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(-) Description

Title :  CRYSTAL STRUCTURE OF NON-NEUTRALIZING VERSION OF 4E10 (WDWD) WITH EPITOPE BOUND
 
Authors :  J. M. M. Caaveiro, E. Rujas, J. L. Nieva, K. Tsumoto
Date :  13 Jul 15  (Deposition) - 23 Sep 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Broadly Neutralizing Antibody, Recombinant Fab, Env-Peptide, Hiv-1, Epitope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rujas, N. Gulzar, K. Morante, K. Tsumoto, J. K. Scott, J. L. Nieva, J. M. M. Caaveiro
Structural And Thermodynamic Basis Of Epitope Binding By Neutralizing And Nonneutralizing Forms Of The Anti-Hiv-1 Antibody 4E10
J. Virol. V. 89 11975 2015
PubMed-ID: 26378169  |  Reference-DOI: 10.1128/JVI.01793-15

(-) 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
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 4E10 LIGHT 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 - PEPTIDE FROM THE MPER REGION OF THE ENV PROTEIN OF HIV-1
    Chains: P
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:174 , PRO H:175 , SER H:186 , LEU H:187 , SER H:188 , HOH H:402 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178binding site for residue GOL H 301
2AC2SOFTWARESER H:82B , ARG H:83 , GLY L:157binding site for residue CL H 302
3AC3SOFTWARELYS H:213 , GLN L:11 , ARG L:18 , ALA L:19 , THR L:20binding site for residue GOL L 301
4AC4SOFTWAREARG L:45 , ALA L:59 , HOH L:574binding site for residue CL L 302
5AC5SOFTWAREGLY L:9 , GLY L:101binding site for residue ACT L 303

(-) 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, 5)

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 5CIL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CIL)

(-) 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.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cil H    2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGDGDLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  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
                5cil 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:13
                                              
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                5cil P  671 NWFDITNWLWYIK  683
                                   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 5CIL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  5cil
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  ENV_HV1H2 | P04578
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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 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08

(-) Related Entries Specified in the PDB File

5cin 5cip