3J47 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   FORMATION OF AN INTRICATE HELICAL BUNDLE DICTATES THE ASSEMBLY OF THE 26S PROTEASOME LID

Authors :   E. Estrin, J. R. Lopez-Blanco, P. Chacon, A. Martin

Date :   27 Jun 13 (Deposition) - 28 Aug 13 (Release) - 02 Oct 13 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   NOT APPLICABLE

Chains :   Asym./Biol. Unit : O,P,Q,R,S,T,U,V

Keywords :   Alpha Helix Bundle, Hybrid Method, Flexible Fitting, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Estrin, J. R. Lopez-Blanco, P. Chacon, A. Martin
Formation Of An Intricate Helical Bundle Dictates The Assembly Of The 26S Proteasome Lid.
Structure V. 21 1624 2013
PubMed-ID: 23911091 | Reference-DOI: 10.1016/J.STR.2013.06.023

Molecule 1 - 26S PROTEASOME REGULATORY SUBUNIT RPN11
	Chains	:	V
	Fragment	:	LAST THREE C-TERMINAL HELICES (UNP RESIDUES 230-298)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	PROTEIN MPR1

Molecule 2 - 26S PROTEASOME REGULATORY SUBUNIT RPN8
	Chains	:	U
	Fragment	:	LAST THREE C-TERMINAL HELICES (UNP RESIDUES 188-308)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

Molecule 3 - 26S PROTEASOME REGULATORY SUBUNIT RPN9
	Chains	:	O
	Fragment	:	C-TERMINAL HELIX (UNP RESIDUES 360-387)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	PROTEASOME NON-ATPASE SUBUNIT 7

Molecule 4 - 26S PROTEASOME REGULATORY SUBUNIT RPN5
	Chains	:	P
	Fragment	:	C-TERMINAL HELIX (UNP RESIDUES 409-442)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	PROTEASOME NON-ATPASE SUBUNIT 5

Molecule 5 - 26S PROTEASOME REGULATORY SUBUNIT RPN6
	Chains	:	Q
	Fragment	:	C-TERMINAL HELIX (UNP RESIDUES 407-431)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	PROTEASOME NON-ATPASE SUBUNIT 4

Molecule 6 - 26S PROTEASOME REGULATORY SUBUNIT RPN7
	Chains	:	R
	Fragment	:	C-TERMINAL HELIX (UNP RESIDUES 397-422)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

Molecule 7 - 26S PROTEASOME REGULATORY SUBUNIT RPN3
	Chains	:	S
	Fragment	:	C-TERMINAL HELIX (UNP RESIDUES 455-478)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

Molecule 8 - 26S PROTEASOME REGULATORY SUBUNIT RPN12
	Chains	:	T
	Fragment	:	C-TERMINAL HELIX (UNP RESIDUES 256-272)
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	NUCLEAR INTEGRITY PROTEIN 1

		1	2	3	4	5	6	7	8
Asymmetric/Biological Unit	:	O	P	Q	R	S	T	U	V

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3J47)

(no "Site" information available for 3J47)

(no "SS Bond" information available for 3J47)

(no "Cis Peptide Bond" information available for 3J47)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_RPN11_YEAST_002 *	A	239	T	RPN11_YEAST	---	---	V	A	239	T
2	UniProt	VAR_RPN11_YEAST_003 *	T	262	S	RPN11_YEAST	---	---	V	T	262	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3J47)

(no "Exon" information available for 3J47)

Asymmetric/Biological 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 O from PDB  Type:PROTEIN  Length:28
 aligned with RPN9_YEAST | Q04062 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:28
                                   369       379        
           RPN9_YEAST   360 GDQITKMKDRLVEWNDQVEKLGKKMEAR 387
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 3j47 O 360 GDQITKMKDRLVEWNDQVEKLGKKMEAR 387
                                   369       379

Chain P from PDB  Type:PROTEIN  Length:34
 aligned with RPN5_YEAST | Q12250 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:34
                                   418       428       438    
           RPN5_YEAST   409 SQLLNEWSHNVDELLEHIETIGHLITKEEIMHGL 442
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3j47 P 409 SQLLNEWSHNVDELLEHIETIGHLITKEEIMHGL 442
                                   418       428       438

Chain Q from PDB  Type:PROTEIN  Length:25
 aligned with RPN6_YEAST | Q12377 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:25
                                   416       426     
           RPN6_YEAST   407 ATYDSALELVGQLNKVVDQLFEKAS 431
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 3j47 Q 407 ATYDSALELVGQLNKVVDQLFEKAS 431
                                   416       426

Chain R from PDB  Type:PROTEIN  Length:26
 aligned with RPN7_YEAST | Q06103 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:26
                                   406       416      
           RPN7_YEAST   397 NAQYHLLVKQGDGLLTKLQKYGAAVR 422
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 3j47 R 397 NAQYHLLVKQGDGLLTKLQKYGAAVR 422
                                   406       416

Chain S from PDB  Type:PROTEIN  Length:24
 aligned with RPN3_YEAST | P40016 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:24
                                   464       474    
           RPN3_YEAST   455 EDPQQVFDERIKFANQLHDEYLVS 478
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 3j47 S 455 EDPQQVFDERIKFANQLHDEYLVS 478
                                   464       474

