G:630 , HOH G:636BINDING SITE FOR MONO-SACCHARIDE NAG G 502 BOUND TO ASN G 262
08AC8SOFTWAREGLU G:275 , ASN G:276 , SER G:278 , ILE L:29 , GLY L:30 , ASP L:32 , GLN L:90 , TYR L:91BINDING SITE FOR MONO-SACCHARIDE NAG G 503 BOUND TO ASN G 276
09AC9SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , LYS G:348 , SO4 G:510BINDING SITE FOR MONO-SACCHARIDE NAG G 504 BOUND TO ASN G 289
10BC1SOFTWAREASN G:295 , THR G:297 , GLU G:332 , LYS G:442 , HOH G:643 , HOH G:738BINDING SITE FOR MONO-SACCHARIDE NAG G 505 BOUND TO ASN G 295
11BC2SOFTWAREGLU G:83 , HIS G:85 , ASN G:334 , THR G:336 , LYS G:337 , SO4 G:513BINDING SITE FOR MONO-SACCHARIDE NAG G 506 BOUND TO ASN G 334
12BC3SOFTWAREGLU G:347 , ASN G:355BINDING SITE FOR MONO-SACCHARIDE NAG G 507 BOUND TO ASN G 355
13BC4SOFTWAREASN G:386 , THR G:388 , HOH G:687 , HOH G:740BINDING SITE FOR MONO-SACCHARIDE NAG G 508 BOUND TO ASN G 386
14BC5SOFTWARETHR G:388 , GLN G:389 , ASN G:392 , THR G:394BINDING SITE FOR MONO-SACCHARIDE NAG G 509 BOUND TO ASN G 392

(-) SS Bonds  (14, 14)

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:331 -G:418
7G:331 -G:385
8G:378 -G:445
9G:385 -G:418
10G:395 -G:410
11H:22 -H:92
12H:140 -H:196
13L:23 -L:88
14L:134 -L:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LSR)

(-) 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:345
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhhheee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee............eeee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh.....eeee......hhhhhheeeee..eeeee.hhhhhh..........eeeeeeeee.eee......eee........eeeeeeeeeeeeee...........eeeeee....hhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsr G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENISDNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGNTGNNSRTNETFRPGGGNIKDNWRSELYKYKVVQI  494
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348      |359       369       379       389      |409       419       429       439       449       459       469       479       489     
                                                                                                          124|                                                                                                    301|                            355|                                    396|                                                                                       
                                                                                                           198                                                                                                     324                             357                                     407                                                                                       


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eee.....eeeeee...........eeeeee......eeeeee......eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsr H    1 QVQLVQSGAAVRKPGASVTVSCKFAEDDDAPEHFIHFLRQAPGQQLEWLAWMNPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCARAQKRGRSEWAYAHWGQGTPVVVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30     |  39        49   |    58        68        78    ||| 85        95     |100E       110       120      |136       146       156       166       176       186       196       206       
                                                      28A|   35A               52A                            82A||               100A||||                        127|                                                                               
                                                        30                                                     82B|                100B|||                         134                                                                               
                                                                                                                82C                 100C||                                                                                                           
                                                                                                                                     100D|                                                                                                           
                                                                                                                                      100E                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsr L    1 DIQMTQSPSSLSASLGDRVTITCQASRGIGKDLNWYQQKAGKAPKLLVSDASTLEGGVPSRFSGSGFHQDFSLTISSLQAEDVATYFCQQYETFGQGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90||     104       114       124       134       144       154       164       174       184       194       204        
                                                                                                                     91|                                                                                                                    
                                                                                                                      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 4LSR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
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  4lsr
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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 4lsu 4olu 4olv 4olw 4olx 4oly 4olz 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

3ngb 3se8 3se9 4j6r 4jb9 4jpv 4jpw