2Z4D - JenaLib

Title :   NMR STRUCTURES OF YEAST PROTEASOME COMPONENT RPN13

Authors :   N. Zhang, K. J. Walters

Date :   15 Jun 07 (Deposition) - 20 May 08 (Release) - 19 Jan 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (8x)

Keywords :   Proteasome, Nmr, Ph Domain, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Husnjak, S. Elsasser, N. Zhang, X. Chen, L. Randles, Y. Shi, K. Hofmann, K. J. Walters, D. Finley, I. Dikic
Proteasome Subunit Rpn13 Is A Novel Ubiquitin Receptor.
Nature V. 453 481 2008
PubMed-ID: 18497817 | Reference-DOI: 10.1038/NATURE06926
(for further references see the PDB file header)

Compounds

Molecule 1 - 26S PROTEASOME REGULATORY SUBUNIT RPN13
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 6-101
	Gene	:	RPN13
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PROTEASOME COMPONENT RPN13, PROTEASOME NON-ATPASE SUBUNIT 13

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:96
 aligned with RPN13_YEAST | O13563 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:96
                                    15        25        35        45        55        65        75        85        95      
          RPN13_YEAST     6 TVIKFRAGVCEYNEDSRLCTPIPVQGEIEIKPNEEEELGFWDFEWRPTEKPVGRELDPISLILIPGETMWVPIKSSKSGRIFALVFSSNERYFFWL 101
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------Proteasom_Rpn13-2z4dA01 A:13-101                                                          Pfam domains
         Sec.struct. author ..eee....eeee....eeee......eeeee........eeeee.............eee.......eee.........eeeee......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2z4d A   6 TVIKFRAGVCEYNEDSRLCTPIPVQGEIEIKPNEEEELGFWDFEWRPTEKPVGRELDPISLILIPGETMWVPIKSSKSGRIFALVFSSNERYFFWL 101
                                    15        25        35        45        55        65        75        85        95

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (RPN13_YEAST | O13563)

molecular function
	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:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
	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: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:0000502	proteasome complex	A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
	GO:0008541	proteasome regulatory particle, lid subcomplex	The subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.
	GO:0034515	proteasome storage granule	A multisubunit proteasome complex that localizes in the cytoplasm as dot-like structures when cells are in a quiescent state.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1fho	SOLUTION STRUCTURE OF THE PH DOMAIN FROM THE C. ELEGANS MUSCLE PROTEIN UNC-89
1ubq	STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION
2coc	SOLUTION STRUCTURE OF THE C-TERMINAL PH DOMAIN OF FYVE, RHOGEF AND PH DOMAIN CONTAINING PROTEIN 3 (FGD3) FROM HUMAN
2d9v	SOLUTION STRUCTURE OF THE PH DOMAIN OF PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN FAMILY B MEMBER 1 FROM MOUSE
2dhk	SOLUTION STRUCTURE OF THE PH DOMAIN OF TBC1 DOMAIN FAMILY MEMBER 2 PROTEIN FROM HUMAN
2hth	STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY THE HUMAN EAP45/ESCRT-II GLUE DOMAIN

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