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- PDB-7qo6: 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state -

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Basic information

Entry
Database: PDB / ID: 7qo6
Title26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state
Components
  • (26S proteasome ...Proteasome) x 17
  • (Proteasome endopeptidase ...) x 2
  • (Proteasome subunit beta type- ...) x 3
  • BJ4_G0020160.mRNA.1.CDS.1
  • BJ4_G0021480.mRNA.1.CDS.1
  • BJ4_G0043800.mRNA.1.CDS.1
  • EM14S01-3B_G0035190.mRNA.1.CDS.1
  • EM14S01-3B_G0050020.mRNA.1.CDS.1
  • HLJ1_G0013750.mRNA.1.CDS.1
  • HLJ1_G0030700.mRNA.1.CDS.1
  • HLJ1_G0039880.mRNA.1.CDS.1
  • HLJ1_G0048980.mRNA.1.CDS.1
  • Polyubiquitin-B
  • Probable proteasome subunit alpha type-7
  • Proteasome subunit beta
  • Ubiquitin carboxyl-terminal hydrolase
KeywordsMOTOR PROTEIN / proteasome / ubiquitin / Ubp6 / allostery / deubiquitination
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) ...SAGA complex localization to transcription regulatory region / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / regulation of protein catabolic process / protein deubiquitination / proteasome storage granule / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / enzyme regulator activity / mRNA export from nucleus / protein folding chaperone / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / double-strand break repair via homologous recombination / metallopeptidase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / ubiquitin protein ligase binding / structural molecule activity / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 12 / Proteasome subunit Rpn10 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit P45-like ...26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 12 / Proteasome subunit Rpn10 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit P45-like / Ubiquitin carboxyl-terminal hydrolase 14-like / Rpn9, C-terminal helix / Rpn9 C-terminal helix / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome subunit RPN2, N-terminal domain / DSS1_SEM1 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / HEAT repeats / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / VWFA domain profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / TPR repeat profile. / MPN domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PRE5 isoform 1 / RPN13 isoform 1 / RPN10 isoform 1 / RPT1 isoform 1 / 26S proteasome regulatory subunit RPN11 / RPT6 isoform 1 / PRE9 isoform 1 / PUP2 isoform 1 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PRE5 isoform 1 / RPN13 isoform 1 / RPN10 isoform 1 / RPT1 isoform 1 / 26S proteasome regulatory subunit RPN11 / RPT6 isoform 1 / PRE9 isoform 1 / PUP2 isoform 1 / Ubiquitin carboxyl-terminal hydrolase / SCL1 isoform 1 / RPT3 isoform 1 / RPN5 isoform 1 / PRE7 isoform 1 / Proteasome subunit beta / PRE6 isoform 1 / RPN7 isoform 1 / RPT2 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 / proteasome endopeptidase complex / RPT5 isoform 1 / RPT4 isoform 1 / PUP3 isoform 1 / RPN6 isoform 1 / RPN3 isoform 1 / PRE8 isoform 1 / RPN12 isoform 1 / Ubiquitin B / 26S proteasome complex subunit SEM1 / Proteasome subunit beta type-7 / 26S proteasome regulatory subunit RPN2 / Proteasome subunit beta type-1 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsHung, K.Y.S. / Klumpe, S. / Eisele, M.R. / Elsasser, S. / Geng, T.T. / Cheng, T.C. / Joshi, T. / Rudack, T. / Sakata, E. / Finley, D.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)SFB1035/Project A01 Germany
German Research Foundation (DFG)CRC889/Project A11 Germany
Other governmentMarie Curie Career Integration grant (PCIG14-GA-2013-631577)
Other governmentNational Institutes of Health R01 GM043601
CitationJournal: Nat Commun / Year: 2022
Title: Allosteric control of Ubp6 and the proteasome via a bidirectional switch.
Authors: Ka Ying Sharon Hung / Sven Klumpe / Markus R Eisele / Suzanne Elsasser / Geng Tian / Shuangwu Sun / Jamie A Moroco / Tat Cheung Cheng / Tapan Joshi / Timo Seibel / Duco Van Dalen / Xin-Hua ...Authors: Ka Ying Sharon Hung / Sven Klumpe / Markus R Eisele / Suzanne Elsasser / Geng Tian / Shuangwu Sun / Jamie A Moroco / Tat Cheung Cheng / Tapan Joshi / Timo Seibel / Duco Van Dalen / Xin-Hua Feng / Ying Lu / Huib Ovaa / John R Engen / Byung-Hoon Lee / Till Rudack / Eri Sakata / Daniel Finley /
Abstract: The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by ...The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / em_software ...atom_site / em_software / entity / entity_name_com / entity_src_nat / pdbx_audit_support / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _entity.pdbx_description / _entity.pdbx_mutation / _entity_src_nat.strain / _pdbx_audit_support.country / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Description: Polymer backbone linkage / Provider: author / Type: Coordinate replacement

