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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE RICE TOPLESS RELATED PROTEIN 2 (TPR2) N-TERMINAL TOPLESS DOMAIN (1-209) IN COMPLEX WITH RICE D53 REPRESSOR EAR PEPTIDE MOTIF
 
Authors :  J. Ke, H. Ma, X. Gu, J. S. Brunzelle, H. E. Xu, K. Melcher
Date :  10 Apr 16  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Transcription Repression, Transcriptional Corepressor Topless, Alpha- Helical Structure, Tetramer, Transcriptional Repressor D53, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ma, J. Duan, J. Ke, Y. He, X. Gu, T. H. Xu, H. Yu, Y. Wang, J. S. Brunzelle Y. Jiang, S. B. Rothbart, H. E. Xu, J. Li, K. Melcher
A D53 Repression Motif Induces Oligomerization Of Topless Corepressors And Promotes Assembly Of A Corepressor-Nucleosome Complex.
Sci Adv V. 3 01217 2017
PubMed-ID: 28630893  |  Reference-DOI: 10.1126/SCIADV.1601217
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TPR1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL TOPLESS DOMAIN (UNP RESIDUES 1-209)
    Gene: TPR1, ASPR2, TPR2, OS01G0254100, LOC_OS01G15020, OSJ_01134, OSNPB_010254100, P0705D01.10-1
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530
    Synonym: ABERRANT SPIKELET AND PANICLE1-RELATED 2,PROTEIN ASP1- RELATED 2,OSASPR2,TOPLESS-RELATED PROTEIN 1,TOPLESS-RELATED PROTEIN 2,OSTPR2
 
Molecule 2 - RICE D53 PEPTIDE 794-808
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530
    Other Details: DNLIYLDLNLQ

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:183 , CYS A:186 , HIS A:202 , CYS A:204binding site for residue ZN A 401
2AC2SOFTWAREHIS B:183 , CYS B:186 , HIS B:202 , CYS B:204binding site for residue ZN B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J9K)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Pro A:189 -Arg A:190
2Gly B:134 -Asp B:135
3Lys B:187 -Asn B:188
4Pro B:189 -Arg B:190
5Leu D:801 -Asn D:802

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J9K)

(-) Exons   (0, 0)

(no "Exon" information available for 5J9K)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j9k A   1 MSSLSRELVFLILQFLDEEKFKETVHKLEQESGFFFNMKYFEEKVHAGEWDEVEKYLSGFTKVDDNRYSMKIFFEIRKQKYLEALDRHDRAKAVDILVKDLKVFSTFNEELYKEITQLLTLENFRENEQLSKYGDTKSARSIMLIELKKLIEANPLFREKLVFPTLKASRLRTLINQSLNWQHQLCKNPRPNPDIKTLFTDHTCT 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j9k B   1 MSSLSRELVFLILQFLDEEKFKETVHKLEQESGFFFNMKYFEEKVHAGEWDEVEKYLSGFTKVDDNRYSMKIFFEIRKQKYLEALDRHDRAKAVDILVKDLKVFSTFNEELYKEITQLLTLENFRENEQLSKYGDTKSARSIMLIELKKLIEANPLFREKLVFPTLKASRLRTLINQSLNWQHQLCKNPRPDIKTLFTDHTCT 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190|      202   
                                                                                                                                                                                                                       190|            
                                                                                                                                                                                                                        193            


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               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
                 5j9k C 795 NLIYLDLNL 803


Chain D from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5j9k D 795 NLIYLDLN 802
   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 5J9K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J9K)

(-) Gene Ontology  (1, 1)

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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly B:134 - Asp B:135   [ RasMol ]  
    Leu D:801 - Asn D:802   [ RasMol ]  
    Lys B:187 - Asn B:188   [ RasMol ]  
    Pro A:189 - Arg A:190   [ RasMol ]  
    Pro B:189 - Arg B:190   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5j9k
    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
  TPR1_ORYSJ | Q5NBT9
    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
  TPR1_ORYSJ | Q5NBT9
    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
        TPR1_ORYSJ | Q5NBT9: 4zhe 5c6q 5c6v 5c7e 5c7f 5ja5 5jgc 5jhp

(-) Related Entries Specified in the PDB File

5ja5 5jgc 5jhp