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 :  STRUCTURAL BASIS FOR ELICITING A CYTOTOXIC EFFECT IN HER2-OVEREXPRESSING CANCER CELLS VIA BINDING TO THE EXTRACELLULAR DOMAIN OF HER2
 
Authors :  C. Jost, J. Schilling, A. Plueckthun
Date :  28 Oct 12  (Deposition) - 16 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Transferase-De Novo Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Jost, J. Schilling, R. Tamaskovic, M. Schwill, A. Honegger, A. Plueckthun
Structural Basis For Eliciting A Cytotoxic Effect In Her2-Overexpressing Cancer Cells Via Binding To The Extracellular Domain Of Her2.
Structure V. 21 1 2013
PubMed-ID: 24095059  |  Reference-DOI: 10.1016/J.STR.2013.08.020

(-) Compounds

Molecule 1 - RECEPTOR TYROSINE-PROTEIN KINASE ERBB-2
    ChainsC
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFL
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentN-TERMINAL EXTRACELLULAR DOMAIN I, UNP RESIDUES 24-219
    GeneERBB2, HER2, MLN19, NEU, NGL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMETASTATIC LYMPH NODE GENE 19 PROTEIN, MLN 19, PROTO- ONCOGENE NEU, PROTO-ONCOGENE C-ERBB-2, TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2, P185ERBB2
 
Molecule 2 - DESIGNED ANKYRIN REPEAT PROTEIN 9_29
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainXL1-BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificSYNTHETIC
    Organism Taxid32630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4HRL)

(-) Sites  (0, 0)

(no "Site" information available for 4HRL)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1C:4 -C:31
2C:140 -C:170
3C:173 -C:182
4C:177 -C:190

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HRL)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hrl A   7 HHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNAHDFYGITPLHLAANFGHLEIVEVLLKHGADVNAFDYDNTPLHLAADAGHLEIVEVLLKYGADVNASDRDGHTPLHLAAREGHLEIVEVLLKNGADVNAQDKFGKTPFDLAIDNGNEDIAEVLQKAA 168
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166  

Chain C from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee............hhhhhhhhhh...ee...eeee.......hhhhh...ee...eeee.............ee....hhhh.eeeeee..................ee...eeeee......hhhhhhhhhhhhhhhh...eee................hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hrl C   2 QVCTGTDMKLRLPPTHLDMLRHLYQGCQVVQGNLELTYLPTDASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDSPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTCHPCSPMCSRCWGESSEDCQ 191
                                    11  |||   24        34        44        54        64        74        84        94    || 115       125       135       145       155       170      |182         
                                       14||                                                                              99|                                                  164|    177|           
                                        17|                                                                              111                                                   170     180           
                                         19                                                                                                                                                          

   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 4HRL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (73, 73)

Asymmetric/Biological Unit(hide GO term definitions)

 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 4hrl)
 
  Sites
(no "Sites" information available for 4hrl)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hrl)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4hrl
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ERBB2_HUMAN | P04626
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ERBB2_HUMAN | P04626
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ERBB2_HUMAN | P046261mfg 1mfl 1mw4 1n8z 1ovc 1qr1 1s78 2a91 2jwa 2ks1 2l4k 2n2a 3be1 3h3b 3mzw 3n85 3pp0 3rcd 3wlw 3wsq 4gfu 4hrm 4hrn 4nnd 5k33 5kwg

(-) Related Entries Specified in the PDB File

1n8z 1s78 3h3b 3mzw 4hrm 4hrn