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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT 4E10 EXPRESSED IN ESCHERICHIA COLI WITH EPITOPE BOUND
 
Authors :  E. Rujas, K. Morante, K. Tsumoto, J. L. Nieva, J. M. M. Caaveiro
Date :  16 Nov 14  (Deposition) - 25 Mar 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Broad Neutralizing Antobody, Recombinant Fab, Epitope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Apellaniz, E. Rujas, S. Serrano, K. Morante, K. Tsumoto, J. M. Caaveiro, M. A. Jimenez, J. L. Nieva
The Atomic Structure Of The Hiv-1 Gp41 Transmembrane Domain And Its Connection To The Immunogenic Membrane-Proximal External Region.
J. Biol. Chem. V. 290 12999 2015
PubMed-ID: 25787074  |  Reference-DOI: 10.1074/JBC.M115.644351

(-) Compounds

Molecule 1 - FAB 4E10 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-DUET1
    Expression System Taxid: 469008
    Expression System Variant: T7 SHUFFLE
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 4E10LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-DUET1
    Expression System Taxid: 469008
    Expression System Variant: T7 SHUFFLE
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP160
    Chains: P
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Fragment: UNP RESIDUES 662-674
    Gene: ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B
    Organism Taxid: 11705
    Strain: ISOLATE WMJ22
    Synonym: ENV POLYPROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS H:213 , GLN L:11 , ARG L:18 , ALA L:19 , THR L:20binding site for residue GOL L 301
2AC2SOFTWAREPHE H:174 , PRO H:175 , SER H:186 , LEU H:187 , SER H:188 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178 , HOH L:485binding site for residue GOL L 302

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:148 -Pro H:149
2Glu H:150 -Pro H:151
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 4WY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WY7)

(-) Exons   (0, 0)

(no "Exon" information available for 4WY7)

(-) 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:220
                                                                                                                                                                                                                                                             
               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........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh.eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wy7 H    2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |||100G|||    107       117       127|      145       156||     171       182       192       205       215      |227
                                                                             52A                            82A||               100A|||||100J                        127|               154|||    169|      180|               200||              222|  
                                                                                                             82B|                100B|||||||                          136                156||     171       182                203|               225  
                                                                                                              82C                 100C||||||                                              157|                                   205                    
                                                                                                                                   100D|||||                                               162                                                          
                                                                                                                                    100E||||                                                                                                            
                                                                                                                                     100F|||                                                                                                            
                                                                                                                                      100G||                                                                                                            
                                                                                                                                       100H|                                                                                                            
                                                                                                                                        100I                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wy7 L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209  
                                                     27A                                                                                                                                                                                        


Chain P from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                4wy7 P  671 NWFDITNWLWYIKKK  685
                                   680
   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 4WY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WY7)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4wy7
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1W2 | P05880: 2fx7 2fx8 2fx9

(-) Related Entries Specified in the PDB File

2fx7 PROTEIN OBTAINED FROM IGG