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(-) Description

Title :  X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT3G22680
 
Authors :  G. E. Wesenberg, D. W. Smith, G. N. Phillips Jr. , K. A. Johnson, C. A. Bin S. T. M. Allard, Center For Eukaryotic Structural Genomics (Ces
Date :  06 May 04  (Deposition) - 18 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Unknown Function, Psi, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Allard, C. A. Bingman, K. A. Johnson, G. E. Wesenberg, E. Bitto, W. B. Jeon, G. N. Phillips
Structure At 1. 6 A Resolution Of The Protein From Gene Locu At3G22680 From Arabidopsis Thaliana.
Acta Crystallogr. , Sect. F V. 61 647 2005
PubMed-ID: 16511118  |  Reference-DOI: 10.1107/S1744309105019743

(-) Compounds

Molecule 1 - EXPRESSED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AT3G22680
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1CPS2Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:38 , ARG A:40 , ARG A:41 , GLY A:59 , SER A:60 , HOH A:471 , HOH A:563BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWARELYS A:50 , THR A:100 , ASP A:101 , SER A:132 , HIS A:133 , HOH A:465 , HOH A:467 , HOH A:515BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREPRO A:55 , THR A:56 , ASN A:57 , HOH A:485 , HOH A:497BINDING SITE FOR RESIDUE SO4 A 302
4AC4SOFTWAREARG A:41 , TYR A:45 , TYR A:48 , PRO A:63 , SER A:73 , GLN A:76 , ILE A:153 , EDO A:403 , HOH A:451 , HOH A:452 , HOH A:477BINDING SITE FOR RESIDUE CPS A 200
5AC5SOFTWAREPRO A:81 , ASP A:151 , PRO A:152 , ILE A:153 , HOH A:442 , HOH A:443BINDING SITE FOR RESIDUE EDO A 401
6AC6SOFTWARELEU A:85 , ARG A:92 , TRP A:93 , HIS A:127 , HOH A:434 , HOH A:447 , HOH A:545BINDING SITE FOR RESIDUE EDO A 402
7AC7SOFTWARESER A:73 , GLN A:76 , ILE A:153 , CPS A:200 , HOH A:487 , HOH A:547BINDING SITE FOR RESIDUE EDO A 403
8AC8SOFTWARELYS A:75 , ASN A:87 , SER A:148 , PHE A:149 , ILE A:150 , ASP A:151 , HOH A:492BINDING SITE FOR RESIDUE EDO A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VK5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VK5)

(-) Exons   (0, 0)

(no "Exon" information available for 1VK5)

(-) 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:121
 aligned with RDM1_ARATH | Q9LUJ3 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:121
                                    51        61        71        81        91       101       111       121       131       141       151       161 
           RDM1_ARATH    42 GSLLRRAEMYQDYMKQVPIPTNRGSLIPFTSWVGLSISMKQLYGQPLHYLTNVLLQRWDQSRFGTDSEEQRLDSIIHPTKAEATIWLVEEIHRLTPSHLHMALLWRSDPMYHSFIDPIFPE 162
               SCOP domains d1vk5a_ A: Hypothetical protein At3g22680                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --DUF1950-1vk5A01 A:38-156                                                                                                Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..............hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk5 A  36 GSLLRRAEMYQDYMKQVPIPTNRGSLIPFTSWVGLSISMKQLYGQPLHYLTNVLLQRWDQSRFGTDSEEQRLDSIIHPTKAEATIWLVEEIHRLTPSHLHMALLWRSDPMYHSFIDPIFPE 156
                                    45        55        65        75        85        95       105       115       125       135       145       155
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VK5)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF1950] (2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (RDM1_ARATH | Q9LUJ3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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).
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0070918    production of small RNA involved in gene silencing by RNA    The process in which a double-stranded RNA precursor is processed into short (20-30 nt) fragments. RNA cleavage is catalyzed by a Dicer endonuclease.
    GO:0044030    regulation of DNA methylation    Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
cellular component
    GO:0000419    DNA-directed RNA polymerase V complex    RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits.
    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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        RDM1_ARATH | Q9LUJ3: 2q3t 3gan

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