Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  PUF3 RNA BINDING DOMAIN BOUND TO COX17 RNA 3' UTR RECOGNITION SEQUENCE SITE A
 
Authors :  D. Zhu, C. R. Stumpf, J. M. Krahn, M. Wickens, T. M. T Hall
Date :  05 Oct 09  (Deposition) - 27 Oct 09  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Puf3, Pumilio, Rna Binding, Mitochondrial Mrna, Membrane, Mitochondrion, Mitochondrion Outer Membrane, Phosphoprotein, Rna- Binding, Rna Binding Protein - Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Zhu, C. R. Stumpf, J. M. Krahn, M. Wickens, T. M. Hall
A 5' Cytosine Binding Pocket In Puf3P Specifies Regulation Of Mitochondrial Mrnas.
Proc. Natl. Acad. Sci. Usa V. 106 20192 2009
PubMed-ID: 19918084  |  Reference-DOI: 10.1073/PNAS.0812079106

(-) Compounds

Molecule 1 - MRNA-BINDING PROTEIN PUF3
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PTYB3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 511-879
    Gene: L1325, PUF3, YLL013C
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: GENOMIC DNA
    Synonym: PUMILIO HOMOLOGY DOMAIN FAMILY MEMBER 3
 
Molecule 2 - RNA (5'-R(P*CP*UP*UP*GP*UP*AP*UP*AP*UP*A)-3')
    Chains: B, D, F
    Engineered: YES
    Other Details: COX17 SITE A
    Other Details - Source: RNA OLIGONUCLEOTIDES WERE OBTAINED FROM DHARMACON, INC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3K4E)

(-) Sites  (0, 0)

(no "Site" information available for 3K4E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K4E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K4E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K4E)

(-) PROSITE Motifs  (1, 24)

Asymmetric Unit (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF3_YEAST538-573
 
 
574-609
 
 
610-646
 
 
682-717
 
 
647-681
 
 
718-759
 
 
760-795
 
 
807-844
 
 		  24A:538-573
C:538-573
E:538-573
A:574-609
C:574-609
E:574-609
A:610-646
C:610-646
E:610-646
A:682-717
C:682-717
E:682-717
A:647-681
C:647-681
E:647-681
A:718-759
C:718-759
E:718-759
A:760-795
C:760-795
E:760-795
A:807-844
C:807-844
E:807-844
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF3_YEAST538-573
 
 
574-609
 
 
610-646
 
 
682-717
 
 
647-681
 
 
718-759
 
 
760-795
 
 
807-844
 
 		  8A:538-573
-
-
A:574-609
-
-
A:610-646
-
-
A:682-717
-
-
A:647-681
-
-
A:718-759
-
-
A:760-795
-
-
A:807-844
-
-
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF3_YEAST538-573
 
 
574-609
 
 
610-646
 
 
682-717
 
 
647-681
 
 
718-759
 
 
760-795
 
 
807-844
 
 		  8-
C:538-573
-
-
C:574-609
-
-
C:610-646
-
-
C:682-717
-
-
C:647-681
-
-
C:718-759
-
-
C:760-795
-
-
C:807-844
-
Biological Unit 3 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF3_YEAST538-573
 
 
574-609
 
 
610-646
 
 
682-717
 
 
647-681
 
 
718-759
 
 
760-795
 
 
807-844
 
 		  8-
-
E:538-573
-
-
E:574-609
-
-
E:610-646
-
-
E:682-717
-
-
E:647-681
-
-
E:718-759
-
-
E:760-795
-
-
E:807-844

(-) Exons   (0, 0)

(no "Exon" information available for 3K4E)

(-) 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:343
 aligned with PUF3_YEAST | Q07807 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:361
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874 
           PUF3_YEAST   515 SPLLEQLRNSSSDKNSNSNMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKLAALVE 875
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k4eA00 A:        515-875 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.--------.........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------PUM  PDB: A:538-573 UniProt: 538-573PUM  PDB: A:574-609 UniProt: 574-609PUM  PDB: A:610-646 UniProt: 610-646 PUM  PDB: A:647-681                PUM  PDB: A:682-717 UniProt: 682-717PUM  PDB: A:718-759 UniProt: 718-759      PUM  PDB: A:760-795 UniProt: 760-795-----------PUM  PDB: A:807-844 UniProt: 807-844  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4e A 515 SPLLEQLRNS--------NMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKL----------LASVEKLAALVE 875
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844        |-       864       874 
                                   524      533                                                                                                                                                                                                                                                                                                                             853        864           


Chain B from PDB  Type:RNA  Length:10
                                          
                 3k4e B   1 CUUGUAUAUA  10
                                    10


Chain C from PDB  Type:PROTEIN  Length:343
 aligned with PUF3_YEAST | Q07807 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:361
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874 
           PUF3_YEAST   515 SPLLEQLRNSSSDKNSNSNMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKLAALVE 875
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k4eC00 C:        515-875 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.--------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------PUM  PDB: C:538-573 UniProt: 538-573PUM  PDB: C:574-609 UniProt: 574-609PUM  PDB: C:610-646 UniProt: 610-646 PUM  PDB: C:647-681                PUM  PDB: C:682-717 UniProt: 682-717PUM  PDB: C:718-759 UniProt: 718-759      PUM  PDB: C:760-795 UniProt: 760-795-----------PUM  PDB: C:807-844 UniProt: 807-844  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4e C 515 SPLLEQLRNS--------NMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKL----------LASVEKLAALVE 875
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844        |-       864       874 
                                   524      533                                                                                                                                                                                                                                                                                                                             853        864           