Chain T from PDB  Type:PROTEIN  Length:17
 aligned with RPN12_YEAST | P32496 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:17
                                   265       
          RPN12_YEAST   256 KTNIIEKAMDYAISIEN 272
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 3j47 T 256 KTNIIEKAMDYAISIEN 272
                                   265

Chain U from PDB  Type:PROTEIN  Length:91
 aligned with RPN8_YEAST | Q08723 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:121
                                   197       207       217       227       237       247       257       267       277       287       297       307 
           RPN8_YEAST   188 IRLTNQLKSLKGLQSKLKDVVEYLDKVINKELPINHTILGKLQDVFNLLPNLGTPDDDEIDVENHDRINISNNLQKALTVKTNDELMVIYISNLVRSIIAFDDLIENKIQNKKIQEQRVKD 308
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh-------.hhhhhhhhhhhh-----------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3j47 U 188 IRLTNQLKSLKGLQSKLKDVVEYLDKVI-------HTILGKLQDVFNL-----------------------NNLQKALTVKTNDELMVIYISNLVRSIIAFDDLIENKIQNKKIQEQRVKD 308
                                   197       207       | -     | 227       | -         -         - |     267       277       287       297       307 
                                                     215     223         235                     259

Chain V from PDB  Type:PROTEIN  Length:63
 aligned with RPN11_YEAST | P43588 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:69
                                   239       249       259       269       279       289         
          RPN11_YEAST   230 YEEKEESNLAATKSMVKIAEQYSKRIEEEKELTEEELKTRYVGRQDPKKHLSETADETLENNIVSVLTA 298
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------T----------------------S------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 3j47 V 230 YEEKEESNLAATKSMVKIAEQYSKRIEEEKELTEEELKTR------PKKHLSETADETLENNIVSVLTA 298
                                   239       249       259       269      |279       289         
                                                                 269    276

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 '\|'

(no "SCOP Domain" information available for 3J47)

(no "CATH Domain" information available for 3J47)

(no "Pfam Domain" information available for 3J47)

Asymmetric/Biological Unit(hide GO term definitions)

Chain O (RPN9_YEAST | Q04062)

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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0043248	proteasome assembly	The aggregation, arrangement and bonding together of a mature, active proteasome 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: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: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.

Chain P (RPN5_YEAST | Q12250)

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:0043161	proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
	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:0008180	COP9 signalosome	A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome.
	GO:0031595	nuclear proteasome complex	A proteasome found in the nucleus of a cell.
	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.

Chain Q (RPN6_YEAST | Q12377)

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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0043248	proteasome assembly	The aggregation, arrangement and bonding together of a mature, active proteasome 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: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.

Chain R (RPN7_YEAST | Q06103)

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:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0043161	proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
	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: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.

Chain S (RPN3_YEAST | P40016)

molecular function
	GO:0030234	enzyme regulator activity	Binds to and modulates the activity of an enzyme.
	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:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0042176	regulation of protein catabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	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: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.

Chain T (RPN12_YEAST | P32496)

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:0043248	proteasome assembly	The aggregation, arrangement and bonding together of a mature, active proteasome complex.
	GO:0043161	proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	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: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:0005838	proteasome regulatory particle	A multisubunit complex, which caps one or both ends of the proteasome core complex. This complex recognizes and unfolds ubiquitinated proteins, and translocates them to the proteasome core complex.
	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.

Chain U (RPN8_YEAST | Q08723)

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:0043161	proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
	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: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.

Chain V (RPN11_YEAST | P43588)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino 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:0004843	thiol-dependent ubiquitin-specific protease activity	Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
	GO:0036459	thiol-dependent ubiquitinyl hydrolase activity	Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
biological process
	GO:0000266	mitochondrial fission	The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
	GO:0016559	peroxisome fission	The division of a mature peroxisome within a cell to form two or more separate peroxisome compartments.
	GO:1902906	proteasome storage granule assembly	The aggregation, arrangement and bonding together of a set of components to form a proteasome storage granule.
	GO:0043161	proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
	GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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: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.
	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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3j47)

	Sites
(no "Sites" information available for 3j47)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3j47)

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	3j47
		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
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	RPN11_YEAST \| P43588
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN12_YEAST \| P32496
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN3_YEAST \| P40016
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN5_YEAST \| Q12250
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN6_YEAST \| Q12377
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN7_YEAST \| Q06103
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN8_YEAST \| Q08723
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RPN9_YEAST \| Q04062
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
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		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
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Access by UniProt ID/Accession number
	RPN11_YEAST \| P43588
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN12_YEAST \| P32496
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN3_YEAST \| P40016
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN5_YEAST \| Q12250
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN6_YEAST \| Q12377
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN7_YEAST \| Q06103
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN8_YEAST \| Q08723
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RPN9_YEAST \| Q04062
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4b4t	26S YEAST PROTEASOME FLEXIBLY FITTED MODEL

Description

Compounds

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

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (29, 77)

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Still Images

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File