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- PDB-5gjq: Structure of the human 26S proteasome bound to USP14-UbAl -

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Basic information

Entry
Database: PDB / ID: 5gjq
TitleStructure of the human 26S proteasome bound to USP14-UbAl
Components
  • (26S protease regulatory subunit ...) x 6
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome complex subunit DSS1Proteasome
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 14
KeywordsHYDROLASE / protein complex / human proteasome
Function / homology
Function and homology information


negative regulation of ERAD pathway / positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / regulation of chemotaxis ...negative regulation of ERAD pathway / positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / regulation of chemotaxis / meiosis I / purine ribonucleoside triphosphate binding / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of programmed cell death / regulation of endopeptidase activity / female meiosis I / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / proteasome core complex / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / Somitogenesis / Impaired BRCA2 binding to RAD51 / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / immune system process / myofibril / female gonad development / proteasome binding / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / transcription factor binding / polyubiquitin modification-dependent protein binding / general transcription initiation factor binding / endopeptidase activator activity / NF-kappaB binding / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / enzyme regulator activity / mRNA export from nucleus / energy homeostasis / regulation of neuron apoptotic process / : / inclusion body / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / negative regulation of inflammatory response to antigenic stimulus / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / response to organonitrogen compound / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-like / : / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 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 ...Ubiquitin carboxyl-terminal hydrolase 14-like / : / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 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 subunit 7, OB domain / 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 / Ubiquitin-interacting motif. / PCI/PINT associated module / von Willebrand factor type A domain / Proteasome subunit alpha 1 / 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. / von Willebrand factor (vWF) type A domain / 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 / MPN domain / MPN domain profile. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / Papain-like cysteine peptidase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin conserved site / Ubiquitin domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 ...ADENOSINE-5'-DIPHOSPHATE / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / Ubiquitin carboxyl-terminal hydrolase 14 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / Proteasome subunit beta type-7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.35 Å
AuthorsHuang, X.L. / Luan, B. / Wu, J.P. / Shi, Y.G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31130002 China
National Natural Science Foundation of China31321062 China
National Natural Science Foundation of China31430020 China
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: An atomic structure of the human 26S proteasome.
Authors: Xiuliang Huang / Bai Luan / Jianping Wu / Yigong Shi /
Abstract: We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory ...We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function.
History
DepositionJul 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: cell / citation ...cell / citation / citation_author / em_entity_assembly / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_version
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _em_entity_assembly.entity_id_list / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.status_code / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 24, 2018Group: Data collection / Refinement description
Category: refine / refine_hist ...refine / refine_hist / refine_ls_restr / refine_ls_shell
Item: _refine.pdbx_refine_id / _refine_hist.pdbx_refine_id ..._refine.pdbx_refine_id / _refine_hist.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id
Revision 1.3Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
a: Proteasome subunit beta type-6
B: Proteasome subunit alpha type-6
b: Proteasome subunit beta type-7
C: Proteasome subunit alpha type-2
c: Proteasome subunit beta type-3
D: Proteasome subunit alpha type-4
d: Proteasome subunit beta type-2
E: Proteasome subunit alpha type-7
e: Proteasome subunit beta type-5
F: Proteasome subunit alpha type-5
f: Proteasome subunit beta type-1
G: Proteasome subunit alpha type-1
g: Proteasome subunit beta type-4
H: 26S protease regulatory subunit 7
h: Proteasome subunit alpha type-6
I: 26S protease regulatory subunit 4
i: Proteasome subunit alpha type-2
J: 26S protease regulatory subunit 8
j: Proteasome subunit alpha type-4
K: 26S protease regulatory subunit 6B
k: Proteasome subunit alpha type-7
L: 26S protease regulatory subunit 10B
l: Proteasome subunit alpha type-5
M: 26S protease regulatory subunit 6A
m: Proteasome subunit alpha type-1
N: 26S proteasome non-ATPase regulatory subunit 1
n: Proteasome subunit alpha type-3
O: 26S proteasome non-ATPase regulatory subunit 13
o: Proteasome subunit beta type-6
P: 26S proteasome non-ATPase regulatory subunit 12
p: Proteasome subunit beta type-7
Q: 26S proteasome non-ATPase regulatory subunit 11
q: Proteasome subunit beta type-3
R: 26S proteasome non-ATPase regulatory subunit 6
r: Proteasome subunit beta type-2
S: 26S proteasome non-ATPase regulatory subunit 3
s: Proteasome subunit beta type-5
T: 26S proteasome non-ATPase regulatory subunit 8
t: Proteasome subunit beta type-1
U: 26S proteasome non-ATPase regulatory subunit 7
u: Proteasome subunit beta type-4
V: 26S proteasome non-ATPase regulatory subunit 14
W: 26S proteasome non-ATPase regulatory subunit 4
X: Proteasome subunit alpha type-3
Y: 26S proteasome complex subunit DSS1
Z: 26S proteasome non-ATPase regulatory subunit 2
x: Ubiquitin carboxyl-terminal hydrolase 14
y: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,730,31154
Polymers1,727,74848
Non-polymers2,5636
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules aobpcqdresftgu

