[English] 日本語
Yorodumi
- PDB-5ef3: RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 25.0 MGy -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ef3
TitleRADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 25.0 MGy
Components
  • (GAGUU)10GAG 53-NUCLEOTIDE RNA
  • Transcription attenuation protein MtrB
KeywordsRNA BINDING PROTEIN / protein-RNA complex / radiation damage
Function / homology
Function and homology information


DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function
TRAP-like / Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRYPTOPHAN / RNA / RNA (> 10) / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBury, C.S. / McGeehan, J.E. / Garman, E.F. / Shevtsov, M.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: RNA protects a nucleoprotein complex against radiation damage.
Authors: Bury, C.S. / McGeehan, J.E. / Antson, A.A. / Carmichael, I. / Gerstel, M. / Shevtsov, M.B. / Garman, E.F.
#1: Journal: Acta Crystallogr D Biol Crystallogr. / Year: 2002
Title: Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences
Authors: Hopcroft, N.H. / Wendt, A.L. / Gollnick, P. / Antson, A.A.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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: Transcription attenuation protein MtrB
B: Transcription attenuation protein MtrB
C: Transcription attenuation protein MtrB
D: Transcription attenuation protein MtrB
E: Transcription attenuation protein MtrB
F: Transcription attenuation protein MtrB
G: Transcription attenuation protein MtrB
H: Transcription attenuation protein MtrB
I: Transcription attenuation protein MtrB
J: Transcription attenuation protein MtrB
K: Transcription attenuation protein MtrB
L: Transcription attenuation protein MtrB
M: Transcription attenuation protein MtrB
N: Transcription attenuation protein MtrB
O: Transcription attenuation protein MtrB
P: Transcription attenuation protein MtrB
Q: Transcription attenuation protein MtrB
R: Transcription attenuation protein MtrB
S: Transcription attenuation protein MtrB
T: Transcription attenuation protein MtrB
U: Transcription attenuation protein MtrB
V: Transcription attenuation protein MtrB
W: (GAGUU)10GAG 53-NUCLEOTIDE RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,06245
Polymers199,56923
Non-polymers4,49322
Water13,385743
1
A: Transcription attenuation protein MtrB
B: Transcription attenuation protein MtrB
C: Transcription attenuation protein MtrB
D: Transcription attenuation protein MtrB
E: Transcription attenuation protein MtrB
F: Transcription attenuation protein MtrB
G: Transcription attenuation protein MtrB
H: Transcription attenuation protein MtrB
I: Transcription attenuation protein MtrB
J: Transcription attenuation protein MtrB
K: Transcription attenuation protein MtrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,07822
Polymers90,83111
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25350 Å2
ΔGint-105 kcal/mol
Surface area27720 Å2
MethodPISA
2
L: Transcription attenuation protein MtrB
M: Transcription attenuation protein MtrB
N: Transcription attenuation protein MtrB
O: Transcription attenuation protein MtrB
P: Transcription attenuation protein MtrB
Q: Transcription attenuation protein MtrB
R: Transcription attenuation protein MtrB
S: Transcription attenuation protein MtrB
T: Transcription attenuation protein MtrB
U: Transcription attenuation protein MtrB
V: Transcription attenuation protein MtrB
W: (GAGUU)10GAG 53-NUCLEOTIDE RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,98423
Polymers108,73812
Non-polymers2,24611
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37390 Å2
ΔGint-142 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.230, 111.160, 138.290
Angle α, β, γ (deg.)90.000, 117.370, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ...
Transcription attenuation protein MtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein


Mass: 8257.377 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mtrB / Plasmid: PTZSTMTRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6
#2: RNA chain (GAGUU)10GAG 53-NUCLEOTIDE RNA


Mass: 17906.479 Da / Num. of mol.: 1 / Fragment: (GAGUU)10GAG 53-NUCLEOTIDE RNA / Source method: obtained synthetically / Details: SYNTHETIC RNA. IN-VITRO TRANSCRIPTION / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 22 / Fragment: Trp ligands / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Potassium phosphate,L-tryptophan,potassium glutamate,triethanolamine,MgCl2,monomethyl ether PEG 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.98→62.71 Å / Num. obs: 130840 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.08 / Net I/σ(I): 7.2 / Num. measured all: 472868 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.98-2.013.42.3910.52156063870.2271.49497.6
10.84-62.713.50.02526.927617970.9990.01694

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
REFMACrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gtf

1gtf


Resolution: 1.98→47.674 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 6573 5.04 %5% random selection
Rwork0.2395 123866 --
obs0.241 130439 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.1 Å2 / Biso mean: 47.5281 Å2 / Biso min: 24.71 Å2
Refinement stepCycle: final / Resolution: 1.98→47.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11789 968 330 743 13830
Biso mean--39.55 54.86 -
Num. residues----1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02413392
X-RAY DIFFRACTIONf_angle_d2.27618220
X-RAY DIFFRACTIONf_chiral_restr0.1692108
X-RAY DIFFRACTIONf_plane_restr0.0122156
X-RAY DIFFRACTIONf_dihedral_angle_d15.6494912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.979-2.00150.40892180.41913908412694
2.0015-2.0250.42242240.42554037426197
2.025-2.04970.4272250.41454041426697
2.0497-2.07570.41922050.40094100430598
2.0757-2.1030.432130.38814071428498
2.103-2.13180.40822240.37024067429198
2.1318-2.16230.36482420.3644100434299
2.1623-2.19450.35192200.34724104432499
2.1945-2.22880.37871970.33514123432099
2.2288-2.26540.35522190.32354105432499
2.2654-2.30440.36182280.32374159438799
2.3044-2.34630.34481960.29964124432099
2.3463-2.39150.36662270.30864105433299
2.3915-2.44030.30492330.2844146437999
2.4403-2.49330.33892200.28544121434199
2.4933-2.55130.33292050.29014168437399
2.5513-2.61510.33152200.28394132435299
2.6151-2.68580.31382400.26654119435999
2.6858-2.76490.30622100.265941704380100
2.7649-2.85410.28421970.256441854382100
2.8541-2.95610.29382170.256541894406100
2.9561-3.07440.29422140.24641884402100
3.0744-3.21430.27392430.230941664409100
3.2143-3.38370.25682090.21244150435999
3.3837-3.59570.24952150.195641964411100
3.5957-3.87320.21562080.186741914399100
3.8732-4.26270.21732350.188841744409100
4.2627-4.8790.19092390.16824148438799
4.879-6.1450.19832110.18444160437198
6.145-47.68790.25042190.22464219443898

+
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