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(-) Description

Title :  CRYSTAL STRUCTURE OF NAS2 N-TERMINAL DOMAIN
 
Authors :  T. Satoh, Y. Saeki, T. Hiromoto, Y. -H. Wang, Y. Uekusa, H. Yagi, H. Yoshi M. Yagi-Utsumi, T. Mizushima, K. Tanaka, K. Kato
Date :  26 Aug 13  (Deposition) - 26 Mar 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Proteasome Assembly Chaperone, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Satoh, Y. Saeki, T. Hiromoto, Y. H. Wang, Y. Uekusa, H. Yagi, H. Yoshihara, M. Yagi-Utsumi, T. Mizushima, K. Tanaka, K. Kato
Structural Basis For Proteasome Formation Controlled By An Assembly Chaperone Nas2
Structure 2014
PubMed-ID: 24685148  |  Reference-DOI: 10.1016/J.STR.2014.02.014

(-) Compounds

Molecule 1 - PROBABLE 26S PROTEASOME REGULATORY SUBUNIT P27
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD-MBP
    Expression System Strain: BL21-CODONPLUS(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-120
    Gene: NAS2, YIL007C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: PROTEASOME NON-ATPASE SUBUNIT 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CD5Ligand/IonCADMIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:27 , GLN A:54 , TYR A:69 , ASP A:75 , HIS A:95 , GLN A:98 , ARG A:99 , CD A:204 , HOH A:320BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARELYS A:30 , LYS A:38 , THR A:39 , GLU A:42 , HIS A:107 , CD A:205 , HOH A:312 , HOH A:318 , HOH A:335BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREASP A:73 , ASP A:92 , HOH A:302 , HOH A:305 , HOH A:341BINDING SITE FOR RESIDUE CD A 203
4AC4SOFTWAREASP A:27 , ASP A:75 , HIS A:95 , SO4 A:201BINDING SITE FOR RESIDUE CD A 204
5AC5SOFTWARELYS A:38 , GLU A:42 , HIS A:107 , SO4 A:202 , HOH A:330BINDING SITE FOR RESIDUE CD A 205
6AC6SOFTWAREGLU A:5 , ASP A:16 , HOH A:382BINDING SITE FOR RESIDUE CD A 206
7AC7SOFTWAREASP A:109BINDING SITE FOR RESIDUE CD A 207

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WHJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3WHJ)

(-) 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:111
 aligned with PSMD9_YEAST | P40555 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
          PSMD9_YEAST     1 MEEEELSKLLANVKIDPSLTSRISQIDSFKLSELMVLKTDIETQLEAYFSVLEQQGIGMDSALVTPDGYPRSDVDVLQVTMIRKNVNMLKNDLNHLLQRSHVLLNQHFDNMNVKSNQ 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.......------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3whj A   1 MEEEELSKLLANVKIDPSLTSRISQIDSFKLSELMVLKTDIETQLEAYFSVLEQQGIGMDSA------YPRSDVDVLQVTMIRKNVNMLKNDLNHLLQRSHVLLNQHFDNMNVKSNQ 117
                                    10        20        30        40        50        60 |      70        80        90       100       110       
                                                                                        62     69
   Legend:   → Mismatch (orange background)
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  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 3WHJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WHJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WHJ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PSMD9_YEAST | P40555)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0070682    proteasome regulatory particle assembly    The aggregation, arrangement and bonding together of a mature, active proteasome regulatory particle complex.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.
    GO:0008540    proteasome regulatory particle, base subcomplex    The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PSMD9_YEAST | P40555: 3whl 4o06

(-) Related Entries Specified in the PDB File

2dzn 3acp 3h4m 3vld 3vle 3vlf 3whk 3whl