[English] 日本語
Yorodumi
- PDB-2nbw: Solution structure of the Rpn1 T1 site with the Rad23 UBL domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nbw
TitleSolution structure of the Rpn1 T1 site with the Rad23 UBL domain
Components
  • 26S proteasome regulatory subunit RPN1
  • UV excision repair protein RAD23
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


PNGase complex / nucleotide-excision repair factor 2 complex / ubiquitin-dependent glycoprotein ERAD pathway / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding ...PNGase complex / nucleotide-excision repair factor 2 complex / ubiquitin-dependent glycoprotein ERAD pathway / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / regulation of protein catabolic process / proteasome storage granule / polyubiquitin modification-dependent protein binding / enzyme regulator activity / : / Neutrophil degranulation / proteasome complex / ubiquitin binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / 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 ...UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / 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 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 / 26S proteasome regulatory subunit RPN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChen, X. / Walters, K.J.
CitationJournal: Structure / Year: 2016
Title: Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.
Authors: Chen, X. / Randles, L. / Shi, K. / Tarasov, S.G. / Aihara, H. / Walters, K.J.
History
DepositionMar 14, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN1
B: UV excision repair protein RAD23


Theoretical massNumber of molelcules
Total (without water)22,3482
Polymers22,3482
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


Mass: 13636.592 Da / Num. of mol.: 1 / Fragment: residues 482-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: RPN1, HRD2, NAS1, RPD1, YHR027C / Production host: Escherichia coli (E. coli) / References: UniProt: P38764
#2: Protein UV excision repair protein RAD23


Mass: 8711.100 Da / Num. of mol.: 1 / Fragment: residues 1-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: RAD23, YEL037C, SYGP-ORF29 / Production host: Escherichia coli (E. coli) / References: UniProt: P32628

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-13C HSQC aliphatic
1442D 1H-13C HSQC aliphatic
1533D 1H-13C NOESY aliphatic
1643D 1H-13C NOESY aliphatic
1733D 13C-half filter NOESY
1843D 13C-half filter NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.04-0.6 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O100% D2O
40.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.3 mMentity_1-1[U-100% 15N]1
mMentity_2-20.04-1.21
50 mMHEPES-31
50 mMsodium chloride-41
1 mMEDTA-51
2 mMDTT-61
0.1 %sodium azide-71
mMentity_1-80.04-0.62
0.3 mMentity_2-9[U-100% 15N]2
50 mMHEPES-102
50 mMsodium chloride-112
1 mMEDTA-122
2 mMDTT-132
0.1 %sodium azide-142
0.6 mMentity_1-15[U-13C]3
0.6 mMentity_2-163
50 mMHEPES-173
50 mMsodium chloride-183
1 mMEDTA-193
2 mMDTT-203
0.1 %sodium azide-213
0.6 mMentity_1-224
0.6 mMentity_2-23[U-13C]4
50 mMHEPES-244
50 mMsodium chloride-254
1 mMEDTA-264
2 mMDTT-274
0.1 %sodium azide-284
Sample conditionsIonic strength: 50 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8501
Bruker AvanceBrukerAvance8002

-
Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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