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(-) Description

Title :  STRUCTURE OF THE GAR1 DOMAIN OF NAF1
 
Authors :  N. Leulliot, K. S. Godin, C. Hoareau-Aveilla, S. Quevillon-Cheruel, G. Varani, Y. Henry, H. Van Tilbeurgh
Date :  19 Jun 07  (Deposition) - 10 Jul 07  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  B,E  (1x)
Keywords :  Ribosomal Protein, Naf1, Gar1, Snornp, Phosphorylation, Hypothetical Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Leulliot, K. S. Godin, C. Hoareau-Aveilla, S. Quevillon-Cheruel, G. Varani, Y. Henry, H. Van Tilbeurgh
The Box H/Aca Rnp Assembly Factor Naf1P Contains A Domain Homologous To Gar1P Mediating Its Interaction With Cbf5P.
J. Mol. Biol. V. 371 1338 2007
PubMed-ID: 17612558  |  Reference-DOI: 10.1016/J.JMB.2007.06.031

(-) Compounds

Molecule 1 - NAF1
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: GOLD (DE3),
    Expression System Taxid: 562
    Fragment: RESIDUES 109-232
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: HYPOTHETICAL 54.9 KDA PROTEIN IN SPC98-TOM70 INTERGENIC REGION

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A    F
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):  B  E 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:146 , PHE A:147 , GLU A:148 , PHE A:205 , LYS A:209BINDING SITE FOR RESIDUE SO4 A1221
2AC2SOFTWAREARG B:194 , LYS B:196 , PRO E:187BINDING SITE FOR RESIDUE SO4 B1221
3AC3SOFTWAREPHE C:147 , GLU C:148 , LYS C:209BINDING SITE FOR RESIDUE SO4 C1221
4AC4SOFTWAREPHE D:147 , GLU D:148BINDING SITE FOR RESIDUE SO4 D1221
5AC5SOFTWAREPRO C:187 , ARG D:194 , LYS D:196BINDING SITE FOR RESIDUE SO4 D1222
6AC6SOFTWAREALA E:146 , PHE E:147 , GLU E:148 , LYS E:209BINDING SITE FOR RESIDUE SO4 E1221
7AC7SOFTWAREPHE F:147 , GLU F:148 , PHE F:205 , LYS F:209BINDING SITE FOR RESIDUE SO4 F1221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V3M)

(-) Exons   (1, 6)

Asymmetric Unit (1, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL124W1YNL124W.1XIV:392894-3943721479NAF1_YEAST1-4924926A:122-220 (gaps)
B:122-220 (gaps)
C:120-220
D:120-220 (gaps)
E:120-220
F:124-220 (gaps)		99
99
101
101
101
97

(-) 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:94
 aligned with NAF1_YEAST | P53919 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:99
                                   131       141       151       161       171       181       191       201       211         
           NAF1_YEAST   122 VPELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCLEDRTLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeeee..eeeeee.-----.......eeee....eeee..eee......eeeee.hhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:122-220 (gaps) UniProt: 1-492 [INCOMPLETE]                                         Transcript 1
                 2v3m A 122 VPELPEDYEISEKTIITPIGVLKSAFENNIIIHAT-----RVLKEGSIFCLEDRTLIGmLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
                                   131       141       151    |    -|      171       181       191       201       211         
                                                            156   162               180-MSE                                    


Chain B from PDB  Type:PROTEIN  Length:86
 aligned with NAF1_YEAST | P53919 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:99
                                   131       141       151       161       171       181       191       201       211         
           NAF1_YEAST   122 VPELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCLEDRTLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeee..eeeee-------------.eeee....eeee..eee......eeeee.hhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:122-220 (gaps) UniProt: 1-492 [INCOMPLETE]                                         Transcript 1
                 2v3m B 122 VPELPEDYEISEKTIITPIGVLKSAFENNIIIH-------------SIFCLEDRTLIGmLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
                                   131       141       151  |      -      |171       181       191       201       211         
                                                          154           168         180-MSE                                    