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
a: BJ4_G0020160.mRNA.1.CDS.1
b: HLJ1_G0039880.mRNA.1.CDS.1
c: BJ4_G0021480.mRNA.1.CDS.1
d: HLJ1_G0048980.mRNA.1.CDS.1
e: EM14S01-3B_G0035190.mRNA.1.CDS.1
f: BJ4_G0043800.mRNA.1.CDS.1
g: Probable proteasome subunit alpha type-7
h: Proteasome subunit beta type-1
i: Proteasome endopeptidase complex
j: Proteasome endopeptidase complex
k: Proteasome subunit beta
l: Proteasome subunit beta type-5
m: HLJ1_G0013750.mRNA.1.CDS.1
n: Proteasome subunit beta type-7
A: BJ4_G0020160.mRNA.1.CDS.1
B: HLJ1_G0039880.mRNA.1.CDS.1
C: BJ4_G0021480.mRNA.1.CDS.1
D: HLJ1_G0048980.mRNA.1.CDS.1
E: EM14S01-3B_G0035190.mRNA.1.CDS.1
F: BJ4_G0043800.mRNA.1.CDS.1
G: Probable proteasome subunit alpha type-7
1: Proteasome subunit beta type-1
2: Proteasome endopeptidase complex
3: Proteasome endopeptidase complex
4: Proteasome subunit beta
5: Proteasome subunit beta type-5
6: HLJ1_G0013750.mRNA.1.CDS.1
7: Proteasome subunit beta type-7
W: 26S proteasome regulatory subunit RPN10
V: 26S proteasome regulatory subunit RPN11
T: EM14S01-3B_G0050020.mRNA.1.CDS.1
X: HLJ1_G0030700.mRNA.1.CDS.1
Y: 26S proteasome complex subunit SEM1
Z: 26S proteasome regulatory subunit RPN1
N: 26S proteasome regulatory subunit RPN2
S: 26S proteasome regulatory subunit RPN3
P: 26S proteasome regulatory subunit RPN5
Q: 26S proteasome regulatory subunit RPN6
R: 26S proteasome regulatory subunit RPN7
U: 26S proteasome regulatory subunit RPN8
O: 26S proteasome regulatory subunit RPN9
H: 26S proteasome regulatory subunit 7 homolog
I: 26S proteasome regulatory subunit 4 homolog
K: 26S proteasome regulatory subunit 6B homolog
L: 26S proteasome subunit RPT4
M: 26S proteasome regulatory subunit 6A
J: 26S proteasome regulatory subunit 8 homolog
8: Ubiquitin carboxyl-terminal hydrolase
9: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,761,61661
Polymers1,758,50849
Non-polymers3,10912
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 13 types, 22 molecules aAbBcCdDeEfFgGk4m6TX89

#1: Protein BJ4_G0020160.mRNA.1.CDS.1 / HLJ1_G0019920.mRNA.1.CDS.1 / Proteasome subunit alpha type-1


