[English] 日本語
Yorodumi
- PDB-6isu: Crystal structure of Lys27-linked di-ubiquitin in complex with it... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6isu
TitleCrystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3
Components
  • (Ubiquitin) x 2
  • Ubiquitin carboxyl-terminal hydrolase isozyme L3
KeywordsHYDROLASE / Ubiquitination / UCHL3 / Lys27-linked di-ubiquitin
Function / homology
Function and homology information


deNEDDylase activity / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / post-translational protein modification / ubiquitin binding / protein catabolic process / UCH proteinases ...deNEDDylase activity / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / post-translational protein modification / ubiquitin binding / protein catabolic process / UCH proteinases / Neddylation / peptidase activity / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / Golgi apparatus / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like ...: / Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily / Ubiquitin family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin carboxyl-terminal hydrolase isozyme L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.866 Å
AuthorsDing, S. / Pan, M. / Zheng, Q. / Ren, Y. / Hong, D.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China21532004 China
National Natural Science Foundation of China91753205 China
National Natural Science Foundation of China31640016 China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27-linked Ubiquitin Chains.
Authors: Pan, M. / Zheng, Q. / Ding, S. / Zhang, L. / Qu, Q. / Wang, T. / Hong, D. / Ren, Y. / Liang, L. / Chen, C. / Mei, Z. / Liu, L.
History
DepositionNov 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L3
B: Ubiquitin
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)43,3843
Polymers43,3843
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-11 kcal/mol
Surface area16690 Å2
Unit cell
Length a, b, c (Å)91.407, 94.204, 91.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-446-

HOH

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L3 / UCH-L3 / Ubiquitin thioesterase L3


Mass: 26213.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15374, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#3: Protein Ubiquitin


Mass: 8593.862 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350 (w/v), 400 mM Ca(AC)2

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9792 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.866→41.85 Å / Num. obs: 29404 / % possible obs: 88.82 % / Redundancy: 3.2 % / Net I/σ(I): 31.32
Reflection shellResolution: 1.866→1.933 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XD3

1xd3


Resolution: 1.866→41.85 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 33.09
RfactorNum. reflection% reflection
Rfree0.2644 1467 4.99 %
Rwork0.2091 --
obs0.2121 29404 88.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.866→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 0 292 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073076
X-RAY DIFFRACTIONf_angle_d0.8614154
X-RAY DIFFRACTIONf_dihedral_angle_d7.9341892
X-RAY DIFFRACTIONf_chiral_restr0.055472
X-RAY DIFFRACTIONf_plane_restr0.006542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8656-1.93230.41990.33561986X-RAY DIFFRACTION64
1.9323-2.00960.3151760.28351662X-RAY DIFFRACTION53
2.0096-2.10110.39911470.31253022X-RAY DIFFRACTION97
2.1011-2.21190.27011590.2283087X-RAY DIFFRACTION100
2.2119-2.35050.32421710.2683020X-RAY DIFFRACTION96
2.3505-2.53190.30881780.25052965X-RAY DIFFRACTION96
2.5319-2.78670.29271250.23862559X-RAY DIFFRACTION82
2.7867-3.18990.28241750.22893142X-RAY DIFFRACTION100
3.1899-4.01860.24371760.17153176X-RAY DIFFRACTION100
4.0186-47.1170.21331610.17623306X-RAY DIFFRACTION100

+
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