Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN OF THE MUTANT EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII, AT LIQUID NITROGEN TEMPERATURE
 
Authors :  R. C. Landry, A. C. Klimowicz, S. J. Lavictoire, S. Borisova, D. T. Kottachchi, I. A. Lorimer, S. V. Evans
Date :  14 Mar 01  (Deposition) - 14 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Antibody-Peptide Complex, Immunoglobulin Fold, Peptide Antigen, Type Ii' Beta Turn. , Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Landry, A. C. Klimowicz, S. J. Lavictoire, S. Borisova, D. T. Kottachchi, I. A. Lorimer, S. V. Evans
Antibody Recognition Of A Conformational Epitope In A Peptide Antigen: Fv-Peptide Complex Of An Antibody Fragment Specific For The Mutant Egf Receptor, Egfrviii.
J. Mol. Biol. V. 308 883 2001
PubMed-ID: 11352579  |  Reference-DOI: 10.1006/JMBI.2001.4628
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TG1
    Expression System Taxid: 562
    Expression System Vector Type: M13KO7 HELPER PHAGE
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DSFV MR1 VARIABLE DOMAIN LIGHT CHAIN
 
Molecule 2 - EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TG1
    Expression System Taxid: 562
    Expression System Vector Type: M13KO7 HELPER PHAGE
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DSFV MR1 VARIABLE DOMAIN HEAVY CHAIN
 
Molecule 3 - EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN
    Chains: C
    Engineered: YES
    Fragment: N-TERMINAL FRAGMENT
    Other Details: THE PEPTIDE SEQUENCE IS FROM THE N-TERMINAL OF THE MUTANT EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII
    Synonym: EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1I8K)

(-) Sites  (0, 0)

(no "Site" information available for 1I8K)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:100 -B:344
3B:322 -B:396

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Val A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I8K)

(-) Exons   (0, 0)

(no "Exon" information available for 1I8K)

(-) 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 A from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d1i8ka_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                      SCOP domains
               CATH domains 1i8kA00 A:1-106 Immunoglobulins                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1i8k A   1 DIELTQSPASLSVATGEKVTIRCMTSTDIDDDMNWYQQKPGEPPKFLISEGNTLRPGVPSRFSSSGTGTDFVFTIENTLSEDVGDYYCLQSFNVPLTFGCGTKLEI 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with HVM58_MOUSE | P18529 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:119
                                                                                                                           117                     
                                    29        39        49        59        69        79        89        99       109       | -         -         
          HVM58_MOUSE    20 EVHLVESGGGLVKPGGSLKLSCVVSGFTFNKYAMSWVRQTPEKRLEWVATISSGGLYTYYPDSVKGRFTISRDNAGNTLYLQMSSLRSEDTAMYYCAR---------------------   -
               SCOP domains d1i8kb_ B: Immunoglobulin heavy chain variable domain, VH                                                               SCOP domains
               CATH domains 1i8kB00 B:301-419 Immunoglobulins                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeee..eeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8k B 301 QVKLQQSGGGLVKPGASLKLSCVTSGFTFRKFGMSWVRQTSDKCLEWVASISTGGYNTYYSDNVKGRFTISRENAKNTLYLQMSSLKSEDTALYYCTRGYSSTSYAMDYWGQGTTVTVS 419
                                   310       320       330       340       350       360       370       380       390       400       410         


Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 1i8k C 501 KKGNYVVTDH 510
                                   510
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I8K)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (HVM58_MOUSE | P18529)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1i8k)
 
  Sites
(no "Sites" information available for 1i8k)
 
  Cis Peptide Bonds
    Ser A:7 - Pro A:8   [ RasMol ]  
    Val A:94 - Pro A:95   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1i8k
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HVM58_MOUSE | P18529
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  KV3A8_MOUSE | P01660
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  HVM58_MOUSE | P18529
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  KV3A8_MOUSE | P01660
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HVM58_MOUSE | P18529: 1bfv 1i8i
        KV3A8_MOUSE | P01660: 1ejo 1i8i 1j05 1moe 1qfw 2r29 2r69 2r6p 2vl5 3bsz 4nja

(-) Related Entries Specified in the PDB File

1i8i SAME PROTEIN, AT ROOM TEMPERATURE