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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC08 IN COMPLEX WITH HIV-1 CLADE A STRAIN Q842.D12 GP120
 
Authors :  T. Zhou, S. Srivatsan, P. D. Kwong
Date :  15 Jan 15  (Deposition) - 29 Apr 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Antibody, Hiv-1, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Wu, Z. Zhang, C. A. Schramm, M. G. Joyce, Y. Do Kwon, T. Zhou, Z. Sheng B. Zhang, S. O'Dell, K. Mckee, I. S. Georgiev, G. Y. Chuang, N. S. Longo, R. M. Lynch, K. O. Saunders, C. Soto, S. Srivatsan, Y. Yang, R. T. Bailer M. K. Louder, J. C. Mullikin, M. Connors, P. D. Kwong, J. R. Mascola, L. Shapiro
Maturation And Diversity Of The Vrc01-Antibody Lineage Over 15 Years Of Chronic Hiv-1 Infection.
Cell V. 161 470 2015
PubMed-ID: 25865483  |  Reference-DOI: 10.1016/J.CELL.2015.03.004

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160,ENVELOPE GLYCOPROTEIN GP160, ENVELOPE GLYCOPROTEIN GP160
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 GNTI-
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-122, 195-297, 319-481
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: Q842.D12
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY VRC08
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY VRC08
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    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, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1BU32Ligand/Ion(R,R)-2,3-BUTANEDIOL
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU G:370 , SER G:375 , BU3 G:513 , HOH G:675binding site for residue BU3 G 512
02AC2SOFTWAREMET G:426 , TRP G:427 , GLY G:473 , BU3 G:512 , ARG H:53 , GLY H:54binding site for residue BU3 G 513
03AC3SOFTWARELYS G:229 , GLU G:231 , ASN G:241binding site for Mono-Saccharide NAG G 501 bound to ASN G 241
04AC4SOFTWAREGLU G:211 , PRO G:212 , LYS G:252 , ASN G:262 , ASN G:377 , CYS G:445 , GLU G:446 , SER G:447 , NAG G:511 , HOH G:602 , HOH G:611 , HOH G:672 , HOH G:681 , HOH G:763 , HOH G:788 , HOH G:844binding site for Mono-Saccharide NAG G 502 bound to ASN G 262
05AC5SOFTWAREASN G:276 , HOH G:792 , ILE L:28 , THR L:29 , ARG L:31 , HIS L:32binding site for Mono-Saccharide NAG G 503 bound to ASN G 276
06AC6SOFTWARELYS G:293 , ASN G:295 , GLU G:446 , HOH G:630 , ARG L:108 , LYS L:169 , ASP L:170 , SER L:171 , HOH L:314binding site for Mono-Saccharide NAG G 504 bound to ASN G 295
07AC7SOFTWAREASN G:334 , GLU G:337 , HOH G:765 , LYS L:169binding site for Mono-Saccharide NAG G 505 bound to ASN G 334
08AC8SOFTWAREASN G:339 , ASN G:340binding site for Mono-Saccharide NAG G 506 bound to ASN G 339
09AC9SOFTWAREASN G:356binding site for Mono-Saccharide NAG G 507 bound to ASN G 356
10AD1SOFTWARELYS G:117 , ASN G:363 , SER G:364 , ASN G:386 , THR G:388 , NAG G:509 , NAG G:510 , HOH G:721 , HOH G:739 , HOH G:778binding site for Mono-Saccharide NAG G 508 bound to ASN G 363
11AD2SOFTWAREGLN G:114 , LYS G:117 , ASN G:386 , THR G:388 , NAG G:508 , HOH G:618 , HOH G:620 , HOH G:700 , HOH G:714 , HOH G:836binding site for Mono-Saccharide NAG G 509 bound to ASN G 386
12AD3SOFTWAREASN G:392 , NAG G:508binding site for Mono-Saccharide NAG G 510 bound to ASN G 392
13AD4SOFTWAREASN G:262 , PRO G:291 , ASN G:448 , NAG G:502 , HOH G:604 , HOH G:795binding site for Mono-Saccharide NAG G 511 bound to ASN G 448

(-) SS Bonds  (13, 13)

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
8H:22 -H:92
9H:98 -H:100J
10H:99 -H:100E
11H:140 -H:196
12L:23 -L:88
13L: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 4XMP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XMP)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee.......hhhhhhhhhheee.......eee....eeee...hhhhhhhhhhhhhhhhhhh...eee.....ee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhh.....eeee......hhhhhheeeee..eeeee.......eee.....eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmp G   45 WKEAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTGGSAITQACPKVTFEPIPIHYCAPAGFAILKCKDEEFNGIGPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKEVKIRCENITNNAKTIIVQLVNPVKINCTRPNDIRQAHCNVNRTEWNNTLHQVVEQLRKHFNKTINFANSTGGDLEITTHSFNCGGEFFYCNTTNLFNSTWNHTADTIILPCRIKQIINMWQRVGQAMYAPPIRGVIRCESNITGLILTRDGGNTNSTRETFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    54        64        74        84        94       104       114       124|      207       217       227       237       247       257       267       277       287       297  ||   331       341       351 ||    363       373       383       393     ||415       425       435       445       455       465       475       485       
                                                                                                         124|                                                                                                   300|                         353|                                        399|                                                                                
                                                                                                          198                                                                                                    325                          356                                         412                                                                                


Chain H from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee...........hhhhh......ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmp H    1 xVQLVQSGTQMKEPGASVTISCVTSGYEFVEILINWVRQVPGRGLEWMGWMNPRGGGVNYARQFQGKVTMTRDVYRDTAYLTLSGLTSGDTAKYFCVRGRSCCGGRRHCNGADCFNWDFQHWGQGTLVIVSPASTKGPSVFPLAPKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||||101       111       121    || 133       143       153       163       173       183       193       203       213  
                            1-PCA                                             52A                            82A||               100A|||||100J|||||                       126|                                                                                      
                                                                                                              82B|                100B|||||100K||||                        129                                                                                      
                                                                                                               82C                 100C|||||100L|||                                                                                                                 
                                                                                                                                    100D|||||100M||                                                                                                                 
                                                                                                                                     100E|||| 100N|                                                                                                                 
                                                                                                                                      100F|||  100O                                                                                                                 
                                                                                                                                       100G||                                                                                                                       
                                                                                                                                        100H|                                                                                                                       
                                                                                                                                         100I                                                                                                                       


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee....hhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xmp L    1 YIGVTQSPAILSVSLGERVTLSCKTSQAITPRHLVWHRQKGGQAPSLVMTGTSERASGIPDRFIGSGSGTDFTLTITRLEAEDFAVYYCQCLEAFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20       |29        39        49        59        69        79        89 ||    103       113       123       133       143       153       163       173       183       193       203       213 
                                                     27A                                                              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 4XMP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xmp
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  Q8JDI3_9HIV1 | Q8JDI3
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHG1_HUMAN | P01857: 1aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e
        IGKC_HUMAN | P01834: 1a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qqk 2qql 2qqn 2qsc 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d3c 4d9r 4hix 4nm4 4nm8 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5ewi 5veb 5viy
UniProtKB/TrEMBL
        Q8JDI3_9HIV1 | Q8JDI3: 4rx4 4xny

(-) Related Entries Specified in the PDB File

4xny 4xnz