[English] 日本語
Yorodumi
- PDB-8dy8: Crystal structure of the R178Q mutant of ubiquitin carboxy termin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dy8
TitleCrystal structure of the R178Q mutant of ubiquitin carboxy terminal hydrolase L1 (UCH-L1)
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE / deubiquitinase / cysteine hydrolase
Function / homology
Function and homology information


axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination / negative regulation of MAP kinase activity / regulation of macroautophagy / axon cytoplasm / positive regulation of glycolytic process / ubiquitin binding / response to ischemia / protein catabolic process / UCH proteinases / cellular response to xenobiotic stimulus / ribosome binding / omega peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / neuronal cell body / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / 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 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase isozyme L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKenny, S. / Brown, K.J. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132024 United States
CitationJournal: To Be Published
Title: Enhanced catalytic activity of the UCHL1R178Q mutant is due to a more reactive active site
Authors: Kenny, S. / Brown, K.J. / Das, C.
History
DepositionAug 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7886
Polymers50,4752
Non-polymers3124
Water1,78399
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4303
Polymers25,2381
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3583
Polymers25,2381
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.385, 109.385, 79.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-458-

HOH

31A-459-

HOH

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L1 / UCH-L1 / Neuron cytoplasmic protein 9.5 / PGP 9.5 / PGP9.5 / Ubiquitin thioesterase L1


Mass: 25237.734 Da / Num. of mol.: 2 / Mutation: R178Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09936, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Ammonium Sulfate, 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→48.92 Å / Num. obs: 26476 / % possible obs: 92.41 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.02 / Net I/σ(I): 18.29
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 1559 / Rpim(I) all: 0.44 / % possible all: 55.28

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ETL

2etl


Resolution: 2.1→48.92 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 1956 7.39 %
Rwork0.2218 --
obs0.2249 26475 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 16 99 3320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023275
X-RAY DIFFRACTIONf_angle_d0.5264438
X-RAY DIFFRACTIONf_dihedral_angle_d4.997446
X-RAY DIFFRACTIONf_chiral_restr0.04505
X-RAY DIFFRACTIONf_plane_restr0.003586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.373750.3662932X-RAY DIFFRACTION50
2.15-2.210.35861040.34571320X-RAY DIFFRACTION71
2.21-2.280.31091250.29791560X-RAY DIFFRACTION84
2.28-2.350.27651350.2911698X-RAY DIFFRACTION91
2.35-2.430.30661440.27751795X-RAY DIFFRACTION97
2.43-2.530.31071480.25771866X-RAY DIFFRACTION99
2.53-2.650.31011510.29541877X-RAY DIFFRACTION100
2.65-2.780.29431480.2931861X-RAY DIFFRACTION100
2.79-2.960.32421510.28341891X-RAY DIFFRACTION100
2.96-3.190.321500.26461890X-RAY DIFFRACTION100
3.19-3.510.26261520.22461907X-RAY DIFFRACTION100
3.51-4.020.22161530.17711919X-RAY DIFFRACTION100
4.02-5.060.20721550.16031943X-RAY DIFFRACTION100
5.06-48.920.26311650.20682060X-RAY DIFFRACTION100
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)
12.1456-1.32371.30814.01171.35186.1385-0.1472-0.2088-0.45940.75290.12840.60010.8402-0.26760.00230.50070.04030.14350.37570.10530.493533.72356.348718.4975
24.8135-0.4706-1.01535.7287-0.68043.1262-0.04480.95050.3546-0.51390.2389-0.51820.0176-0.1331-0.07190.2956-0.07180.02130.4917-0.01150.32342.827515.48561.8651
33.4593-0.23090.66963.3122-1.48123.6051-0.1915-0.25110.28230.52210.13440.2331-0.4743-0.17320.09870.46520.12770.01550.253-0.01840.300234.749623.490317.0487
49.9166-3.92171.87487.38095.91817.9596-0.0392-0.2549-0.20130.49490.016-0.13250.03510.3916-0.24510.64010.20590.06170.62340.05360.325343.920315.083628.1693
56.6672-1.86322.88375.6927-1.47114.07610.02820.1550.0402-0.0728-0.1087-0.0806-0.11940.02750.05250.2643-0.0080.04780.2625-0.00150.239435.952215.75666.0698
67.69110.50581.09566.7708-2.37048.35860.37630.598-0.1681-0.42720.12860.4975-0.3360.0918-0.4310.4704-0.0208-0.08510.3524-0.04920.436730.5656.73071.6842
79.1106-5.0416-2.49416.88392.99672.95220.40691.6904-0.3538-0.431-0.23990.0021-0.327-0.8482-0.18530.4319-0.04240.08570.26690.07080.417938.34113.81798.0236
84.8413-0.36191.28243.1836-1.15377.0064-0.2952-0.4940.58950.43260.0268-0.4495-0.52310.60830.17520.42340.0902-0.07850.4478-0.08110.436321.26354.400731.6721
99.2978-1.2004-0.72592.83051.65782.998-0.80280.6096-0.5107-0.25610.3112-0.01140.50590.340.37310.6534-0.00120.06790.46470.00450.402120.638.276719.6254
101.9774-0.7564-0.78731.0128-0.42032.7663-0.4933-1.0434-0.67450.5411-0.0493-0.23960.96561.36630.3440.77240.41760.08410.84480.14850.472227.215339.41735.1387
113.4024-0.3503-1.50242.0882-1.96568.1439-0.2584-0.81690.38130.25970.45880.07040.05540.1017-0.14040.34860.0614-0.04310.4206-0.05610.307416.344746.228433.7247
125.706-2.4349-2.78727.9294-0.02175.23030.0810.57060.3491-0.34140.003-0.45680.11980.31670.02170.43110.04510.03310.56850.06830.303526.042548.86817.5815
131.22491.64231.90943.842.08244.6710.13310.80120.12970.21370.2633-0.0244-0.15810.6107-0.67680.45330.0228-0.01150.4284-0.03490.550916.371456.716524.132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 189 )
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 222 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 136 )
11X-RAY DIFFRACTION11chain 'B' and (resid 137 through 168 )
12X-RAY DIFFRACTION12chain 'B' and (resid 169 through 207 )
13X-RAY DIFFRACTION13chain 'B' and (resid 208 through 222 )

+
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