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- PDB-6avo: Cryo-EM structure of human immunoproteasome with a novel noncompe... -

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Entry
Database: PDB / ID: 6avo
TitleCryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / complex / immunoproteasome / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyProteasome beta subunits C terminal / Proteasome subunit beta type 10 / Proteasome subunit alpha 3 / Proteasome subunit beta type 8 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 ...Proteasome beta subunits C terminal / Proteasome subunit beta type 10 / Proteasome subunit alpha 3 / Proteasome subunit beta type 8 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit beta type 9 / Proteasome subunit A N-terminal signature / Proteasome subunit alpha5 / Proteasome beta 3 subunit / Nucleophile aminohydrolases, N-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / Proteasome, subunit alpha/beta / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit / Proteasome alpha-type subunits signature. / Asymmetric localization of PCP proteins / Vpu mediated degradation of CD4 / ABC-family proteins mediated transport / Regulation of ornithine decarboxylase (ODC) / Autodegradation of the E3 ubiquitin ligase COP1 / FCERI mediated NF-kB activation / Separation of Sister Chromatids / Regulation of activated PAK-2p34 by proteasome mediated degradation / Downstream TCR signaling / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / Vif-mediated degradation of APOBEC3G / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Proteasome beta-type subunits signature. / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / Cross-presentation of soluble exogenous antigens (endosomes) / ER-Phagosome pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Activation of NF-kappaB in B cells / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Peptidase T1A, proteasome beta-subunit / AUF1 (hnRNP D0) binds and destabilizes mRNA / RUNX1 regulates transcription of genes involved in differentiation of HSCs / CDT1 association with the CDC6:ORC:origin complex / Regulation of expression of SLITs and ROBOs / Neddylation / Regulation of PTEN stability and activity / Ub-specific processing proteases / Degradation of AXIN / Neutrophil degranulation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-dependent degradation of Cyclin D1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of RUNX3 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of RUNX2 expression and activity / UCH proteinases / Defective CFTR causes cystic fibrosis / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Negative regulation of NOTCH4 signaling / Degradation of DVL / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Antigen processing: Ubiquitination & Proteasome degradation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Interleukin-1 signaling / Interferon alpha/beta signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / regulation of cysteine-type endopeptidase activity / spermatoproteasome complex / purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / proteasome core complex / immune system process / fat cell differentiation / myofibril / humoral immune response / antigen processing and presentation / NF-kappaB binding / proteasome complex
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsLi, H. / Santos, R. / Bai, L.
CitationJournal: Nat Commun / Year: 2017
Title: Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
Authors: Ruda de Luna Almeida Santos / Lin Bai / Pradeep K Singh / Naoka Murakami / Hao Fan / Wenhu Zhan / Yingrong Zhu / Xiuju Jiang / Kaiming Zhang / Jean Pierre Assker / Carl F Nathan / Huilin Li / Jamil Azzi / Gang Lin
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 4, 2017 / Release: Dec 6, 2017

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Assembly

Deposited unit
A: Proteasome subunit beta type-9
B: Proteasome subunit beta type-10
C: Proteasome subunit beta type-8
D: Proteasome subunit beta type-8
E: Proteasome subunit beta type-10
F: Proteasome subunit beta type-9
G: Proteasome subunit alpha type-1
H: Proteasome subunit alpha type-5
I: Proteasome subunit alpha type-7
J: Proteasome subunit alpha type-3
K: Proteasome subunit alpha type-6
L: Proteasome subunit alpha type-1
M: Proteasome subunit alpha type-5
N: Proteasome subunit alpha type-7
O: Proteasome subunit alpha type-4
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-3
R: Proteasome subunit alpha type-6
S: Proteasome subunit beta type-1
T: Proteasome subunit beta type-2
U: Proteasome subunit beta type-3
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-4
X: Proteasome subunit beta type-1
Y: Proteasome subunit beta type-3
Z: Proteasome subunit alpha type-4
a: Proteasome subunit beta type-4
b: Proteasome subunit alpha type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)716,69030
Polyers715,60528
Non-polymers1,0852
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)110300
ΔGint (kcal/M)-413
Surface area (Å2)207100

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Components

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

#1: Protein/peptide Proteasome subunit beta type-9 / / Proteasome subunit beta type-6 / Low molecular mass protein 2 / Macropain chain 7 / Multicatalytic endopeptidase complex chain 7 / Proteasome chain 7 / Proteasome subunit beta-1i / Really interesting new gene 12 protein


Mass: 21295.000 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P28065, proteasome endopeptidase complex
#2: Protein/peptide Proteasome subunit beta type-10 / / Proteasome subunit beta type-7 / Low molecular mass protein 10 / Macropain subunit MECl-1 / Multicatalytic endopeptidase complex subunit MECl-1 / Proteasome MECl-1 / Proteasome subunit beta-2i


Mass: 24674.248 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P40306, proteasome endopeptidase complex
#3: Protein/peptide Proteasome subunit beta type-8 / / Proteasome subunit beta type-5 / Low molecular mass protein 7 / Macropain subunit C13 / Multicatalytic endopeptidase complex subunit C13 / Proteasome component C13 / Proteasome subunit beta-5i / Really interesting new gene 10 protein


Mass: 22685.633 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P28062, proteasome endopeptidase complex
#11: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#12: Protein/peptide 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: (natural) Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#13: Protein/peptide 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: (natural) Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#14: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 24414.740 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex

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

#4: Protein/peptide Proteasome subunit alpha type-1 / / 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: (natural) Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#5: Protein/peptide 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: (natural) Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#6: Protein/peptide Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#7: Protein/peptide 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: (natural) Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex
#8: Protein/peptide Proteasome subunit alpha type-6 / / 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: (natural) Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#9: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#10: Protein/peptide 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: (natural) Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex

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Non-polymers , 1 types, 2 molecules

#15: Chemical ChemComp-BZ7 / N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-tert-butyl-N~2~-(3-phenylpropanoyl)-L-aspartamide / PKS21004


Mass: 542.669 Da / Num. of mol.: 2 / Formula: C32H38N4O4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 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
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
5GctfCTF correction
13RELION1.4classification
14RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 75017 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00849104
ELECTRON MICROSCOPYf_angle_d0.84466591
ELECTRON MICROSCOPYf_dihedral_angle_d7.57837450
ELECTRON MICROSCOPYf_chiral_restr0.0487504
ELECTRON MICROSCOPYf_plane_restr0.0058603

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