[English] 日本語
Yorodumi
- PDB-5l4k: The human 26S proteasome lid -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5l4k
TitleThe human 26S proteasome lid
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • 26S proteasome complex subunit DSS1
KeywordsSTRUCTURAL PROTEIN / proteostasis / AAA-ATPase / structural protein
Function / homology26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / SCF(Skp2)-mediated degradation of p27/p21 / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Vpu mediated degradation of CD4 / Vif-mediated degradation of APOBEC3G / Degradation of beta-catenin by the destruction complex ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / SCF(Skp2)-mediated degradation of p27/p21 / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Vpu mediated degradation of CD4 / Vif-mediated degradation of APOBEC3G / Degradation of beta-catenin by the destruction complex / ER-Phagosome pathway / Downstream TCR signaling / Regulation of activated PAK-2p34 by proteasome mediated degradation / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of ornithine decarboxylase (ODC) / ABC-family proteins mediated transport / Cross-presentation of soluble exogenous antigens (endosomes) / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Asymmetric localization of PCP proteins / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Ubiquitin interaction motif / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / 26S proteasome subunit RPN7 / von Willebrand factor type A domain / Activation of NF-kappaB in B cells / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / VWFA domain profile. / MPN domain profile. / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / 26S proteasome regulatory subunit Rpn6, N-terminal / Regulation of PTEN stability and activity / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Neddylation / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Negative regulation of NOTCH4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / HEAT repeats / RPN1/RPN2 N-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / Ubiquitin-dependent degradation of Cyclin D1 / Orc1 removal from chromatin / Degradation of DVL / Hedgehog 'on' state / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Regulation of RAS by GAPs / CDT1 association with the CDC6:ORC:origin complex / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / Defective CFTR causes cystic fibrosis / MAPK6/MAPK4 signaling / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / 6S proteasome subunit Rpn6, C-terminal helix domain / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN2, C-terminal / Rpn11/EIF3F, C-terminal / Proteasome component (PCI) domain / Proteasome/cyclosome repeat / von Willebrand factor, type A / Ubiquitin interacting motif / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / 26S proteasome regulatory subunit, C-terminal / Armadillo-type fold / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / CSN8/PSMD8/EIF3K / 26S Proteasome non-ATPase regulatory subunit 7/8
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSchweitzer, A. / Aufderheide, A. / Rudack, T. / Beck, F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure of the human 26S proteasome at a resolution of 3.9 Å.
Authors: Andreas Schweitzer / Antje Aufderheide / Till Rudack / Florian Beck / Günter Pfeifer / Jürgen M Plitzko / Eri Sakata / Klaus Schulten / Friedrich Förster / Wolfgang Baumeister
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 25, 2016 / Release: Sep 7, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 7, 2016Structure modelrepositoryInitial release
1.1Sep 21, 2016Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collectionem_software_em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4002
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
W: 26S proteasome non-ATPase regulatory subunit 4
V: 26S proteasome non-ATPase regulatory subunit 14
T: 26S proteasome non-ATPase regulatory subunit 8
Y: 26S proteasome complex subunit DSS1
Z: 26S proteasome non-ATPase regulatory subunit 2
N: 26S proteasome non-ATPase regulatory subunit 1
S: 26S proteasome non-ATPase regulatory subunit 3
P: 26S proteasome non-ATPase regulatory subunit 12
Q: 26S proteasome non-ATPase regulatory subunit 11
R: 26S proteasome non-ATPase regulatory subunit 6
U: 26S proteasome non-ATPase regulatory subunit 7
O: 26S proteasome non-ATPase regulatory subunit 13


Theoretical massNumber of molelcules
Total (without water)616,87312
Polyers616,87312
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)49450
ΔGint (kcal/M)-290
Surface area (Å2)220080
MethodPISA

-
Components

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

#1: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / 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: (natural) Homo sapiens (human) / References: UniProt: P55036
#2: Protein/peptide 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: (natural) Homo sapiens (human)
References: UniProt: O00487, Hydrolases, Acting on peptide bonds (peptidases), Omega peptidases
#3: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: P48556
#5: Protein/peptide 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: 100313.625 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13200
#6: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: Q99460
#7: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: O43242
#8: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: O00232
#9: Protein/peptide 26S proteasome non-ATPase regulatory subunit 11 / 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: (natural) Homo sapiens (human) / References: UniProt: O00231
#10: Protein/peptide 26S proteasome non-ATPase regulatory subunit 6 / 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: (natural) Homo sapiens (human) / References: UniProt: Q15008
#11: Protein/peptide 26S proteasome non-ATPase regulatory subunit 7 / 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: (natural) Homo sapiens (human) / References: UniProt: P51665
#12: Protein/peptide 26S proteasome non-ATPase regulatory subunit 13 / 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: (natural) Homo sapiens (human) / References: UniProt: Q9UNM6

-
Protein/peptide , 1 types, 1 molecules Y

#4: Protein/peptide 26S proteasome complex subunit DSS1 / 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: (natural) Homo sapiens (human) / References: UniProt: P60896

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: human 26S proteasome lid / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenDetails: This sample was monodisperse. / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 45 e/Å2 / Film or detector model: OTHER / Number of grids imaged: 19 / Number of real images: 40211
Image scansWidth: 4096 / Height: 4096