Chain D from PDB  Type:RNA  Length:10
                                          
                 3k4e D   1 CUUGUAUAUA  10
                                    10


Chain E from PDB  Type:PROTEIN  Length:343
 aligned with PUF3_YEAST | Q07807 from UniProtKB/Swiss-Prot  Length:879

    Alignment length:361
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874 
           PUF3_YEAST   515 SPLLEQLRNSSSDKNSNSNMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKLAALVE 875
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k4eE00 E:        515-875 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE01 E:760-794              --------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE02 E:760-794              --------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE03 E:760-794              --------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE04 E:760-794              --------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE05 E:760-794              --------------------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE06 E:760-794              --------------------------------------------------------------------------------- Pfam domains (6)
           Pfam domains (7) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE07 E:760-794              --------------------------------------------------------------------------------- Pfam domains (7)
           Pfam domains (8) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE08 E:760-794              --------------------------------------------------------------------------------- Pfam domains (8)
           Pfam domains (9) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE09 E:760-794              --------------------------------------------------------------------------------- Pfam domains (9)
          Pfam domains (10) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE10 E:760-794              --------------------------------------------------------------------------------- Pfam domains (10)
          Pfam domains (11) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE11 E:760-794              --------------------------------------------------------------------------------- Pfam domains (11)
          Pfam domains (12) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE12 E:760-794              --------------------------------------------------------------------------------- Pfam domains (12)
          Pfam domains (13) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE13 E:760-794              --------------------------------------------------------------------------------- Pfam domains (13)
          Pfam domains (14) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE14 E:760-794              --------------------------------------------------------------------------------- Pfam domains (14)
          Pfam domains (15) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE15 E:760-794              --------------------------------------------------------------------------------- Pfam domains (15)
          Pfam domains (16) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE16 E:760-794              --------------------------------------------------------------------------------- Pfam domains (16)
          Pfam domains (17) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE17 E:760-794              --------------------------------------------------------------------------------- Pfam domains (17)
          Pfam domains (18) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3k4eE18 E:760-794              --------------------------------------------------------------------------------- Pfam domains (18)
         Sec.struct. author hhhhhhhhh.--------.........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------PUM  PDB: E:538-573 UniProt: 538-573PUM  PDB: E:574-609 UniProt: 574-609PUM  PDB: E:610-646 UniProt: 610-646 PUM  PDB: E:647-681                PUM  PDB: E:682-717 UniProt: 682-717PUM  PDB: E:718-759 UniProt: 718-759      PUM  PDB: E:760-795 UniProt: 760-795-----------PUM  PDB: E:807-844 UniProt: 807-844  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4e E 515 SPLLEQLRNS--------NMSLKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVSEGEGKKLIVIAIRAYLDKL----------LASVEKLAALVE 875
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844        |-       864       874 
                                   524      533                                                                                                                                                                                                                                                                                                                             853        864           


Chain F from PDB  Type:RNA  Length:10
                                          
                 3k4e F   1 CUUGUAUAUA  10
                                    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 3K4E)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 18)

Asymmetric Unit
(-)
Clan: TPR (230)
(-)
Family: PUF (24)
(-)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (2)
1aPUF-3k4eE01E:760-794
1bPUF-3k4eE02E:760-794
1cPUF-3k4eE03E:760-794
1dPUF-3k4eE04E:760-794
1ePUF-3k4eE05E:760-794
1fPUF-3k4eE06E:760-794
1gPUF-3k4eE07E:760-794
1hPUF-3k4eE08E:760-794
1iPUF-3k4eE09E:760-794
1jPUF-3k4eE10E:760-794
1kPUF-3k4eE11E:760-794
1lPUF-3k4eE12E:760-794
1mPUF-3k4eE13E:760-794
1nPUF-3k4eE14E:760-794
1oPUF-3k4eE15E:760-794
1pPUF-3k4eE16E:760-794
1qPUF-3k4eE17E:760-794
1rPUF-3k4eE18E:760-794

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E   (PUF3_YEAST | Q07807)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
biological process
    GO:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:0008298    intracellular mRNA localization    Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
    GO:0051646    mitochondrion localization    Any process in which a mitochondrion or mitochondria are transported to, and/or maintained in, a specific location within the cell.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0000956    nuclear-transcribed mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0032473    cytoplasmic side of mitochondrial outer membrane    The external (cytoplasmic) face of the mitochondrial outer membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 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
(no "Ligands, Modified Residues, Ions" information available for 3k4e)
 
  Sites
(no "Sites" information available for 3k4e)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3k4e)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3k4e
    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
  PUF3_YEAST | Q07807
    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
  PUF3_YEAST | Q07807
    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
        PUF3_YEAST | Q07807: 3k49

(-) Related Entries Specified in the PDB File

3k49 THE SAME PROTEIN COMPLEXED WITH COX17 SITE B