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(-) Description

Title :  CRYSTAL STRUCTURE OF UNBOUND VRC01C-HUGL2 FAB FROM AN HIV-1 NAIVE DONOR AT 1.82 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 :  1.82
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Vrc01-Class Naive Human Germline Antibody, Cd4 Binding Site, Immune System, Anti-Hiv-1 (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 - VRC01C-HUGL2 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 Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - VRC01C-HUGL2 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 Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2GOL7Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU L:17 , LYS L:190 , ARG L:211binding site for residue SO4 H 301
02AC2SOFTWARETYR H:33 , ASN H:52 , SER H:132 , LYS L:207binding site for residue SO4 H 302
03AC3SOFTWAREARG H:82B , ARG H:83 , GLN H:171 , SER H:172 , HOH H:441 , GLN L:160binding site for residue SO4 H 303
04AC4SOFTWAREGLN H:105 , GLY H:106binding site for residue 1PE H 304
05AC5SOFTWARESER H:7 , GLU H:10 , LYS H:19binding site for residue 1PE H 305
06AC6SOFTWAREASP H:208 , LYS H:209 , LYS H:210binding site for residue 1PE H 306
07AC7SOFTWARELYS H:129 , SER L:77 , GLN L:79 , SER L:208 , PHE L:209 , ASN L:210 , HOH L:457binding site for residue 1PE H 307
08AC8SOFTWAREARG H:38 , GLN H:39 , ALA H:40 , GLN H:43 , GLY H:44 , GLU H:46 , HOH H:428binding site for residue GOL H 308
09AC9SOFTWARESER H:96 , SER H:98 , SER H:100 , ASP H:101 , HOH H:401 , LEU L:46 , TYR L:49 , GLU L:55binding site for residue GOL H 309
10AD1SOFTWAREGLU H:148 , HOH H:456 , HOH H:465binding site for residue GOL H 310
11AD2SOFTWARETHR H:160 , SER H:161 , GLY H:162 , VAL H:163 , HIS H:164 , ASP L:167 , LYS L:169binding site for residue GOL H 311
12AD3SOFTWAREGLN L:37 , LYS L:39 , LYS L:45 , PRO L:59 , PHE L:62 , GLU L:81 , ASP L:82binding site for residue GOL L 301
13AD4SOFTWAREARG L:142 , GLU L:143 , ALA L:144 , GLU L:161 , LEU L:175binding site for residue GOL L 302
14AD5SOFTWARESER L:14 , LEU L:15 , GLU L:17 , LYS L:188 , HIS L:189 , LYS L:190 , ARG L:211 , HOH L:401binding site for residue GOL L 303

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L: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 5IFA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IFA)

(-) 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 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.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ifa 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:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeee.......eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ifa L    1 DIVMTQSPDSLAVSLGERATINCKSSQNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKYACEVTHQGLRSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90||     104       114       124       134       144       154       164       174       184     ||195       205       
                                                                                                                     91|                                                                                           190|                    
                                                                                                                      96                                                                                            192
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  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 5IFA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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