Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CSL (RBP-JK) WITH COREPRESSOR KYOT2 BOUND TO DNA
 
Authors :  K. J. Collins, R. A. Kovall
Date :  05 Feb 13  (Deposition) - 06 Nov 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,G,H  (1x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Lim Domain Containing Protein, Transcription Factor Corepressor, Dna Binding, Nucleus, Transcription-Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Collins, Z. Yuan, R. A. Kovall
Structure And Function Of The Csl-Kyot2 Corepressor Complex A Negative Regulator Of Notch Signaling.
Structure V. 22 70 2014
PubMed-ID: 24290140  |  Reference-DOI: 10.1016/J.STR.2013.10.010

(-) Compounds

Molecule 1 - RECOMBINING BINDING PROTEIN SUPPRESSOR OF HAIRLESS
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CORE DOMAIN (UNP RESIDUES 53-474)
    Gene: IGKJRB1, IGKRSBP, RBP-JK, RBPJ, RBPSUH
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CSL, CBF-1, SUPRESSOR OF HAIRLESS, LAG-1, J KAPPA- RECOMBINATION SIGNAL-BINDING PROTEIN, RBP-J KAPPA
 
Molecule 2 - FOUR AND A HALF LIM DOMAINS PROTEIN 1
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Gene: FHL1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: FHL-1, KYOT, RBP-ASSOCIATED MOLECULE 14-1, RAM14-1, SKELETAL MUSCLE LIM-PROTEIN 1, SLIM, SLIM-1
 
Molecule 3 - 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
    Chains: E, G
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 4 - 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
    Chains: F, H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB    GH
Biological Unit 2 (1x):   CDEF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:98 , TYR A:100 , GLN A:242 , TRP A:243BINDING SITE FOR RESIDUE EDO A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J2X)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Cys A:94 -Pro A:95
2Gly A:132 -Asn A:133
3Thr A:378 -Pro A:379
4Asn A:389 -Gly A:390
5Gly A:390 -Gly A:391
6Cys C:94 -Pro C:95
7Thr C:378 -Pro C:379
8Asn C:389 -Gly C:390
9Gly C:390 -Gly C:391
10Asp D:196 -Asn D:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J2X)

(-) Exons   (0, 0)

(no "Exon" information available for 4J2X)

(-) Sequences/Alignments

Asymmetric 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...eeeeeeee.eee..............eeeee.hhhhhhhhhhhhhh.hhhhhheeeeeee.......eee......eee.............ee.eeeeeee....eeeeee...eeee........hhhhhhhh....eeeeeee....hhhhheeeeee..eeeee......eeeeee........eee..........eeeeee.........eeeeee...eee...........eeeeee.....eeeeee..eeeeee.ee......eee.hhhhheeeeeeeeeeeeeee.............eeeeeee.......eeeeeee.....eeeee..ee..eeeee..eeeee..hhhhh..........eeeeeeeee...eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j2x A  53 PPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKKEQMETDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYLCLSQERIIQFQATPCPKEQNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDVAMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGVIYSTSLTFTYTP 472
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472


Chain B from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ..eee.......... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4j2x B 183 SGLVKAPVWWPMKDN 197
                                   192     


Chain C from PDB  Type:PROTEIN  Length:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeeeeeee.eee..............eeeee.hhhhhhhhhhhhh..hhhhhheeeeeee.......eee......eee.............ee.eeeeeee....eeeeee...eeee........hhhhhhhh....eeeeeeeee..eeeeeeeeeee..eeeee......eeeee.........eee..........eeeeee.........eeeeeee..eee...........eeeeee.....eeeeee..eeeeee.ee......eee.hhhhheeeeeeeeeeeeeee.............eeeeeee.......eeeeeee.....eeeee..ee.eeee....eeeee..hhhhh..........eeeeeeeee...eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j2x C  53 PPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKKEQMETDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYLCLSQERIIQFQATPCPKEQNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDVAMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGVIYSTSLTFTYTPE 473
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472 


Chain D from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ..eee.......... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4j2x D 183 SGLVKAPVWWPMKDN 197
                                   192     


Chain E from PDB  Type:DNA  Length:15
                                               
                 4j2x E   1 AATCTTTCCCACAGT  15
                                    10     


Chain F from PDB  Type:DNA  Length:15
                                               
                 4j2x F   1 TTACTGTGGGAAAGA  15
                                    10     


Chain G from PDB  Type:DNA  Length:15
                                               
                 4j2x G   1 AATCTTTCCCACAGT  15
                                    10     


Chain H from PDB  Type:DNA  Length:15
                                               
                 4j2x H   1 TTACTGTGGGAAAGA  15
                                    10
   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 4J2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J2X)

(-) Gene Ontology  (99, 101)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:389 - Gly A:390   [ RasMol ]  
    Asn C:389 - Gly C:390   [ RasMol ]  
    Asp D:196 - Asn D:197   [ RasMol ]  
    Cys A:94 - Pro A:95   [ RasMol ]  
    Cys C:94 - Pro C:95   [ RasMol ]  
    Gly A:132 - Asn A:133   [ RasMol ]  
    Gly A:390 - Gly A:391   [ RasMol ]  
    Gly C:390 - Gly C:391   [ RasMol ]  
    Thr A:378 - Pro A:379   [ RasMol ]  
    Thr C:378 - Pro C:379   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4j2x
    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
  FHL1_MOUSE | P97447
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SUH_MOUSE | P31266
    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
  FHL1_MOUSE | P97447
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SUH_MOUSE | P31266
    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
        SUH_MOUSE | P31266: 3brg 3iag 5eg6

(-) Related Entries Specified in the PDB File

1ttu CRYSTAL STRUCTURE OF CSL BOUND TO DNA
2fo1 CRYSTAL STRUCTURE OF THE CSL-NOTCH-MASTERMIND TERNARY COMPLEX BOUND TO DNA
3brd CSL (LAG-1) BOUND TO DNA WITH LIN-12 RAM PEPTIDE, P212121
3brf CSL (LAG-1) BOUND TO DNA WITH LINK-12 RAM PEPTIDE, C2221
3brg CSL (RBP-JK) BOUND TO DNA
3iag CSL (RBP-JK) BOUND TO HES-1 NONCONSENSUS SITE