[English] 日本語
Yorodumi
- PDB-4wlq: Crystal structure of mUCH37-hRPN13 CTD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wlq
TitleCrystal structure of mUCH37-hRPN13 CTD complex
Components
  • Proteasomal ubiquitin receptor ADRM1
  • Ubiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsPROTEIN BINDING / UCH37 RPN13 Proteasome INO80 DUB
Function / homology
Function and homology information


lateral ventricle development / UCH proteinases / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / positive regulation of smoothened signaling pathway / midbrain development ...lateral ventricle development / UCH proteinases / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity / molecular function inhibitor activity / proteasome binding / protein deubiquitination / regulation of DNA replication / regulation of embryonic development / endopeptidase activator activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome assembly / regulation of DNA repair / regulation of proteasomal protein catabolic process / positive regulation of DNA repair / telomere maintenance / proteasome complex / transcription elongation by RNA polymerase II / UCH proteinases / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA recombination / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / regulation of cell cycle / chromatin remodeling / DNA repair / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proteasomal ubiquitin receptor ADRM1 / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.85 Å
AuthorsHemmis, C.W. / Hill, C.P. / VanderLinden, R. / Whitby, F.G.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM059135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM098401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM097452 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA042014 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR001209 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase.
Authors: VanderLinden, R.T. / Hemmis, C.W. / Schmitt, B. / Ndoja, A. / Whitby, F.G. / Robinson, H. / Cohen, R.E. / Yao, T. / Hill, C.P.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
B: Proteasomal ubiquitin receptor ADRM1


Theoretical massNumber of molelcules
Total (without water)47,9242
Polymers47,9242
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-36 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.935, 96.843, 98.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin C-terminal hydrolase UCH37 / Ubiquitin thioesterase L5


Mass: 37533.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uchl5, Uch37 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUP7, ubiquitinyl hydrolase 1
#2: 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: 10390.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16186

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 20% PEG 3350, 200 mM Mg(OAC)2,100 mM HEPES / Temp details: constant temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: single wavelength
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 2, 2010
RadiationMonochromator: VariMax-HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→38.26 Å / Num. obs: 14095 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 86.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.042 / Net I/σ(I): 12.2 / Num. measured all: 110961 / Scaling rejects: 173
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.85-37.61.0032.41529920110.8610.375100
9.01-38.266.80.07726.535045150.9960.03199

-
Processing

Software
NameVersionClassification
CrystalClear0.1.26data collection
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.85→38.144 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1253 8.98 %
Rwork0.1918 12699 -
obs0.1996 13952 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 358.99 Å2 / Biso mean: 112.4345 Å2 / Biso min: 41.99 Å2
Refinement stepCycle: final / Resolution: 2.85→38.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 0 0 3082
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093139
X-RAY DIFFRACTIONf_angle_d1.2124243
X-RAY DIFFRACTIONf_chiral_restr0.041474
X-RAY DIFFRACTIONf_plane_restr0.006558
X-RAY DIFFRACTIONf_dihedral_angle_d15.9711179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8501-2.96420.41121320.292213721504
2.9642-3.09910.32521380.25413751513
3.0991-3.26240.33351330.232713921525
3.2624-3.46660.3261400.20513861526
3.4666-3.73410.2911370.190614131550
3.7341-4.10950.27831390.187113911530
4.1095-4.70320.27051400.163914271567
4.7032-5.92190.29191450.185514261571
5.9219-38.14760.23291490.187815171666
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.16571.6642.67777.0775-1.91978.18130.07390.4384-0.7753-0.9442-0.01050.52430.3122-0.56-0.05021.1960.02890.03170.5953-0.09250.5772-14.9355-1.995716.6563
27.7802-0.2731.78334.75970.1067.1469-0.3881-1.23150.40881.37450.12261.07580.1097-1.1190.13961.03370.09430.1811.1003-0.02270.6448-19.32874.922331.9257
38.7166-0.18383.69788.57662.89833.22540.42580.0677-0.2324-0.7427-0.0510.2802-0.05590.1559-0.62120.9894-0.06460.1920.58110.01070.6386-8.66715.764324.3209
45.49045.87130.87258.83850.49279.6638-0.05260.3030.0504-1.0017-0.0954-0.71790.03180.56250.23390.88550.14820.21310.5457-0.03840.5589-4.85017.83919.4336
59.1598-1.7636.73756.70963.83929.13590.55391.9325-0.52420.1849-0.54490.30440.46110.74260.08641.7366-0.1112-0.07110.88330.01520.6097-17.9142.9995.4254
68.46754.20012.18849.47041.88429.0420.0743-0.80250.26760.6997-0.54960.94990.2227-1.39540.4620.56730.00920.25310.715-0.10340.5539-13.17099.450332.3857
76.6380.3314-1.44472.6551-0.24614.8690.8838-1.31740.1850.7464-0.28170.73790.1248-1.4937-0.08840.6840.02450.32161.0885-0.17750.6538-24.38033.475732.3344
89.1043-3.65793.13153.5721-4.49946.1044-0.01890.17171.67261.1913-0.0033-1.2372-0.49850.60230.19131.5953-0.0118-0.06820.5438-0.08150.6703-2.6278-22.812934.8944
97.9579-6.69875.55188.2034-5.86214.4105-0.8542-0.43170.0868-0.16720.0495-0.02360.8167-1.35450.39461.276-0.1156-0.01950.6175-0.01750.696-14.9686-19.55723.5563
102.71890.6699-2.08644.196-3.04363.17590.28572.24260.0191-0.39030.67641.77450.0352-0.869-1.10740.9052-0.01610.0841.27880.08651.1519-38.726-11.0839-5.5113
118.2897-0.83184.42251.2454-1.27052.94750.2628-1.3685-1.68880.46450.49540.24210.0319-2.4306-0.39721.8143-0.69790.34892.049-0.21951.0198-41.7068-14.86391.9769
127.8558-1.83291.85158.0193-0.23889.4379-0.1647-0.49640.7551.1281-0.45270.4208-0.8876-0.71870.42340.9630.03830.03350.701-0.1930.6232-31.993-9.0058-3.468
130.7739-0.6381-1.41040.54661.15776.8720.78210.218-2.1818-1.2232-1.46532.6694-0.6798-2.79111.00070.92230.1988-0.13691.8368-0.10291.9619-45.4334-2.777-10.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 71 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 85 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 133 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 162 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 196 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 226 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 254 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 255 through 288 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 289 through 314 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 286 through 303 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 370 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 371 through 384 )B0

+
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