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYC9
#2: Protein HLJ1_G0039880.mRNA.1.CDS.1 / Proteasome subunit alpha type-2


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1BIF8
#3: Protein BJ4_G0021480.mRNA.1.CDS.1 / Proteasome subunit alpha type-3


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXC6
#4: Protein HLJ1_G0048980.mRNA.1.CDS.1 / Proteasome subunit alpha type-4


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q273
#5: Protein EM14S01-3B_G0035190.mRNA.1.CDS.1 / HLJ1_G0035780.mRNA.1.CDS.1 / Proteasome subunit alpha type-5 / SX2_G0040870.mRNA.1.CDS.1 / XXYS1_4_ ...HLJ1_G0035780.mRNA.1.CDS.1 / Proteasome subunit alpha type-5 / SX2_G0040870.mRNA.1.CDS.1 / XXYS1_4_G0037780.mRNA.1.CDS.1 / Y55_G0035760.mRNA.1.CDS.1


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXN2
#6: Protein BJ4_G0043800.mRNA.1.CDS.1 / Proteasome subunit alpha type-6


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTH4
#7: Protein Probable proteasome subunit alpha type-7


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q4M4
#11: Protein Proteasome subunit beta /


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q0W2, proteasome endopeptidase complex
#13: Protein HLJ1_G0013750.mRNA.1.CDS.1 / Proteasome subunit beta type-6 / SX2_G0013730.mRNA.1.CDS.1 / Y55_G0013890.mRNA.1.CDS.1


Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0P3
#17: Protein EM14S01-3B_G0050020.mRNA.1.CDS.1 / Y55_G0050750.mRNA.1.CDS.1


Mass: 31952.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9BXZ7
#18: Protein HLJ1_G0030700.mRNA.1.CDS.1 / HN1_G0030480.mRNA.1.CDS.1 / SX2_G0030420.mRNA.1.CDS.1


Mass: 17919.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTW0
#34: Protein Ubiquitin carboxyl-terminal hydrolase


Mass: 57188.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS2079, PACBIOSEQ_LOCUS2095, PACBIOSEQ_LOCUS2109, PACBIOSEQ_LOCUS2117, PACBIOSEQ_LOCUS2154, SCNYR20_0015006200, SCP684_0015006000
Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PXS0, ubiquitinyl hydrolase 1
#35: Protein Polyubiquitin-B


Mass: 8560.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39

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Proteasome subunit beta type- ... , 3 types, 6 molecules h1l5n7

#8: Protein Proteasome subunit beta type-1 / PSMB1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 23573.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-5 / PSMB5


Mass: 31670.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q5W3, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-7 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P30657

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Proteasome endopeptidase ... , 2 types, 4 molecules i2j3

#9: Protein Proteasome endopeptidase complex /


Mass: 28299.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q449, proteasome endopeptidase complex
#10: Protein Proteasome endopeptidase complex /


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6L0YA22, proteasome endopeptidase complex

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26S proteasome ... , 17 types, 17 molecules WVYZNSPQRUOHIKLMJ

#15: Protein 26S proteasome regulatory subunit RPN10


Mass: 29776.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUA1
#16: Protein 26S proteasome regulatory subunit RPN11


Mass: 34442.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PWR8
#19: Protein 26S proteasome complex subunit SEM1 / Proteasome


Mass: 10397.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O94742
#20: Protein 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


Mass: 109601.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38764
#21: Protein 26S proteasome regulatory subunit RPN2


Mass: 104351.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32565
#22: Protein 26S proteasome regulatory subunit RPN3 / SX2_G0000950.mRNA.1.CDS.1


Mass: 60464.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1AUZ6
#23: Protein 26S proteasome regulatory subunit RPN5 / HLJ1_G0042390.mRNA.1.CDS.1 / SX2_G0042290.mRNA.1.CDS.1


