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(-) Description

Title :  ONTOGENY OF RECOGNITION SPECIFICITY AND FUNCTIONALITY FOR THE ANTI-HIV NEUTRALIZING ANTIBODY 4E10
 
Authors :  K. A. K. Finton
Date :  13 Aug 13  (Deposition) - 08 Oct 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B,C,H,L,S
Biol. Unit 1:  A,B,S  (1x)
Biol. Unit 2:  C,H,L  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),H (1x),L (1x),S (1x)
Keywords :  Hiv, 4E10, Gep, Germline, Fv, Immunoglobulin, Antibody, 4E10 Epitope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Finton, D. Friend, J. Jaffe, M. Gewe, M. A. Holmes, H. B. Larman, A. Stuart, K. Larimore, P. D. Greenberg, S. J. Elledge, L. Stamatatos, R. K. Strong
Ontogeny Of Recognition Specificity And Functionality For The Broadly Neutralizing Anti-Hiv Antibody 4E10.
Plos Pathog. V. 10 04403 2014
PubMed-ID: 25254371  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004403

(-) Compounds

Molecule 1 - GEP1 FV HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - GEP1 FV LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-129
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IG KAPPA CHAIN V-III REGION HIC
 
Molecule 3 - 4E10 EPITOPE SCAFFOLD T117
    Chains: C, S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHLS
Biological Unit 1 (1x): AB   S
Biological Unit 2 (1x):   CHL 
Biological Unit 3 (1x): A (1x)B (1x)C (1x)H (1x)L (1x)S (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4M8Q)

(-) Sites  (0, 0)

(no "Site" information available for 4M8Q)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:22 -A:92
2B:23 -B:88
3H:22 -H:92
4L:23 -L:88

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser B:7 -Pro B:8
2Ser B:94 -Pro B:95
3Glu C:67 -Pro C:68
4Ser L:7 -Pro L:8
5Ser L:94 -Pro L:95
6Glu S:67 -Pro S:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M8Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M8Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4M8Q)

(-) 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:125
                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeeee...eeeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeeee......eeeeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                4m8q A    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCAREGTTGWGGKPIGAFAYWGQGTLVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100H||     108     
                                                                              52A                            82A||               100A|||||||             
                                                                                                              82B|                100D||||||             
                                                                                                               82C                 100E|||||             
                                                                                                                                    100F||||             
                                                                                                                                     100G|||             
                                                                                                                                      100H||             
                                                                                                                                       100I|             
                                                                                                                                        100J             


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                4m8q B    1 EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPSTFGQGTKVE  105
                                    10        20       |29        39        49        59        69        79        89        99      
                                                     27A                                                                              


Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..ee.....eee....hhhhh...eeeeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m8q C   13 HFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDSKYVRQNAISVGILAEPVNFEDAGGEPDPVPVRVVFMLALGNWFDITNVLWWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRIS  160
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152        


Chain H from PDB  Type:PROTEIN  Length:125
                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeeee.......eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                4m8q H    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCAREGTTGWGWGKPIGAFAYWGQGTLVTVS  112
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100G|||    107     
                                                                              52A                            82A||               100A||||||||            
                                                                                                              82B|                100B|||||||            
                                                                                                               82C                 100D||||||            
                                                                                                                                    100E|||||            
                                                                                                                                     100F||||            
                                                                                                                                      100G|||            
                                                                                                                                       100H||            
                                                                                                                                        100I|            
                                                                                                                                         100J            


Chain L from PDB  Type:PROTEIN  Length:106
                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeee......ee...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                4m8q L    1 EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPSTFGQGTKVE  105
                                    10        20       |29        39        49        59        69        79        89        99      
                                                     27A                                                                              


Chain S from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..ee.....eee....hhhhh...eeeeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m8q S    8 AMQGIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDSKYVRQNAISVGILAEPVNFEDAGGEPDPVPVRVVFMLALGNWFDITNVLWWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISE  161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
   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 4M8Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M8Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M8Q)

(-) Gene Ontology  (21, 33)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu C:67 - Pro C:68   [ RasMol ]  
    Glu S:67 - Pro S:68   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Ser B:94 - Pro B:95   [ RasMol ]  
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 Related Entries

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        KV320_HUMAN | P01619: 1dh5 4lrn 4m62 4ob5 4odx

(-) Related Entries Specified in the PDB File

4m62