Chain C from PDB  Type:PROTEIN  Length:101
 aligned with NAF1_YEAST | P53919 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:101
                                   129       139       149       159       169       179       189       199       209       219 
           NAF1_YEAST   120 ETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCLEDRTLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeeee..eeeee..............eee.....eeee..eee......eeeee.hhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:120-220 UniProt: 1-492 [INCOMPLETE]                                                  Transcript 1
                 2v3m C 120 ETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHATmSGEKRVLKEGSIFCLEDRTLIGmLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
                                   129       139       149       159       169       179|      189       199       209       219 
                                                               157-MSE                180-MSE                                    


Chain D from PDB  Type:PROTEIN  Length:94
 aligned with NAF1_YEAST | P53919 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:101
                                   129       139       149       159       169       179       189       199       209       219 
           NAF1_YEAST   120 ETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCLEDRTLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeeee..eeeee.-------......eeee....eeee..eee......eeeee.hhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:120-220 (gaps) UniProt: 1-492 [INCOMPLETE]                                           Transcript 1
                 2v3m D 120 ETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHA-------VLKEGSIFCLEDRTLIGmLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
                                   129       139       149     |   -   |   169       179|      189       199       209       219 
                                                             155     163              180-MSE                                    


Chain E from PDB  Type:PROTEIN  Length:101
 aligned with NAF1_YEAST | P53919 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:101
                                   129       139       149       159       169       179       189       199       209       219 
           NAF1_YEAST   120 ETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCLEDRTLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeeee..eeeee..............eeee....eeee..eee......eeeee.hhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:120-220 UniProt: 1-492 [INCOMPLETE]                                                  Transcript 1
                 2v3m E 120 ETVPELPEDYEISEKTIITPIGVLKSAFENNIIIHATmSGEKRVLKEGSIFCLEDRTLIGmLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
                                   129       139       149       159       169       179|      189       199       209       219 
                                                               157-MSE                180-MSE                                    


Chain F from PDB  Type:PROTEIN  Length:91
 aligned with NAF1_YEAST | P53919 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:97
                                   133       143       153       163       173       183       193       203       213       
           NAF1_YEAST   124 ELPEDYEISEKTIITPIGVLKSAFENNIIIHATMSGEKRVLKEGSIFCLEDRTLIGMLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Gar1-2v3mF01 F:124-220                                                                            Pfam domains (1)
           Pfam domains (2) Gar1-2v3mF02 F:124-220                                                                            Pfam domains (2)
           Pfam domains (3) Gar1-2v3mF03 F:124-220                                                                            Pfam domains (3)
           Pfam domains (4) Gar1-2v3mF04 F:124-220                                                                            Pfam domains (4)
           Pfam domains (5) Gar1-2v3mF05 F:124-220                                                                            Pfam domains (5)
           Pfam domains (6) Gar1-2v3mF06 F:124-220                                                                            Pfam domains (6)
         Sec.struct. author .............eeeeeeeeeee..eeeeee.------......eeee....eeee..eee......eeeee.hhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:124-220 (gaps) UniProt: 1-492 [INCOMPLETE]                                       Transcript 1
                 2v3m F 124 ELPEDYEISEKTIITPIGVLKSAFENNIIIHAT------VLKEGSIFCLEDRTLIGmLTEVFGPLQNPFYRIKLPDSKKNLFDELKVRLGEKAFIVT 220
                                   133       143       153  |    163       173      |183       193       203       213       
                                                          156    163              180-MSE
   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 2V3M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V3M)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: Gar1] (3)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NAF1_YEAST | P53919)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0000493    box H/ACA snoRNP assembly    The aggregation, arrangement and bonding together of proteins and a box H/ACA snoRNA to form a box H/ACA small nucleolar ribonucleoprotein (snoRNP) complex.
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  2v3m
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