#1: Protein Proteasome subunit beta type-6 / / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 25377.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#3: Protein Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 30000.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#5: Protein Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#7: Protein Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-5 / PSMB5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 28510.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-1 / PSMB1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 26522.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / PSMB4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 29231.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex

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Proteasome subunit alpha type- ... , 7 types, 14 molecules BhCiDjEkFlGmnX

#2: Protein Proteasome subunit alpha type-6 / / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-4 / / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#8: Protein Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#10: Protein Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#12: Protein Proteasome subunit alpha type-1 / / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#21: Protein Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex

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26S protease regulatory subunit ... , 6 types, 6 molecules HIJKLM

#14: Protein 26S protease regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 48700.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35998
#15: Protein 26S protease regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 49260.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62191
#16: Protein 26S protease regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 45694.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62195
#17: Protein 26S protease regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ...26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 47426.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43686
#18: Protein 26S protease regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 44241.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62333
#19: Protein 26S protease regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / ...26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 49266.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17980

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26S proteasome non-ATPase regulatory subunit ... , 11 types, 11 molecules NOPQRSTUVWZ

#20: Protein 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105958.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99460
#22: Protein 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome ...26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


Mass: 42995.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNM6
#23: Protein 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


Mass: 52979.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00232
#24: Protein 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome ...26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


Mass: 47526.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00231
#25: Protein 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer- ...26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


Mass: 45592.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15008
#26: Protein 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 61066.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43242
#27: Protein 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 39667.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48556
#28: Protein 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein ...26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


Mass: 37086.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51665
#29: Protein 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 34620.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O00487, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#30: Protein 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 40781.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55036
#32: Protein 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome ...26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 100313.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13200

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Protein , 3 types, 3 molecules Yxy

#31: Protein 26S proteasome complex subunit DSS1 / Proteasome / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot ...Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60896
#33: Protein Ubiquitin carboxyl-terminal hydrolase 14 / Deubiquitinating enzyme 14 / Ubiquitin thioesterase 14 / Ubiquitin-specific-processing protease 14


Mass: 56133.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP14, TGT / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P54578, ubiquitinyl hydrolase 1
#34: Protein Polyubiquitin-B


Mass: 8560.831 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB
Details (production host): this source was bought from Boston Biochem
Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 1 types, 6 molecules

#35: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: human 26S proteasome bound to USP14-UbAl / Type: COMPLEX
Details: cryo-EM map of human 26S proteasome bound to USP14-UbAl by single particle reconstruction
Entity ID: #1-#34 / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HClTrisTris-HClTris1
2150 mMsodium chlorideNaClSodium chloride1
35 mMDTTDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Preliminary grid screening was performed manually
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 70 K
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 37 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 26 / Used frames/image: 1-26

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7Chimera1.10.1model fitting
9REFMAC4.5model refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 534096
3D reconstructionResolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141293 / Num. of class averages: 1 / Symmetry type: POINT
RefinementResolution: 4.5→321 Å / Cor.coef. Fo:Fc: 0.9 / SU B: 45.871 / SU ML: 0.604
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.32584 --
obs0.32584 354865 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 200.756 Å2
Baniso -1Baniso -2Baniso -3
1--4.81 Å20.33 Å2-1.72 Å2
2--14.06 Å2-18.22 Å2
3----9.25 Å2
Refinement stepCycle: 1 / Total: 99374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0160.019100883
ELECTRON MICROSCOPYr_bond_other_d0.0030.0294055
ELECTRON MICROSCOPYr_angle_refined_deg1.7681.967136522
ELECTRON MICROSCOPYr_angle_other_deg0.9733215287
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.845513422
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.64324.0383848
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.7331516129
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.05615577
ELECTRON MICROSCOPYr_chiral_restr0.0910.215847
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.02115504
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0221969
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it22.71420.61253926
ELECTRON MICROSCOPYr_mcbond_other22.71420.61253927
ELECTRON MICROSCOPYr_mcangle_it36.72130.73667214
ELECTRON MICROSCOPYr_mcangle_other36.7230.73767215
ELECTRON MICROSCOPYr_scbond_it24.77321.37146957
ELECTRON MICROSCOPYr_scbond_other24.77321.37146958
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other40.99531.43569309
ELECTRON MICROSCOPYr_long_range_B_refined60.556432509
ELECTRON MICROSCOPYr_long_range_B_other60.556432508
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.5→4.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.338 26212 -
Rfree-0 -
obs--100 %

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