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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING VH1-46 GERMLINE-DERIVED CD4-BINDING SITE-DIRECTED ANTIBODY CH235.09 IN COMPLEX WITH HIV-1 CLADE A/E 93TH057 GP120
 
Authors :  M. G. Joyce, J. R. Mascola, P. D. Kwong
Date :  10 Dec 15  (Deposition) - 16 Mar 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Antibody Evolution Hiv-1 Broadly Neutralizing Cd4 Binding Site, 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 Taxid: 9606
    Gene: HIV-1 ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - CH235.9 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CH235.09 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    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  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (41, 41)

Asymmetric Unit (41, 41)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA G:60 , GLU G:62 , THR G:63 , THR G:71 , HIS G:72 , GLY G:367 , ASP G:368 , GLU G:370 , ILE G:423 , ASN G:425 , GLN G:432 , HOH G:664 , HOH G:696 , HOH G:697 , HOH G:711 , TYR H:71binding site for residue 15P G 515
02AC2SOFTWAREASN G:88binding site for Mono-Saccharide NAG G 501 bound to ASN G 88
03AC3SOFTWAREASN G:234 , THR G:236 , SER G:274 , ASN G:276 , NAG G:505binding site for Mono-Saccharide NAG G 502 bound to ASN G 234
04AC4SOFTWAREASN G:229 , ASN G:241binding site for Mono-Saccharide NAG G 503 bound to ASN G 241
05AC5SOFTWARELEU G:261 , ASN G:262 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:512 , HOH G:622binding site for Mono-Saccharide NAG G 504 bound to ASN G 262
06AC6SOFTWAREASN G:276 , ASN G:279 , HIS G:352 , NAG G:502binding site for Mono-Saccharide NAG G 505 bound to ASN G 276
07AC7SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS G:348binding site for Mono-Saccharide NAG G 506 bound to ASN G 289
08AC8SOFTWAREASN G:295 , TYR G:330 , GLU G:332binding site for Mono-Saccharide NAG G 507 bound to ASN G 295
09AC9SOFTWAREPRO G:81 , GLU G:83 , ASN G:334 , THR G:336 , HOH G:748binding site for Mono-Saccharide NAG G 508 bound to ASN G 334
10AD1SOFTWARELYS G:350 , ASN G:355binding site for Mono-Saccharide NAG G 509 bound to ASN G 355
11AD2SOFTWAREMET G:373 , ASN G:386binding site for Mono-Saccharide NAG G 510 bound to ASN G 386
12AD3SOFTWAREASN G:392 , THR G:394 , LYS G:408 , CYS G:410binding site for Mono-Saccharide NAG G 511 bound to ASN G 392
13AD4SOFTWARESER G:291 , LYS G:408 , ASN G:448 , NAG G:504binding site for Mono-Saccharide NAG G 512 bound to ASN G 448
14AD5SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
15AD6SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
16AD7SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
17AD8SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
18AD9SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
19AE1SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
20AE2SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
21AE3SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
22AE4SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
23AE5SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
24AE6SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
25AE7SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
26AE8SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
27AE9SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
28AF1SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
29AF2SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
30AF3SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
31AF4SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
32AF5SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
33AF6SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
34AF7SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
35AF8SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
36AF9SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
37AG1SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
38AG2SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
39AG3SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
40AG4SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514
41AG5SOFTWARECYS G:54 , ALA G:73 , GLN G:103 , ASP G:107 , ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:684binding site for residues EPE G 513 and EPE G 514

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1G:54 -G:74
2G:119 -G:205
3G:218 -G:247
4G:228 -G:239
5G:378 -G:445
6G:385 -G:418
7G:395 -G:410
8H:22 -H:96
9H:149 -H:205
10L:23 -L:88
11L:133 -L:193

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:155 -Pro H:156
2Glu H:157 -Pro H:158
3Ser L:7 -Pro L:8
4Tyr L:139 -Pro L:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F9O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F9O)

(-) Exons   (0, 0)

(no "Exon" information available for 5F9O)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhhhhee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee......hhhhh.......eeeeeeeee.eee.....eeee........eeeeeeeeeeeeee........eeeeee...hhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f9o G  44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCITMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQI 491
                                    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    || 410       420       430       440       450       460       470       480       490 
                                                                                                            126|                                                                                                 300|                           355|                                    396|                                                                                     
                                                                                                             200                                                                                                  325                            357                                     406                                                                                     


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.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeeeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f9o H   1 QVRLLQYGGGVKRPGASMTISCVASGYNFNDYYIHWVRQAPGQGLELMGWIDPSGGRTDYAGAFGDRVSMYRDKSMNTLYMDLRSLRSGDTAMYYCVRNVGTAGSLLHYDHWGLGVMVTVSSTKTKGPSVFPLAPSSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |143       153       163       173       183       193       203       213       223
                                                                                                                                                                  137|                                                                                  
                                                                                                                                                                   141                                                                                  


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f9o L   1 EIVLTQSPATLSVSPGERVTLSCRASQSVRNNLAWYRQKRGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSMQSEDFAVYYCQQYNNWWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 5F9O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F9O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F9O)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F9O)

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  Cis Peptide Bonds
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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 5f96 5f9w 5fcu 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5F9O)