[English] 日本語
Yorodumi
- PDB-6lvs: USP14 catalytic domain mutant C114S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lvs
TitleUSP14 catalytic domain mutant C114S
ComponentsUbiquitin carboxyl-terminal hydrolase 14
KeywordsHYDROLASE / Ubiquitin Dependent Protein Catabolic Process / Protein Deubiquitination
Function / homology
Function and homology information


negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / negative regulation of ubiquitin-dependent protein catabolic process / proteasome complex ...negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / negative regulation of ubiquitin-dependent protein catabolic process / proteasome complex / Regulation of NF-kappa B signaling / chemical synaptic transmission / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / innate immune response / synapse / cell surface / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-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. / Cysteine proteinases / Cathepsin B; Chain A ...Ubiquitin carboxyl-terminal hydrolase 14-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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FORMIC ACID / Ubiquitin carboxyl-terminal hydrolase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsLin, H.C. / Lin, T.H. / Chou, C.Y.
CitationJournal: To Be Published
Title: USP14 catalytic domain mutant C114S
Authors: Lin, H.C.
History
DepositionFeb 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 14
B: Ubiquitin carboxyl-terminal hydrolase 14
C: Ubiquitin carboxyl-terminal hydrolase 14
D: Ubiquitin carboxyl-terminal hydrolase 14
E: Ubiquitin carboxyl-terminal hydrolase 14
F: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,90395
Polymers281,8946
Non-polymers4,01089
Water6,377354
1
A: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,59014
Polymers46,9821
Non-polymers60713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,92121
Polymers46,9821
Non-polymers93920
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78319
Polymers46,9821
Non-polymers80118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,37310
Polymers46,9821
Non-polymers3919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,85419
Polymers46,9821
Non-polymers87218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,38212
Polymers46,9821
Non-polymers40011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.506, 160.422, 90.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 14 / Deubiquitinating enzyme 14 / Ubiquitin thioesterase 14 / Ubiquitin-specific-processing protease 14


Mass: 46982.258 Da / Num. of mol.: 6 / Fragment: catalytic domain / Mutation: C114S, deletion of 223-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP14, TGT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54578, ubiquitinyl hydrolase 1

-
Non-polymers , 6 types, 443 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M HcooNa, 0.1M BICINE, 20% PEGmme 5000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 62014 / % possible obs: 99.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.4
Reflection shellResolution: 2.73→2.83 Å / Num. unique obs: 6191 / CC1/2: 0.844

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AYN

2ayn


Resolution: 2.73→28.49 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.948 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27677 3065 5 %RANDOM
Rwork0.197 ---
obs0.20093 58008 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.24 Å2
2---0.14 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.73→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15925 0 231 354 16510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01316375
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715267
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.64421969
X-RAY DIFFRACTIONr_angle_other_deg1.0761.57835511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84651957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95223.061846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.746153009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4381588
X-RAY DIFFRACTIONr_chiral_restr0.140.22087
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.254.8677903
X-RAY DIFFRACTIONr_mcbond_other2.254.8677904
X-RAY DIFFRACTIONr_mcangle_it3.8467.2799835
X-RAY DIFFRACTIONr_mcangle_other3.8467.2799836
X-RAY DIFFRACTIONr_scbond_it2.1115.1828472
X-RAY DIFFRACTIONr_scbond_other2.1115.1828473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6237.61412135
X-RAY DIFFRACTIONr_long_range_B_refined9.77556.5317844
X-RAY DIFFRACTIONr_long_range_B_other9.77556.53417845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.73→2.878 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 372 -
Rwork0.24 7703 -
obs--89.18 %

+
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