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(-) Description

Title :  CRYSTAL STRUCTURE OF AN IMMATURE VRC01-CLASS ANTIBODY DRVIA7 FROM A CHINESE DONOR BOUND TO CLADE A/E HIV-1 GP120 CORE
 
Authors :  L. Kong, I. A. Wilson
Date :  03 Jul 15  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Vrc01, Gp120, Hiv-1, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kong, B. Ju, L. Ren, Y. Chen, J. Liu, L. He, K. Hong, B. Su, Z. Wang, G. Ozorowski, X. Ji, Y. Hua, Y. Chen, M. C. Deller, Y. Hao, Y. Feng, F. Garces, R. Wilson, K. Dai, S. O'Dell, K. Mckee, J. Mascola, A. B. Ward R. T. Wyatt, Y. Li, I. A. Wilson, J. Zhu, Y. Shao
Critical Determinants In The Emergence Of Broadly Neutralizing Cd4-Binding Site Antibodies From An Hiv-1-Infected Chinese Donor
Immunity 2015
PubMed: search

(-) Compounds

Molecule 1 - 93TH057 HIV-1 GP120 CORE
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293S
    Expression System Taxid: 9606
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - DRVIA7 FAB HEAVY CHAIN
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - DRVIA7 FAB LIGHT CHAIN
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:229 , ASN A:241 , SER D:52binding site for residue NAG A 502
02AC2SOFTWARENAG A:516binding site for residue NAG A 517
03AC3SOFTWAREASN A:234 , THR A:236 , GLY A:237 , PRO A:238 , ILE A:272 , HIS A:352binding site for Mono-Saccharide NAG A 501 bound to ASN A 234
04AC4SOFTWAREPRO A:212 , LYS A:252 , ASN A:262 , ARG A:379 , CYS A:445 , VAL A:446 , SER A:447 , NAG A:516binding site for Mono-Saccharide NAG A 503 bound to ASN A 262
05AC5SOFTWARELYS A:240 , ASN A:276 , ILE D:29 , ASP D:30 , ASN D:31 , TRP D:32 , PHE D:91binding site for Mono-Saccharide NAG A 504 bound to ASN A 276
06AC6SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:347binding site for Poly-Saccharide residues NAG A 509 through MAN A 512 bound to ASN A 289
07AC7SOFTWAREASN A:295 , TYR A:330 , GLU A:332 , ASP D:17binding site for Poly-Saccharide residues NAG A 513 through BMA A 515 bound to ASN A 295
08AC8SOFTWAREASN A:334binding site for Mono-Saccharide NAG A 505 bound to ASN A 334
09AC9SOFTWAREASN A:386 , THR A:388binding site for Poly-Saccharide residues NAG A 507 through NAG A 508 bound to ASN A 386
10AD1SOFTWARETHR A:388 , GLN A:389 , ASN A:392 , THR A:394 , CYS A:410binding site for Mono-Saccharide NAG A 506 bound to ASN A 392
11AD2SOFTWAREASN A:262 , LEU A:265 , SER A:291 , ASN A:448 , NAG A:503 , NAG A:517binding site for Mono-Saccharide NAG A 516 bound to ASN A 448

(-) SS Bonds  (12, 12)

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
8A:395 -A:410
9C:22 -C:92
10C:140 -C:196
11D:23 -D:88
12D:136 -D:196

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe C:146 -Pro C:147
2Glu C:148 -Pro C:149
3Ser D:7 -Pro D:8
4Tyr D:142 -Pro D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CD5)

(-) Exons   (0, 0)

(no "Exon" information available for 5CD5)

(-) 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:343
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhh....eee......hhhhhheeeee..eeeee.................eeeeeeee..eee.....eeee........eeeeeeeeeeeeee.........eeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd5 A   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    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 C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd5 C    1 QVQLVESGTQFRRPGASVRLSCEASGYTFISSFIHWIRQGPGQGLEWMGWMNPRHGAVNYPRRFQGKVTMTRDTSIDTAYMELRDLRSDDTAMYFCVTSRTKDYDWDFVWGQGTLVVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123       133       143       153       163       173       183       193       203       213
                                                                              52A                            82A||               100A||                                                                                                                 
                                                                                                              82B|                100B|                                                                                                                 
                                                                                                               82C                 100C                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cd5 D    1 DIQMTQSPVTLSASIGDRVTITCRASQRIDNWVAWYQQKPGRAPKLLIYKASILETGVPSRFSGSGSGTEFTLSINSLQPDDVATYYCQQFEEFGRGTKIDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  213
                                    10        20        30        40        50        60        70        80        90||     106       116       126       136       146       156       166       176       186       196       206       
                                                                                                                     91|    103|                                                                                                           
                                                                                                                      96     106
   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 5CD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CD5)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5CD5)

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

UniProtKB/TrEMBL
        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1r 4s1s 4ybl 4yc2 5f96 5f9o 5f9w 5fcu 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

5cd3