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(-) Description

Title :  CRYSTAL STRUCTURE OF VRC01C-HUGL2 FAB FROM AN HIV-1 NAIVE DONOR IN COMPLEX WITH WITH A GERMLINE-TARGETING GP120 ENGINEERED OUTER DOMAIN EOD-GT8 AT 2.44 A
 
Authors :  A. Sarkar, I. A. Wilson
Date :  25 Feb 16  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B,G,H,I,L
Biol. Unit 1:  A,B,I  (1x)
Biol. Unit 2:  G,H,L  (1x)
Keywords :  Hiv-1 Gp120, Engineered Outer Domain (Eod), Germline Targeting, Cd4 Binding Site, Vrc01-Class Naive Human Germline Antibody, Immune System, Viral-Protein Complex, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Jardine, D. W. Kulp, C. Havenar-Daughton, A. Sarkar, B. Briney, D. Sok, F. Sesterhenn, J. Ereno-Orbea, O. Kalyuzhniy, I. Deresa, X. Hu S. Spencer, M. Jones, E. Georgeson, Y. Adachi, M. Kubitz, A. C. Decamp, J. P. Julien, I. A. Wilson, D. R. Burton, S. Crotty, W. R. Schief
Hiv-1 Broadly Neutralizing Antibody Precursor B Cells Revealed By Germline-Targeting Immunogen.
Science V. 351 1458 2016
PubMed-ID: 27013733  |  Reference-DOI: 10.1126/SCIENCE.AAD9195

(-) Compounds

Molecule 1 - VRC01CHUGL2 FAB HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 FREESTYLE
    Expression System Plasmid: PFUSESS-CHIG-HG1
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - VRC01C-HUGL2 FAB LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 FREESTYLE
    Expression System Plasmid: PFUSESS-CHIG-HG1
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN EOD- GT8
    Chains: G, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293S
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABGHIL
Biological Unit 1 (1x): AB  I 
Biological Unit 2 (1x):   GH L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL H:169 , SER H:179 , GLN L:160 , SER L:162 , SER L:176 , THR L:178binding site for residue PO4 L 301
2AC2SOFTWAREGLN A:3 , SER G:16 , SER G:17 , ASN G:18 , NAG G:1002binding site for Mono-Saccharide NAG G 1001 bound to ASN G 18
3AC3SOFTWAREHIS G:14 , SER G:16 , SER G:17 , ASN G:65 , ASN G:150 , NAG G:1001binding site for Mono-Saccharide NAG G 1002 bound to ASN G 65
4AC4SOFTWAREGLN H:3 , SER I:16 , SER I:17 , ASN I:18 , NAG I:202binding site for Mono-Saccharide NAG I 201 bound to ASN I 18
5AC5SOFTWAREHIS I:14 , SER I:16 , SER I:17 , ASN I:65 , ASN I:150 , NAG I:201binding site for Mono-Saccharide NAG I 202 bound to ASN I 65

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:194
5G:7 -G:158
6G:15 -G:151
7G:51 -G:88
8G:99 -G:105
9H:22 -H:92
10H:140 -H:196
11I:7 -I:158
12I:15 -I:151
13I:51 -I:88
14L:23 -L:88
15L:134 -L:194

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Gly A:133 -Gly A:134
2Phe A:146 -Pro A:147
3Glu A:148 -Pro A:149
4Ser B:7 -Pro B:8
5Tyr B:140 -Pro B:141
6Arg G:8 -Pro G:9
7Phe H:146 -Pro H:147
8Glu H:148 -Pro H:149
9Arg I:8 -Pro I:9
10Ser L:7 -Pro L:8
11Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IF0)

(-) Exons   (0, 0)

(no "Exon" information available for 5IF0)

(-) Sequences/Alignments

Asymmetric 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:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeeee..hhhhheeeeeeee.....eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5if0 A    1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCAKISGSYSFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205         
                                                                              52A                            82A||               100A                                                                                                                  
                                                                                                              82B|                                                                                                                                     
                                                                                                               82C                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5if0 B    1 DIVMTQSPDSLAVSLGERATINCKSSQKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRG  212
                                    10        20      ||32        42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206      
                                                     27|                                                           91|                                                                                                                    
                                                      30                                                            96                                                                                                                    


Chain G from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee........eeeeee...hhhhhhhhh.........eee.........eeee.........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee......hhhhhheeeee..eeeee.hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5if0 G    1 DTITLPCRPAPPPHCSSNITGLILTRQGGYSNANTVIFRPSGGDWRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIASKLREQYGAKTIIFKPSSGGDPEFVNHSFNCGGEFFYCASTQLFASTWF  169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               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...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5if0 H    1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCAKISGSYSFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205         
                                                                              52A                            82A||               100A                                                                                                                  
                                                                                                              82B|                                                                                                                                     
                                                                                                               82C                                                                                                                                     


Chain I from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee........eeeeee...hhhhhhh...........eee.........eeee.........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee......hhhhhheeeee..eeeee.hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5if0 I    1 DTITLPCRPAPPPHCSSNITGLILTRQGGYSNANTVIFRPSGGDWRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIASKLREQYGAKTIIFKPSSGGDPEFVNHSFNCGGEFFYCASTQLFASTWF  169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain L from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               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..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5if0 L    1 DIVMTQSPDSLAVSLGERATINCKSSQKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRG  212
                                    10        20      ||32        42        52        62        72        82        96       106       116       126       136       146       156       166       176       186       196       206      
                                                     27|                                                           91|                                                                                                                    
                                                      30                                                            96
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5IF0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IF0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IF0)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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