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(-) Description

Title :  CRYSTAL STRUCTURE OF BROAD NEUTRALIZING ANTIBODY 10E8 WITH LONG EPITOPE BOUND
 
Authors :  J. M. M. Caaveiro, E. Rujas, K. Morante, J. L. Nieva, K. Tsumoto
Date :  21 Jun 16  (Deposition) - 23 Nov 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Broad Neutralizing Antibody, Recombinant Fab, Epitope, Immune System, Hiv-1, Viral Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rujas, J. M. Caaveiro, A. Partida-Hanon, N. Gulzar, K. Morante, B. Apellaniz, M. Garcia-Porras, M. Bruix, K. Tsumoto, J. K. Scott, M. A. Jimenez, J. L. Nieva
Structural Basis For Broad Neutralization Of Hiv-1 Through The Molecular Recognition Of 10E8 Helical Epitope At The Membrane Interface
Sci Rep V. 6 38177 2016
PubMed-ID: 27905530  |  Reference-DOI: 10.1038/SREP38177

(-) Compounds

Molecule 1 - FAB 10E8 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 10E8 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ENDOGENOUS RETROVIRUS GROUP K MEMBER 8 ENV POLYPROTEIN
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 674-698
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: ENDOGENOUS RETROVIRUS GROUP K MEMBER 113 ENV POLYPROTEIN, ENDOGENOUS RETROVIRUS GROUP K MEMBER 13-1 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 18 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 19 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 21 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 24 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 25 ENV POLYPROTEIN, ENDOGENOUS RETROVIRUS GROUP K MEMBER 6 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 7 ENV POLYPROTEIN,ENDOGENOUS RETROVIRUS GROUP K MEMBER 9 ENV POLYPROTEIN,ENVELOPE GLYCOPROTEIN GP160
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1PO47Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS H:117 , SER H:132 , GLY H:133 , ASP H:144 , HOH H:401 , HOH H:439 , LYS L:130binding site for residue PO4 H 301
2AC2SOFTWARETHR H:116 , SER H:128 , LYS H:129binding site for residue PO4 H 302
3AC3SOFTWAREASP L:83 , LYS L:103 , THR L:105 , TYR L:141 , LYS L:167 , TYR L:173 , HOH L:421binding site for residue PO4 L 301
4AC4SOFTWAREALA H:125 , LYS H:214 , SER L:122 , SER L:123 , GLU L:124 , HOH L:411 , HOH L:414binding site for residue PO4 L 302
5AC5SOFTWARELEU L:28 , ARG L:29 , SER L:30 , HIS L:31 , ALA L:66binding site for residue PO4 L 303
6AC6SOFTWARESER H:130 , SER L:115 , VAL L:116 , LYS L:205 , HOH L:401binding site for residue PO4 L 304
7AC7SOFTWARELYS H:206 , LYS L:150 , ASP L:152 , SER L:193 , GLU L:204 , THR L:206binding site for residue PO4 L 305

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:135 -L:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro H:100F-Pro H:100G
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GHW)

(-) 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:233
                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeee........eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee..........eeeeeee...eeeee........eeeeeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ghw H    1 EVQLVESGGGLVKPGGSLRLSCSASGFDFDNAWMTWVRQPPGKGLEWVGRITGPGEGWSVDYAAPVEGRFTISRLNSINFLYLEMNNLRMEDSGLYFCARTGKYYDFWSGYPPGEEYFQDWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122       132       142       152       162       172       182       192       202       212   
                                                                              52A||                            82A||               100A|||||100J||                                                                                                                   
                                                                               52B|                             82B|                100B|||||100K|                                                                                                                   
                                                                                52C                              82C                 100C|||||100L                                                                                                                   
                                                                                                                                      100D|||||                                                                                                                      
                                                                                                                                       100E||||                                                                                                                      
                                                                                                                                        100F|||                                                                                                                      
                                                                                                                                         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.hhhhh...eeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeee.........ee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ghw L    2 YELTQETGVSVALGRTVTITCRGDSLRSHYASWYQKKPGQAPILLFYGKNNRPSGVPDRFSGSASGNRASLTISGAQAEDDAEYYCSSRDKSGSRLSVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  210
                                   |12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209 
                                   9|                                                                                  95A||                                                                                                                   
                                   11                                                                                   95B|                                                                                                                   
                                                                                                                         95C                                                                                                                   


Chain P from PDB  Type:PROTEIN  Length:21
                                                      
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                5ghw P  669 LWNWFNITNWLWYIKLFIMIV  689
                                   678       688
   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 5GHW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 46)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Pro H:100F - Pro H:100G  [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
 

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  5ghw
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4jpk 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08

(-) Related Entries Specified in the PDB File

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