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 :  CRYSTAL STRUCTURE OF CTCF(ZNF 4-10) WITH 28-MER DNA
 
Authors :  J. R. Horton, X. Cheng
Date :  30 Jan 17  (Deposition) - 24 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Transcription Factor Zinc Finger Protein-Dna Binding Insulator/Chromatin Architecture, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, D. Wang, J. R. Horton, X. Zhang, V. G. Corces, X. Cheng
Structural Basis For The Versatile And Methylation-Dependen Binding Of Ctcf To Dna.
Mol. Cell V. 66 711 2017
PubMed-ID: 28529057  |  Reference-DOI: 10.1016/J.MOLCEL.2017.05.004

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REPRESSOR CTCF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTCF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 11-ZINC FINGER PROTEIN,CCCTC-BINDING FACTOR,CTCFL PARALOG
 
Molecule 2 - DNA (26-MER)
    Chains: C, E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: D, F
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3ZN12Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:353 , CYS A:356 , HIS A:369 , HIS A:373binding site for residue ZN A 601
02AC2SOFTWARECYS A:381 , CYS A:384 , HIS A:397 , HIS A:401binding site for residue ZN A 602
03AC3SOFTWARECYS A:409 , CYS A:412 , HIS A:425 , HIS A:430binding site for residue ZN A 603
04AC4SOFTWARECYS A:439 , CYS A:442 , HIS A:455 , HIS A:460binding site for residue ZN A 604
05AC5SOFTWARECYS A:469 , CYS A:472 , HIS A:485 , HIS A:489binding site for residue ZN A 605
06AC6SOFTWARECYS A:500 , HIS A:513 , HIS A:517binding site for residue ZN A 606
07AC7SOFTWAREDT C:11 , DG D:19binding site for residue EDO D 101
08AC8SOFTWAREDG C:13 , DG D:15binding site for residue EDO D 102
09AC9SOFTWARECYS B:353 , CYS B:356 , HIS B:369 , HIS B:373binding site for residue ZN B 601
10AD1SOFTWARECYS B:381 , CYS B:384 , HIS B:397 , HIS B:401binding site for residue ZN B 602
11AD2SOFTWARECYS B:409 , CYS B:412 , HIS B:425 , HIS B:430binding site for residue ZN B 603
12AD3SOFTWARECYS B:439 , CYS B:442 , HIS B:455 , HIS B:460binding site for residue ZN B 604
13AD4SOFTWARECYS B:469 , CYS B:472 , HIS B:485 , HIS B:489binding site for residue ZN B 605
14AD5SOFTWARECYS B:412 , HIS B:425 , LYS B:429binding site for residue EDO B 606
15AD6SOFTWAREHIS B:441 , HIS B:460 , GLU B:478binding site for residue GOL B 607
16AD7SOFTWAREDT E:11 , DG F:19binding site for residue EDO E 101
17AD8SOFTWAREDG F:15binding site for residue EDO F 101
18AD9SOFTWAREDG F:14binding site for residue EDO F 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UND)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UND)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UND)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UND)

(-) Exons   (0, 0)

(no "Exon" information available for 5UND)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhh................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5und A 348 EKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYACRQERHMIMHKRTHT 518
                                   357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517 


Chain B from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5und B 348 EKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNE 492
                                   357       367       377       387       397       407       417       427       437       447       457       467       477       487     


Chain C from PDB  Type:DNA  Length:26
                                                          
                 5und C   1 CGCCCCCTGCTGGCCTCTGTGGGCAC  26
                                    10        20      


Chain D from PDB  Type:DNA  Length:26
                                                          
                 5und D   3 GTGCCCACAGAGGCCAGCAGGGGGCG  28
                                    12        22      


Chain E from PDB  Type:DNA  Length:26
                                                          
                 5und E   1 CGCCCCCTGCTGGCCTCTGTGGGCAC  26
                                    10        20      


Chain F from PDB  Type:DNA  Length:25
                                                         
                 5und F   4 TGCCCACAGAGGCCAGCAGGGGGCG  28
                                    13        23
   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 5UND)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UND)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UND)

(-) Gene Ontology  (39, 39)

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 ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5und)
 
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
  5und
    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
  CTCF_HUMAN | P49711
    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
  CTCF_HUMAN | P49711
    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
        CTCF_HUMAN | P49711: 1x6h 2ct1 5k5h 5k5i 5k5j 5k5l 5kkq 5t00 5t0u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5UND)