[English] 日本語
Yorodumi
- PDB-4mel: Crystal Structure of the human USP11 DUSP-UBL domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mel
TitleCrystal Structure of the human USP11 DUSP-UBL domains
ComponentsUbiquitin carboxyl-terminal hydrolase 11
KeywordsHYDROLASE / DOMAIN PRESENT IN UBIQUITIN SPECIFIC PROTEASES (DUSP) / UBIQUITIN-LIKE DOMAIN (UBL) / DEUBIQUITINATING ENZYME / DUB / DU FINGER / UBIQUITIN THIOLESTERASE
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / protein deubiquitination / transcription corepressor binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / nucleoplasm ...Association of TriC/CCT with target proteins during biosynthesis / protein deubiquitination / transcription corepressor binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal ...DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsHarper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Catalytic Regulatory Function of Ubiquitin Specific Protease 11 N-Terminal and Ubiquitin-like Domains.
Authors: Harper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 11
B: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)53,6102
Polymers53,6102
Non-polymers00
Water724
1
A: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)26,8051
Polymers26,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)26,8051
Polymers26,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-21 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.725, 131.982, 72.029
Angle α, β, γ (deg.)90.000, 96.710, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological assembly is a monomer. There are 2 biological units in the asymmetric unit (chain A. chain B.)

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 11 / Deubiquitinating enzyme 11 / Ubiquitin thioesterase 11 / Ubiquitin-specific-processing protease 11


Mass: 26804.859 Da / Num. of mol.: 2 / Fragment: DUSP-UBL domains, UNP residues 67-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 9606 / Gene: UHX1, USP11 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51784, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/imidazole, 30 mM Na Nitrate, 30 mM Na phosphate and 30 mM Na sulphate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.899→131.982 Å / Num. all: 11440 / Num. obs: 11440 / % possible obs: 100 % / Redundancy: 9.1 % / Rsym value: 0.116 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.068.90.8320.81503916890.832100
3.06-3.249.20.4961.31418415340.496100
3.24-3.479.10.32921375915200.329100
3.47-3.749.30.1883.51253813490.188100
3.74-4.19.20.1225.41166912750.122100
4.1-4.599.10.097.21057611610.09100
4.59-5.299.30.0847.3931210040.084100
5.29-6.489.10.1115.278448600.111100
6.48-9.1790.05510.561376810.055100
9.17-43.9948.80.04212.732133670.04298.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JYU

3jyu


Resolution: 2.899→37.474 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.46 / Isotropic thermal model: isotropic / σ(F): 1.35 / Phase error: 33.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2967 546 4.78 %RANDOM
Rwork0.2311 ---
obs0.2341 11416 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.43 Å2 / Biso mean: 71.5446 Å2 / Biso min: 11.78 Å2
Refinement stepCycle: LAST / Resolution: 2.899→37.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 4 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033539
X-RAY DIFFRACTIONf_angle_d0.6414824
X-RAY DIFFRACTIONf_chiral_restr0.027515
X-RAY DIFFRACTIONf_plane_restr0.003626
X-RAY DIFFRACTIONf_dihedral_angle_d13.3021280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8985-3.19010.39021330.29322690282399
3.1901-3.65140.35561260.27227142840100
3.6514-4.5990.26841380.217427382876100
4.599-37.47740.27411490.211127282877100
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)
10.09880.0496-0.10160.0444-0.04340.1132-0.0028-0.0629-0.03060.04830.0218-0.0140.00370.00530.03930.65030.01390.0070.52890.36170.717-8.8633-24.3397-58.3327
20.1006-0.0367-0.00760.0446-0.01150.0072-0.0347-0.00660.1185-0.04610.0585-0.01440.1739-0.17190.00310.7031-0.02120.00460.75790.36840.5561-12.6685-17.159-62.5642
30.01270.0058-0.00840.0062-0.00460.009-0.2499-0.0332-0.066-0.11120.23830.12250.0655-0.26720.00020.46880.0083-0.04870.55470.29240.5133-11.768-9.2757-70.5814
40.067-0.00610.01130.1175-0.04680.02220.0918-0.04330.0316-0.2308-0.12450.0014-0.0459-0.0194-0.08620.1270.18370.17450.12880.3099-0.036-4.97328.6815-37.3257
50.3646-0.0948-0.03330.14150.02830.01420.08630.27450.2041-0.1118-0.4136-0.30960.00080.1952-0.5107-0.19440.501-0.0511-0.32170.27480.23020.73350.4536-27.629
60.02930.0117-0.04750.0414-0.03410.12760.0387-0.08220.05790.1-0.172-0.0126-0.36130.3626-0.09210.2517-0.1423-0.0990.15060.27450.1044-14.932133.7637-39.3494
70.1115-0.070.08270.1334-0.12030.18520.0465-0.1163-0.22680.32580.36710.06920.0479-0.03760.57650.58110.4138-0.18860.279-0.05870.2781-0.598315.8292-74.8295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 32 through 43 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 44 through 90 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 91 through 139 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 140 through 162 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 163 through 244 )B0
6X-RAY DIFFRACTION6chain 'A' and (resid 32 through 139 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 244 )A0

+
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