-
Processing

SoftwareName: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement
EM software
IDNameVersionCategory
1TOM Toolboxparticle selection
4CTFFINDCTF correction
7MDFFmodel fitting
12RELION1.43D reconstruction
13PHENIXmodel refinement
Image processingDetails: Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 688742
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 461402 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT
RefineOverall SU ML: 1.03 / Sigma F: 1.57 / Overall phase error: 46.21 / Stereochemistry target values: MLHL
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.4039 / R factor R work: 0.4025 / R factor obs: 0.4025 / Highest resolution: 4.5 Å / Lowest resolution: 9.999 Å / Number reflection R free: 72545 / Number reflection obs: 2910189 / Percent reflection R free: 2.49 / Percent reflection obs: 1
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.03040310
ELECTRON MICROSCOPYf_angle_d2.54254461
ELECTRON MICROSCOPYf_dihedral_angle_d17.76624722
ELECTRON MICROSCOPYf_chiral_restr0.0906190
ELECTRON MICROSCOPYf_plane_restr0.0167022
Refine TLS

Method: refined / Refine ID: ELECTRON MICROSCOPY

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.2520-0.36710.15400.8806-0.00611.47610.0675-1.1644-0.47400.8709-0.08790.62830.4958-0.41480.55121.93330.13580.43881.8545-0.22140.3197104.8521340.5149335.5330
20.64460.02270.00400.57150.28990.16790.0891-0.53740.09830.02940.0973-1.2166-0.34110.1036-0.01790.5615-0.3945-0.2022-0.1600-0.39090.9486181.3667339.0347284.1382
3-0.1402-0.0961-0.26670.7307-0.10380.16070.73430.19111.0317-1.1195-0.5605-0.2179-0.51750.23100.57840.0886-0.95800.7052-3.23872.9049-1.4020148.0504346.8379243.7802
40.92480.2131-0.29210.4787-0.34600.4428-0.08831.2585-0.2601-0.98390.58430.38390.3751-0.69870.20890.74011.0668-1.70410.91800.36690.6416102.2255349.8882230.1998
50.1061-0.1258-0.05610.20850.09620.0782-0.23690.17750.5226-0.15990.08310.6786-0.1123-0.3019-0.00142.69560.9289-0.43671.46100.33362.112891.6655384.4199245.1031
60.0506-0.01720.02240.59500.05170.0425-0.3278-0.26730.00130.8182-0.38820.26670.0558-0.3137-1.2922-0.00360.65530.8967-0.06580.09810.567597.1549314.2907304.3314
70.4753-0.0705-0.32160.05050.03270.3477-0.24300.3227-0.50610.04300.00420.46670.6662-0.47650.4201-1.9924-0.73380.95820.31290.45100.477294.4667291.4467286.2832
80.72970.37140.27630.4775-0.41930.25370.53570.1164-0.4831-0.97870.04711.1394-0.1232-1.07280.3168-0.9436-1.0805-1.35522.92760.16262.478367.1482304.2696250.1638
90.1004-0.0099-0.00850.12130.03770.07270.0371-0.4370-0.10910.27510.0049-0.01240.03020.01510.01561.6305-0.10141.15732.24580.26091.768780.5023302.1103331.8394
100.0848-0.0872-0.05330.07920.05250.06370.00000.2168-0.0933-0.0809-0.04190.1603-0.0259-0.3175-0.00050.95130.1101-0.03201.1937-0.25351.5935131.8604361.6390242.3978
110.2939-0.1599-0.03220.24710.30170.3028-0.09870.8324-0.4750-0.3621-0.18410.1590-0.1218-0.03430.00012.4330-0.7598-0.12593.2502-0.68593.5329128.8382230.9531221.0618
120.7216-0.09920.17941.6316-0.35850.8080-0.35980.4774-0.22910.67690.21961.4146-0.0975-0.32561.26070.0955-0.1250-0.3783-0.1591-1.1648-1.6931108.9813332.4448270.9597
130.49980.0500-0.16420.27510.25870.6934-0.5830-1.0583-0.75870.6160-0.0177-0.82070.15670.2855-0.28920.8247-0.0999-0.69650.4333-0.6485-0.2247159.3045325.9652321.9276
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1ELECTRON MICROSCOPY1(chain O and resseq 1:340 )
2ELECTRON MICROSCOPY2(chain Q and resseq 1:392 )
3ELECTRON MICROSCOPY3(chain R and resseq 1:358 )
4ELECTRON MICROSCOPY4(chain S and resseq 1:466 )
5ELECTRON MICROSCOPY5(chain T and resseq 1:322 )
6ELECTRON MICROSCOPY6(chain U and resseq 1:183 )
7ELECTRON MICROSCOPY7(chain V and resseq 1:229 )
8ELECTRON MICROSCOPY8chain N
9ELECTRON MICROSCOPY9chain W
10ELECTRON MICROSCOPY10chain Y
11ELECTRON MICROSCOPY11chain Z
12ELECTRON MICROSCOPY12(chain O and resseq 341:376 ) or (chain P and resseq 420:456 ) or (chain Q and resseq 393:422 ) or (chain R and resseq 359:389 ) or (chain S and resseq 467:534 ) or (chain T and resseq 323:350 ) or (chain U and resseq 184:324 ) or (chain V and resseq 230:309 )
13ELECTRON MICROSCOPY13(chain P and resseq 1:419 )

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more