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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 4E10 FAB IN COMPLEX WITH ITS PEPTIDE EPITOPE ON HIV-1 GP41; CRYSTALS CRYOPROTECTED WITH PHOSPHATIDYLCHOLINE (03:0 PC)
 
Authors :  A. Irimia, R. L. Stanfield, I. A. Wilson
Date :  18 Dec 14  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  4E10 Fab Anti Hiv-1 Gp41, Phosphatidylcholine, Membrane Lipid, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Irimia, A. Sarkar, R. L. Stanfield, I. A. Wilson
Crystallographic Identification Of Lipid As An Integral Component Of The Epitope Of Hiv Broadly Neutralizing Antibody 4E10.
Immunity V. 44 21 2016
PubMed-ID: 26777395  |  Reference-DOI: 10.1016/J.IMMUNI.2015.12.001

(-) Compounds

Molecule 1 - 4E10 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Plasmid: PDR12
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 4E10 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Plasmid: PDR12
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MODIFIED FRAGMENT OF HIV-1 GLYCOPROTEIN (GP41) INCLUDING THE MPER REGION 671-683
    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  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
143Y4Ligand/Ion[(2R)-3-[OXIDANYL-[2-(TRIMETHYL-$L^{4}-AZANYL)ETHOXY]PHOSPHORYL]OXY-2-PROPANOYLOXY-PROPYL]PROPANOATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE43Y H:301 , GLY L:9 , THR L:10 , GLN L:100 , GLY L:101 , HOH L:414 , HOH L:432 , HOH L:539binding site for residue 43Y L 301
2AC2SOFTWAREARG L:108 , THR L:109 , LYS L:169 , ASP L:170 , SER L:171binding site for residue 43Y L 302
3AC3SOFTWARETHR H:116 , LYS H:117 , GLY H:118 , PRO H:214 , SER H:215 , ASN H:216 , THR H:217 , HOH H:439 , HOH H:450 , 43Y L:301 , HOH L:418binding site for residue 43Y H 301
4AC4SOFTWARESER H:7 , THR H:19 , THR H:70 , TYR H:79 , GLU H:81 , HOH H:429 , GLN L:27 , SER L:27A , SER L:67 , GLY L:68 , THR L:69binding site for residue 43Y H 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
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XCF)

(-) 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........eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xcf H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96 |||||100J       110       120       137       147      |162      |173      |184       194     ||207       217    ||   
                                                                              52A                            82A||              98||||||||                         128|               154|||    169|      180|               200||              222|   
                                                                                                              82B|             100C|||||||                          136                156||     171       182                203|               225   
                                                                                                               82C              100D||||||                                              157|                                   205                     
                                                                                                                                 100E|||||                                               162                                                           
                                                                                                                                  100F||||                                                                                                             
                                                                                                                                   100G|||                                                                                                             
                                                                                                                                    100H||                                                                                                             
                                                                                                                                     100I|                                                                                                             
                                                                                                                                      100J                                                                                                             


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               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..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xcf L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    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:16
                                                 
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                4xcf P  671 NWWDITNWLWYIKKKK  686
                                   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 4XCF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4xcf
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  ENV_HV1MN | P05877
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P05877: 1acy 1ai1 1f58 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xmk

(-) Related Entries Specified in the PDB File

4xaw 4xbe 4xbg 4xbp 4xc1 4xc3 4xcc 4xce 4xcn 4xcy