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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING ANTIBODY 4E10 FAB FRAGMENT IN COMPLEX WITH A HYDROCARBON-STAPLED PEPTIDE CONTAINING THE 4E10 EPITOPE ON GP41.
 
Authors :  A. Irimia, I. A. Wilson
Date :  04 Nov 13  (Deposition) - 03 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunoglobulin Fold, Beta-Sandwich, 4E10 Fab, Antibody-Epitope Complex, Gp41 Hiv-1, Hydrocarbon Staple, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. H. Bird, A. Irimia, G. Ofek, P. D. Kwong, I. A. Wilson, L. D. Walensky
Stapled Hiv-1 Peptides Recapitulate Antigenic Structures An Engage Broadly Neutralizing Antibodies.
Nat. Struct. Mol. Biol. V. 21 1058 2014
PubMed-ID: 25420104  |  Reference-DOI: 10.1038/NSMB.2922

(-) Compounds

Molecule 1 - FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Strain: CHO CELLS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Strain: CHO CELLS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41)
    Chains: P
    Engineered: YES
    Other Details: SYNTHETIC;
THIS SEQUENCE INCLUDES A MODIFIED FRAGMENT OF THE HIV ENVELOPE PROTEIN GP41
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2DIV1Mod. Amino AcidD-ISOVALINE
3MK81Mod. Amino Acid2-METHYL-L-NORLEUCINE
4PO41Ligand/IonPHOSPHATE ION
5TFA2Ligand/IonTRIFLUOROACETIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN P:674 , ILE P:675 , THR P:676 , ASN P:677 , LEU P:679 , MK8 P:681 , ILE P:682BINDING SITE FOR RESIDUE DIV P 678
2AC2SOFTWARETHR H:133 , SER H:134 , VAL L:115 , PHE L:116 , LYS L:207 , HOH L:412BINDING SITE FOR RESIDUE TFA L 301
3AC3SOFTWARESER H:28 , PHE H:29 , SER H:30BINDING SITE FOR RESIDUE PO4 H 301
4AC4SOFTWAREGLN H:39 , ALA H:40 , PRO H:41 , GLY H:42BINDING SITE FOR RESIDUE TFA 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  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Ala L:184 -Asp L:185
4Glu L:213 -Cys L:214
5Gly H:100A-Trp H:100B
6Phe H:148 -Pro H:149
7Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NHC)

(-) 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:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.......eeeee.....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeehhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4nhc H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126   ||  138       148     ||163     ||174     ||185       195    |||208       218   ||   
                                                                              52A                            82A||               100A|||||100J                           130|                  154|||    169|      180|               200||              222|   
                                                                                                              82B|                100B|||||||                             133                   156||     171       182                203|               225   
                                                                                                               82C                 100C||||||                                                    157|                                   205                     
                                                                                                                                    100D|||||                                                     162                                                           
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..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
                4nhc L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    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:17
                                                  
               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
                4nhc P  670 xNWFNITNxLWlIKKKK  686
                            |      679 |     
                          670-ACE 678-DIV    
                                     681-MK8
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4NHC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Cis Peptide Bonds
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    Gly H:100A - Trp H:100B  [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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4ngh CRYSTAL STRUCTURE OF THE HIV-1 NEUTRALIZING ANTIBODY 4E10 FAB FRAGMENT IN COMPLEX WITH A HYDROCARBON-STAPLED PEPTIDE CONTAINING THE 4E10 EPITOPE ON GP41 AND A TETHERED PHOSPHATE MOIETY.