[English] 日本語
Yorodumi
- PDB-6ezc: Crystal Structure of human tRNA-dihydrouridine(20) synthase catal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ezc
TitleCrystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K double mutant
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsFLAVOPROTEIN / RNA BINDING PROTEIN / TRNA PROCESSING / OXIDOREDUCTASE
Function / homology
Function and homology information


tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / NADPH binding / antiviral innate immune response / PKR-mediated signaling / double-stranded RNA binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / NADPH binding / antiviral innate immune response / PKR-mediated signaling / double-stranded RNA binding / FMN binding / flavin adenine dinucleotide binding / tRNA binding / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
DUS2, double-stranded RNA binding domain / : / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / TRIETHYLENE GLYCOL / tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBou-Nader, C. / Bregeon, D. / Vincent, G. / Fontecave, M. / Hamdane, D.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0004-01 France
French National Research AgencyANR-11-LABX-0011-01 France
CitationJournal: Biochemistry / Year: 2018
Title: Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases.
Authors: Bou-Nader, C. / Bregeon, D. / Pecqueur, L. / Fontecave, M. / Hamdane, D.
History
DepositionNov 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,11311
Polymers36,8061
Non-polymers1,30610
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-86 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.990, 84.660, 100.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein tRNA-dihydrouridine(20) synthase [NAD(P)+]-like / Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine ...Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine synthase 2-like / hDUS2


Mass: 36806.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia coli (E. coli) / Variant (production host): pLysS
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 6 types, 240 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% PEG 2000 MME 200 mM ammonium sulfate 50 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980066 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980066 Å / Relative weight: 1
ReflectionResolution: 2→43.17 Å / Num. obs: 22677 / % possible obs: 89.9 % / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.17 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.9 % / Rmerge(I) obs: 2.521 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1135 / CC1/2: 0.413 / Rrim(I) all: 2.665 / % possible all: 43.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS20151015data reduction
STARANISO1.10.15data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XP7

4xp7


Resolution: 2→42.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1124 4.96 %RANDOM
Rwork0.182 ---
obs0.184 22658 83.3 %-
Displacement parametersBiso mean: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.6035 Å20 Å20 Å2
2---5.748 Å20 Å2
3---5.1444 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 79 230 2677
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033360HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d871SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes435HARMONIC5
X-RAY DIFFRACTIONt_it2481HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion16.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion332SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3088SEMIHARMONIC4
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2 -5.07 %
Rwork0.2182 431 -
all0.2174 454 -
obs--20.78 %
Refinement TLS params.Method: refined / Origin x: 19.7569 Å / Origin y: -1.8799 Å / Origin z: -12.6109 Å
111213212223313233
T-0.0196 Å2-0.0174 Å2-0.0126 Å2--0.0655 Å2-0.0044 Å2--0.0624 Å2
L0.7668 °20.2619 °2-0.2993 °2-1.4383 °2-0.5718 °2--1.2257 °2
S0.0315 Å °-0.0644 Å °0.0516 Å °0.054 Å °-0.0293 Å °0.0387 Å °-0.0291 Å °0.0188 Å °-0.0022 Å °
Refinement TLS groupSelection details: { A|* }

+
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