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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING VH1-46 GERMLINE-DERIVED CD4-BINDING SITE-DIRECTED ANTIBODY CH235.12 IN COMPLEX WITH HIV-1 CLADE A/E 93TH057 GP120
 
Authors :  T. Zhou, P. D. Kwong
Date :  09 Dec 15  (Deposition) - 09 Mar 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv-1, Antibody, Ch235 Lineage, Vh1-46 Germline, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bonsignori, T. Zhou, Z. Sheng, L. Chen, F. Gao, M. G. Joyce, G. Ozorowski, G. Y. Chuang, C. A. Schramm, K. Wiehe, S. M. Alam, T. Bradley, M. A. Gladden, K. K. Hwang, S. Iyengar, A. Kumar, X. Lu, K. Luo, M. C. Mangiapani, R. J. Parks, H. Song, P. Acharya, R. T. Bailer, A. Cao, A. Druz, I. S. Georgiev, Y. D. Kwon, M. K. Louder, B. Zhang, A. Zheng, B. J. Hill, R. Kong, C. Soto, J. C. Mullikin, D. C. Douek, D. C. Montefiori, M. A. Moody, G. M. Shaw, B. H. Hahn, G. Kelsoe, P. T. Hraber, B. T. Korber, S. D. Boyd, A. Z. Fire, T. B. Kepler, L. Shapiro, A. B. Ward, J. R. Mascola, H. X. Liao, P. D. Kwong, B. F. Hayne
Maturation Pathway From Germline To Broad Hiv-1 Neutralizer Of A Cd4-Mimic Antibody.
Cell V. 165 449 2016
PubMed-ID: 26949186  |  Reference-DOI: 10.1016/J.CELL.2016.02.022

(-) Compounds

Molecule 1 - CLADE A/E 93TH057 HIV-1 GP120 CORE
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F GNTI-/-
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMIDS
    Gene: HIV-1 ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY CH235.12
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 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 CH235.12
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    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, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG G:327 , LYS G:421 , GLN G:422 , ILE G:423binding site for residue EPE G 513
02AC2SOFTWAREALA G:60 , GLU G:62 , THR G:63 , THR G:71 , HIS G:72binding site for residue EPE G 514
03AC3SOFTWAREILE L:106 , LYS L:107 , ARG L:108 , SER L:168 , LYS L:169 , SER L:171binding site for residue EPE L 301
04AC4SOFTWAREASN G:88 , LYS H:117binding site for Mono-Saccharide NAG G 501 bound to ASN G 88
05AC5SOFTWAREASN G:234 , THR G:236 , PRO G:238 , SER G:274 , ASN G:276 , HIS G:352 , NAG G:505binding site for Mono-Saccharide NAG G 502 bound to ASN G 234
06AC6SOFTWAREGLU G:83 , ASN G:229 , ASN G:241binding site for Mono-Saccharide NAG G 503 bound to ASN G 241
07AC7SOFTWARELEU G:261 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:605 , HOH G:610binding site for Mono-Saccharide NAG G 504 bound to ASN G 262
08AC8SOFTWAREASN G:276 , HIS G:352 , NAG G:502 , HOH G:638 , ARG L:30binding site for Mono-Saccharide NAG G 505 bound to ASN G 276
09AC9SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS G:348 , HOH G:619 , SER H:25binding site for Mono-Saccharide NAG G 506 bound to ASN G 289
10AD1SOFTWAREGLU G:293 , ASN G:295 , GLU G:332binding site for Mono-Saccharide NAG G 507 bound to ASN G 295
11AD2SOFTWAREASN G:334 , LYS G:337binding site for Mono-Saccharide NAG G 508 bound to ASN G 334
12AD3SOFTWAREASN G:355 , SER H:105binding site for Mono-Saccharide NAG G 509 bound to ASN G 355
13AD4SOFTWAREASN G:386 , THR G:388binding site for Mono-Saccharide NAG G 510 bound to ASN G 386
14AD5SOFTWAREASN G:392 , THR G:394 , CYS G:395 , CYS G:410binding site for Mono-Saccharide NAG G 511 bound to ASN G 392
15AD6SOFTWARESER G:291 , ASN G:448binding site for Mono-Saccharide NAG G 512 bound to ASN G 448

(-) SS Bonds  (12, 12)

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: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 5F96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F96)

(-) Exons   (0, 0)

(no "Exon" information available for 5F96)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee......eeee....eeee...hhhhhhhhhhhhhhhhhhh...eee.....ee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhhhhhh....eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5f96 G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296   ||  330       340       350    || 361       371       381       391     ||413       423       433       443       453       463       473       483         
                                                                                                          124|                                                                                                   300|                           355|                                     397|                                                                                  
                                                                                                           198                                                                                                    325                            357                                      410                                                                                  


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5f96 H    1 QVRLAQYGGGVKRLGATMTLSCVASGYTFNDYYIHWVRQAPGQGFELLGYIDPANGRPDYAGALRERLSFYRDKSMETLYMDLRSLRYDDTAMYYCVRNVGTAGSLLHYDHWGSGSPVIVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121      |136       146       156       166       176       186       196       206       216
                                                                              52A                            82A||               100A||||                         128|                                                                                  
                                                                                                              82B|                100B|||                          134                                                                                  
                                                                                                               82C                 100C||                                                                                                               
                                                                                                                                    100D|                                                                                                               
                                                                                                                                     100E                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......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
                5f96 L    1 EIVLTQSPATLSASPGERVTLTCRASRSVRNNVAWYQHKGGQSPRLLIYDASTRAAGVPARFSGSASGTEFTLAISNLESEDFTVYFCLQYNNWWTFGQGTRVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    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)
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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 5F96)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F96)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F96)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F96)

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  5f96
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  A0A0M3KKW9_9 | A0A0M3KKW9
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 Related Entries

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

UniProtKB/TrEMBL
        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1r 4s1s 4ybl 4yc2 5cd5 5f9o 5f9w 5fcu 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

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