[English] 日本語
Yorodumi
- PDB-5ohp: Crystal structure of USP30 (C77A) in complex with Lys6-linked diu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ohp
TitleCrystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 30
KeywordsHYDROLASE / DUB / Ubiquitin / USP / K6
Function / homology
Function and homology information


protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / autophagy of mitochondrion / pexophagy / peroxisomal membrane / symbiont entry into host cell via disruption of host cell glycocalyx / mitochondrial fusion / symbiont entry into host cell via disruption of host cell envelope / virus tail ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / autophagy of mitochondrion / pexophagy / peroxisomal membrane / symbiont entry into host cell via disruption of host cell glycocalyx / mitochondrial fusion / symbiont entry into host cell via disruption of host cell envelope / virus tail / negative regulation of mitophagy / protein deubiquitination / Pexophagy / regulation of protein stability / mitochondrial outer membrane / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleus / cytosol
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Cysteine proteinases / Cathepsin B; Chain A / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily / Ubiquitin family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin carboxyl-terminal hydrolase 30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGersch, M. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Mechanism and regulation of the Lys6-selective deubiquitinase USP30.
Authors: Gersch, M. / Gladkova, C. / Schubert, A.F. / Michel, M.A. / Maslen, S. / Komander, D.
History
DepositionJul 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_close_contact ...diffrn_source / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 17, 2024Group: 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: Ubiquitin carboxyl-terminal hydrolase 30
B: Polyubiquitin-B
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers55,5913
Non-polymers651
Water93752
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-8 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.504, 117.504, 138.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-912-

HOH

21A-926-

HOH

31C-109-

HOH

41C-111-

HOH

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 30 / Deubiquitinating enzyme 30 / Ubiquitin thioesterase 30 / Ubiquitin-specific-processing protease 30 ...Deubiquitinating enzyme 30 / Ubiquitin thioesterase 30 / Ubiquitin-specific-processing protease 30 / Ub-specific protease 30


Mass: 38437.355 Da / Num. of mol.: 1
Fragment: UNP residues 64-178,UNP residues 217-357,UNP residues 432-502
Mutation: construct 13i (C77A, R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP30 / Plasmid: MG-31-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLacI / References: UniProt: Q70CQ3, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLacI / References: UniProt: P0CG47
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.73 M sodium citrate, 0.1 M Hepes pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→82.08 Å / Num. obs: 14395 / % possible obs: 99.18 % / Redundancy: 4.7 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1702 / Rpim(I) all: 0.0863 / Net I/σ(I): 6.99
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.9977 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 1402 / CC1/2: 0.713 / Rpim(I) all: 0.5044 / % possible all: 99.86

-
Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHK

5ohk


Resolution: 2.8→82.077 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 729 5.07 %Random selection
Rwork0.2158 ---
obs0.2176 14379 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→82.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 1 52 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053767
X-RAY DIFFRACTIONf_angle_d0.6955102
X-RAY DIFFRACTIONf_dihedral_angle_d25.0171365
X-RAY DIFFRACTIONf_chiral_restr0.223583
X-RAY DIFFRACTIONf_plane_restr0.004651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-3.01650.34741280.30882686X-RAY DIFFRACTION100
3.0165-3.320.30981530.26212664X-RAY DIFFRACTION100
3.32-3.80050.24711540.22292703X-RAY DIFFRACTION100
3.8005-4.78810.23151480.17782754X-RAY DIFFRACTION100
4.7881-82.1120.21381460.19982843X-RAY DIFFRACTION97

+
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