[English] 日本語
Yorodumi
- PDB-5v1z: Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v1z
TitleCrystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex
Components
  • 26S proteasome non-ATPase regulatory subunit 1
  • Proteasomal ubiquitin receptor ADRM1
  • Ubiquitin
KeywordsPROTEIN BINDING / RPN13 / proteasome / RPN2 / ubiquitin
Function / homology
Function and homology information


proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / symbiont entry into host cell via disruption of host cell glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity ...proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / symbiont entry into host cell via disruption of host cell glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / molecular function inhibitor activity / symbiont entry into host cell via disruption of host cell envelope / virus tail / proteasome binding / regulation of protein catabolic process / proteasome storage granule / endopeptidase activator activity / proteasome assembly / enzyme regulator activity / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / proteasome complex / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / transcription elongation by RNA polymerase II / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / azurophil granule lumen / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Proteasomal ubiquitin receptor Rpn13/ADRM1 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain ...Proteasomal ubiquitin receptor Rpn13/ADRM1 / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / HEAT repeats / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / PH-domain like / Pectin lyase fold / Pectin lyase fold/virulence factor / Armadillo-like helical / Ubiquitin family / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Tail fiber / Proteasomal ubiquitin receptor ADRM1 / 26S proteasome non-ATPase regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHemmis, C.W. / VanderLinden, R.T. / Yao, T. / Robinson, H. / Hill, C.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM059135 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21 CA191929 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.
Authors: VanderLinden, R.T. / Hemmis, C.W. / Yao, T. / Robinson, H. / Hill, C.P.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasomal ubiquitin receptor ADRM1
B: Proteasomal ubiquitin receptor ADRM1
C: Ubiquitin
D: Ubiquitin
F: 26S proteasome non-ATPase regulatory subunit 1
E: 26S proteasome non-ATPase regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)49,3546
Polymers49,3546
Non-polymers00
Water1,45981
1
A: Proteasomal ubiquitin receptor ADRM1
C: Ubiquitin
E: 26S proteasome non-ATPase regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)24,6773
Polymers24,6773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proteasomal ubiquitin receptor ADRM1
D: Ubiquitin
F: 26S proteasome non-ATPase regulatory subunit 1


Theoretical massNumber of molelcules
Total (without water)24,6773
Polymers24,6773
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.852, 100.852, 37.571
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Proteasomal ubiquitin receptor ADRM1 / 110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome ...110 kDa cell membrane glycoprotein / Gp110 / Adhesion-regulating molecule 1 / ARM-1 / Proteasome regulatory particle non-ATPase 13 / hRpn13 / Rpn13 homolog


Mass: 13482.367 Da / Num. of mol.: 2 / Fragment: PRU domain (UNP residues 19-132)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: Q16186
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET3a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: P0CG47
#3: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome ...26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112 / RPN2


Mass: 2617.699 Da / Num. of mol.: 2 / Fragment: C-termimal domain (UNP residues 932-953)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: Q99460
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, pH 4.6, 22.5% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 28875 / % possible obs: 100 % / Redundancy: 4.7 % / Rsym value: 0.098 / Net I/σ(I): 16
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2748 / Num. unique obs: 2748 / Rsym value: 0.628 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2R2Y & 1CMX

2r2y

1cmx


Resolution: 2→33.012 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.1817 1468 5.08 %
Rwork0.1458 --
obs0.1552 28875 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→33.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 81 3297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093308
X-RAY DIFFRACTIONf_angle_d0.8874467
X-RAY DIFFRACTIONf_dihedral_angle_d16.2252050
X-RAY DIFFRACTIONf_chiral_restr0.051484
X-RAY DIFFRACTIONf_plane_restr0.006585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07150.2531460.24592748X-RAY DIFFRACTION94
2.0715-2.15430.27671500.24452730X-RAY DIFFRACTION95
2.1543-2.25220.2671380.21962735X-RAY DIFFRACTION95
2.2522-2.37070.25331560.21072719X-RAY DIFFRACTION95
2.3707-2.51890.22641430.20632795X-RAY DIFFRACTION95
2.5189-2.71290.19831490.18812699X-RAY DIFFRACTION95
2.7129-2.9850.21561380.17142733X-RAY DIFFRACTION95
2.985-3.41470.18331660.14752737X-RAY DIFFRACTION94
3.4147-4.29380.13451370.10982726X-RAY DIFFRACTION95
4.2938-18.87930.14961450.1072752X-RAY DIFFRACTION95

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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