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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 2.16 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 :  2.16
Chains :  Asym./Biol. Unit :  C,H,L
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, 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: 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 Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - VRC01CHUGL2 FAB LIGHT CHAIN
    Chains: 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 Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN EOD- GT8
    Chains: C
    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 Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : CHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER H:96 , SER H:98 , SER H:100 , ASP H:101 , LEU L:46 , GLU L:55binding site for residue GOL H 301
2AC2SOFTWAREGLY H:42 , VAL L:85 , TYR L:87 , GLY L:100 , GLY L:101binding site for residue GOL L 301
3AC3SOFTWARELEU L:15 , SER L:168 , LYS L:169 , SER L:171 , HOH L:403binding site for residue GOL L 302
4AC4SOFTWARESER C:16 , SER C:17 , ASN C:18 , GLU C:96 , NAG C:1002 , GLN H:3binding site for Mono-Saccharide NAG C 1001 bound to ASN C 18
5AC5SOFTWAREHIS C:14 , SER C:16 , SER C:17 , VAL C:57 , ASN C:65 , ASN C:150 , NAG C:1001 , HOH C:1128 , GLN L:42binding site for Mono-Saccharide NAG C 1002 bound to ASN C 65

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1C:7 -C:158
2C:15 -C:151
3C:51 -C:88
4C:99 -C:105
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

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
5Arg C:8 -Pro C:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IES)

(-) 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 C from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee......eeeeee...hhhhhhhhh.........eee.........eee..........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee......hhhhhheeeee..eeeee.hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ies C    1 DTITLPCRPAPPPHCSSNITGLILTRQGGYANTVIFRPSGGDWRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSEDWRDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIASKLREQYGAKTIIFKPSSGGDPEFVNHSFNCGGEFFYCASTQLFASTWF  169
                                    10        20        30|       42        52        62        72        82        92       102       112       122       132       142       152       162       
                                                        30|                                                                                                                                        
                                                         33                                                                                                                                        


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......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ies 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 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.....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
                5ies 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
   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 5IES)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  5ies
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 Related Entries

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(-) Related Entries Specified in the PDB File

5if0 5ifa