Mass: 51840.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYX7
#24: Protein 26S proteasome regulatory subunit RPN6 / EM14S01-3B_G0042150.mRNA.1.CDS.1 / HLJ1_G0042890.mRNA.1.CDS.1 / HN1_G0042730.mRNA.1.CDS.1 / Y55_ ...EM14S01-3B_G0042150.mRNA.1.CDS.1 / HLJ1_G0042890.mRNA.1.CDS.1 / HN1_G0042730.mRNA.1.CDS.1 / Y55_G0042740.mRNA.1.CDS.1


Mass: 49839.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0YP93
#25: Protein 26S proteasome regulatory subunit RPN7


Mass: 49016.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2N6
#26: Protein 26S proteasome regulatory subunit RPN8


Mass: 38365.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08723
#27: Protein 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 45839.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q04062
#28: Protein 26S proteasome regulatory subunit 7 homolog / HLJ1_G0003420.mRNA.1.CDS.1 / HN1_G0003390.mRNA.1.CDS.1 / SX2_G0003430.mRNA.1.CDS.1 / Y55_G0003630.mRNA.1.CDS.1


Mass: 52153.082 Da / Num. of mol.: 1 / Mutation: S164R; T166K / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PV22
#29: Protein 26S proteasome regulatory subunit 4 homolog / EM14S01-3B_G0043310.mRNA.1.CDS.1 / HLJ1_G0043690.mRNA.1.CDS.1 / HN1_G0043500.mRNA.1.CDS.1 / SX2_ ...EM14S01-3B_G0043310.mRNA.1.CDS.1 / HLJ1_G0043690.mRNA.1.CDS.1 / HN1_G0043500.mRNA.1.CDS.1 / SX2_G0043570.mRNA.1.CDS.1 / Y55_G0043530.mRNA.1.CDS.1


Mass: 48898.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q382
#30: Protein 26S proteasome regulatory subunit 6B homolog / EM14S01-3B_G0046630.mRNA.1.CDS.1 / HLJ1_G0047490.mRNA.1.CDS.1 / HN1_G0047230.mRNA.1.CDS.1 / SX2_ ...EM14S01-3B_G0046630.mRNA.1.CDS.1 / HLJ1_G0047490.mRNA.1.CDS.1 / HN1_G0047230.mRNA.1.CDS.1 / SX2_G0047320.mRNA.1.CDS.1 / XXYS1_4_G0049230.mRNA.1.CDS.1 / Y55_G0047290.mRNA.1.CDS.1


Mass: 47953.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYF7
#31: Protein 26S proteasome subunit RPT4 / Proteasome / HLJ1_G0040220.mRNA.1.CDS.1 / HN1_G0040040.mRNA.1.CDS.1 / SX2_G0034800.mRNA.1.CDS.1 / Y55_G0040060.mRNA.1.CDS.1


Mass: 49480.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8D3
#32: Protein 26S proteasome regulatory subunit 6A / HLJ1_G0038940.mRNA.1.CDS.1 / HN1_G0038760.mRNA.1.CDS.1 / SX2_G0033520.mRNA.1.CDS.1 / Y55_G0038760.mRNA.1.CDS.1


Mass: 48315.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q672
#33: Protein 26S proteasome regulatory subunit 8 homolog / EM14S01-3B_G0032480.mRNA.1.CDS.1 / HLJ1_G0032990.mRNA.1.CDS.1 / HN1_G0032830.mRNA.1.CDS.1 / SX2_ ...EM14S01-3B_G0032480.mRNA.1.CDS.1 / HLJ1_G0032990.mRNA.1.CDS.1 / HN1_G0032830.mRNA.1.CDS.1 / SX2_G0038120.mRNA.1.CDS.1 / XXYS1_4_G0035060.mRNA.1.CDS.1 / Y55_G0032950.mRNA.1.CDS.1


Mass: 45342.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PWS2

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Non-polymers , 3 types, 12 molecules

#36: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#37: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state
Type: COMPLEX / Entity ID: #1-#35 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74842 / Symmetry type: POINT

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