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- PDB-5vhr: Conformational Landscape of the p28-Bound Human Proteasome Regula... -

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Entry
Database: PDB / ID: 5vhr
TitleConformational Landscape of the p28-Bound Human Proteasome Regulatory Particle
Descriptor(26S proteasome non-ATPase regulatory subunit ...) x 2
(26S proteasome regulatory subunit ...) x 6
KeywordsHYDROLASE / p28 / 26S proteasome / regulatory particle / 19S / gankyrin
Specimen sourceHomo sapiens / human
MethodElectron microscopy (7.7 Å resolution / Particle / Single particle)
AuthorsLu, Y. / Wu, J. / Dong, Y. / Chen, S. / Sun, S. / Ma, Y.B. / Ouyang, Q. / Finley, D. / Kirschner, M.W. / Mao, Y.
CitationMol. Cell, 2017, 67, 322-333.e6

Mol. Cell, 2017, 67, 322-333.e6 Yorodumi Papers
Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.
Ying Lu / Jiayi Wu / Yuanchen Dong / Shuobing Chen / Shuangwu Sun / Yong-Bei Ma / Qi Ouyang / Daniel Finley / Marc W Kirschner / Youdong Mao

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Release: Aug 23, 2017

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Assembly

Deposited unit
G: 26S proteasome non-ATPase regulatory subunit 10
A: 26S proteasome regulatory subunit 7
B: 26S proteasome regulatory subunit 4
D: 26S proteasome regulatory subunit 6B
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
C: 26S proteasome regulatory subunit 8
f: 26S proteasome non-ATPase regulatory subunit 2


Theoretical massNumber of molelcules
Total (without water)295,8458
Polyers295,8458
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)13100
ΔGint (kcal/M)-24
Surface area (Å2)127510

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Components

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26S proteasome non-ATPase regulatory subunit ... , 2 types, 2 molecules Gf

#1: Polypeptide(L)26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit p28 / Gankyrin / p28(GANK)


Mass: 24142.490 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: O75832

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • apoptotic process (GO: 0006915)
  • cytoplasmic sequestering of NF-kappaB (GO: 0007253)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • negative regulation of apoptotic process (GO: 0043066)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of DNA damage response, signal transduction by p53 class mediator (GO: 0043518)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of MAPK cascade (GO: 0043409)
  • negative regulation of NF-kappaB transcription factor activity (GO: 0032088)
  • negative regulation of release of cytochrome c from mitochondria (GO: 0090201)
  • negative regulation of transcription from RNA polymerase II promoter (GO: 0000122)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of cell growth (GO: 0030307)
  • positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO: 0045737)
  • positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO: 0032436)
  • positive regulation of protein ubiquitination (GO: 0031398)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome regulatory particle assembly (GO: 0070682)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)
#8: Polypeptide(L)26S proteasome non-ATPase regulatory subunit 2 / 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: 93790.188 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: Q13200

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • neutrophil degranulation (GO: 0043312)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)

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26S proteasome regulatory subunit ... , 6 types, 6 molecules ABDEFC

#2: Polypeptide(L)26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 29746.465 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P35998

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • neutrophil degranulation (GO: 0043312)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • osteoblast differentiation (GO: 0001649)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO: 0045899)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
  • viral process (GO: 0016032)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)
#3: Polypeptide(L)26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 29958.395 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P62191

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of neuron death (GO: 1901215)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO: 0045899)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein folding (GO: 0006457)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)
#4: Polypeptide(L)26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 29497.975 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P43686

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • blastocyst development (GO: 0001824)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO: 0045899)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • proteolysis (GO: 0006508)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)
#5: Polypeptide(L)26S proteasome regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 29434.889 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P62333

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO: 0045899)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)
#6: Polypeptide(L)26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 29773.246 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P17980

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • blastocyst development (GO: 0001824)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • modulation by host of viral transcription (GO: 0043921)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • neutrophil degranulation (GO: 0043312)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO: 0045899)
  • positive regulation of transcription from RNA polymerase II promoter (GO: 0045944)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
  • viral process (GO: 0016032)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)
#7: Polypeptide(L)26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 29501.363 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: P62195

Cellular component

Molecular function

Biological process

  • anaphase-promoting complex-dependent catabolic process (GO: 0031145)
  • antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO: 0002479)
  • Fc-epsilon receptor signaling pathway (GO: 0038095)
  • MAPK cascade (GO: 0000165)
  • modulation of chemical synaptic transmission (GO: 0050804)
  • negative regulation of canonical Wnt signaling pathway (GO: 0090090)
  • negative regulation of G2/M transition of mitotic cell cycle (GO: 0010972)
  • negative regulation of programmed cell death (GO: 0043069)
  • negative regulation of transcription, DNA-templated (GO: 0045892)
  • negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO: 0051436)
  • NIK/NF-kappaB signaling (GO: 0038061)
  • positive regulation of canonical Wnt signaling pathway (GO: 0090263)
  • positive regulation of inclusion body assembly (GO: 0090261)
  • positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO: 0045899)
  • positive regulation of transcription, DNA-templated (GO: 0045893)
  • positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition (GO: 0051437)
  • post-translational protein modification (GO: 0043687)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deubiquitination (GO: 0016579)
  • protein polyubiquitination (GO: 0000209)
  • regulation of cellular amino acid metabolic process (GO: 0006521)
  • regulation of hematopoietic stem cell differentiation (GO: 1902036)
  • regulation of mRNA stability (GO: 0043488)
  • regulation of transcription from RNA polymerase II promoter (GO: 0006357)
  • regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO: 0061418)
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO: 0031146)
  • stimulatory C-type lectin receptor signaling pathway (GO: 0002223)
  • T cell receptor signaling pathway (GO: 0050852)
  • transmembrane transport (GO: 0055085)
  • tumor necrosis factor-mediated signaling pathway (GO: 0033209)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
  • Wnt signaling pathway, planar cell polarity pathway (GO: 0060071)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Proteasome regulatory particle / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 14464 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.03419603
ELECTRON MICROSCOPYf_angle_d1.68926435
ELECTRON MICROSCOPYf_dihedral_angle_d8.77512522
ELECTRON MICROSCOPYf_chiral_restr0.0753012
ELECTRON MICROSCOPYf_plane_restr0.0093458

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