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

(-) Description

Title :  STRUCTURE OF U2AF65 D231V VARIANT WITH BRU5 DNA
 
Authors :  A. A. Agrawal, J. L. Jenkins, C. L. Kielkopf
Date :  24 Jun 14  (Deposition) - 26 Nov 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B,E,P
Keywords :  Pre-Mrna Splicing Factor, Rna Recognition Motif, Rna Binding Protein- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Agrawal, K. J. Mclaughlin, J. L. Jenkins, C. L. Kielkopf
Structure-Guided U2Af65 Variant Improves Recognition And Splicing Of A Defective Pre-Mrna.
Proc. Natl. Acad. Sci. Usa V. 111 17420 2014
PubMed-ID: 25422459  |  Reference-DOI: 10.1073/PNAS.1412743111

(-) Compounds

Molecule 1 - SPLICING FACTOR U2AF 65 KDA SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P2
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: U2AF2, U2AF65
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U2 AUXILIARY FACTOR 65 KDA SUBUNIT,HU2AF65,U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT
 
Molecule 2 - DNA (5'-D(*UP*UP*UP*UP*(BRU)P*UP*U)-3')
    Chains: P, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 29)

Asymmetric/Biological Unit (6, 29)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CPQ1Ligand/IonN,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
3DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DU12Mod. Residue
5GOL4Ligand/IonGLYCEROL
6SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:269 , ASN A:271binding site for residue DIO A 401
2AC2SOFTWAREPRO A:144 , TYR A:232 , GLN A:233 , LEU A:325binding site for residue DIO A 402
3AC3SOFTWARELYS A:225 , ARG A:227 , HOH A:577 , HOH A:589binding site for residue SO4 A 403
4AC4SOFTWAREARG A:150 , GLU A:201 , SER A:281 , HOH A:515 , HOH A:537 , DU P:7binding site for residue SO4 A 404
5AC5SOFTWAREARG A:228binding site for residue SO4 A 405
6AC6SOFTWAREILE A:191 , ASN A:192 , GLN A:193 , ASP A:194 , LYS B:329binding site for residue GOL A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TU7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:143 -Pro A:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TU7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TU7)

(-) Exons   (0, 0)

(no "Exon" information available for 4TU7)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhh.........eeeeeee....eeeeee.hhhhhhhhhhhh..ee..ee.eee.............eeee......hhhhhhhhhhh...eeeeeeeee....eeeeeeeeee...hhhhhhhhhhh..ee..ee.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tu7 A 143 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHVYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 336
                                   152       162       172       182       192       202       212       222       232    || 262       272       282       292       302       312       322       332    
                                                                                                                        237|                                                                              
                                                                                                                         258                                                                              


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeee......hhhhhhhhhhhhhhhh.........eeeeeee....eeeeee.hhhhhhhhhhhh..ee..ee.eee.............eeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tu7 B 143 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHVYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 336
                                   152       162       172       182       192       202       212       222       232    || 262       272       282       292       302       312       322       332    
                                                                                                                        237|                                                                              
                                                                                                                         258                                                                              


Chain E from PDB  Type:DNA/OTHER  Length:7
                                       
                 4tu7 E   1 xxxxuxx   7
                            |||||||
                            1-DU|||
                             2-DU||
                              3-DU|
                               4-DU
                                5-BRU
                                 6-DU
                                  7-DU


Chain P from PDB  Type:DNA/OTHER  Length:7
                                       
                 4tu7 P   1 xxxxuxx   7
                            |||||||
                            |||||||
                            1-DU|||
                             2-DU||
                              3-DU|
                               4-DU
                                5-BRU
                                 6-DU
                                  7-DU
   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 4TU7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TU7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TU7)

(-) Gene Ontology  (26, 26)

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
    BRU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CPQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DIO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:143 - Pro A:144   [ 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 | Asym./Biol. Unit - 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
  4tu7
    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
  U2AF2_HUMAN | P26368
    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
  U2AF2_HUMAN | P26368
    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
        U2AF2_HUMAN | P26368: 1jmt 1o0p 1opi 1u2f 2g4b 2hzc 2m0g 2u2f 2yh0 2yh1 3vaf 3vag 3vah 3vai 3vaj 3vak 3val 3vam 4fxw 4tu8 4tu9 5ev1 5ev2 5ev3 5ev4

(-) Related Entries Specified in the PDB File

4tu8 4tu9