[English] 日本語
Yorodumi
- PDB-3jsb: Crystal structure of the N-terminal domain of the Lymphocytic Cho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jsb
TitleCrystal structure of the N-terminal domain of the Lymphocytic Choriomeningitis Virus L protein
ComponentsRNA-directed RNA polymerase
KeywordsRNA BINDING PROTEIN / VIRAL PROTEIN / VIZIER / Structural Genomics / Marseilles Structural Genomics Program @ AFMB / MSGP / Nucleotide-binding / Nucleotidyltransferase / RNA replication / RNA-directed RNA polymerase / Transferase / Virion
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase L, helical domain / Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / de novo design (two linked rop proteins) / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. ...RNA-directed RNA polymerase L, helical domain / Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / de novo design (two linked rop proteins) / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsMorin, B. / Jamal, S. / Ferron, F.P. / Coutard, B. / Bricogne, G. / Canard, B. / Vonrhein, C. / Marseilles Structural Genomics Program @ AFMB (MSGP)
CitationJournal: Plos Pathog. / Year: 2010
Title: The N-terminal domain of the arenavirus L protein is an RNA endonuclease essential in mRNA transcription
Authors: Morin, B. / Coutard, B. / Lelke, M. / Ferron, F.P. / Kerber, R. / Jamal, S. / Frangeul, A. / Baronti, C. / Charrel, R. / de Lamballerie, X. / Vonrhein, C. / Lescar, J. / Bricogne, G. / Gunther, S. / Canard, B.
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Refinement description
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: RNA-directed RNA polymerase
B: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)47,4442
Polymers47,4442
Non-polymers00
Water4,540252
1
A: RNA-directed RNA polymerase

A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)47,4442
Polymers47,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area2040 Å2
ΔGint-15 kcal/mol
Surface area17260 Å2
MethodPISA
2
B: RNA-directed RNA polymerase

B: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)47,4442
Polymers47,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1990 Å2
ΔGint-15 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.010, 159.350, 52.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein RNA-directed RNA polymerase / Protein L


Mass: 23722.172 Da / Num. of mol.: 2 / Fragment: UNP residues 2-197 / Mutation: S107T, N173D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis virus / Strain: Armstrong / Gene: L / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express Iq (biolabs-C3016) / References: UniProt: P14240, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M-0.8M LiSo4, 50mM Citrate, 5-10% Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9835 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9835 Å / Relative weight: 1
ReflectionResolution: 2.13→107.25 Å / Num. obs: 33999 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 48.62 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 27.1 / Num. measured all: 215459
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
BUSTER2.11.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→42.59 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.9353 / Occupancy max: 1 / Occupancy min: 0.11 / SU B: 5.865 / SU ML: 0.151 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.21 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1698 5 %RANDOM
Rwork0.1986 ---
obs0.1997 33931 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 144.99 Å2 / Biso mean: 59.853 Å2 / Biso min: 27.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.4191 Å20 Å20 Å2
2--2.3075 Å20 Å2
3----4.7266 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å
Refinement stepCycle: LAST / Resolution: 2.13→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 0 252 3211
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013073HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144162HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1136SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it3073HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion19.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion401SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3674SEMIHARMONIC4
LS refinement shellResolution: 2.13→2.19 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2041 115 4.59 %
Rwork0.2002 2390 -
all0.2003 2505 -
obs--97.94 %
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)
17.09311.0451-2.08341.2214-0.64441.2586-0.15530.8513-0.4855-0.21940.05070.04580.015-0.22220.1045-0.19930.01430.0051-0.0787-0.0845-0.230414.51838.453331.0167
21.18110.88510.36752.11971.2190.96030.0891-0.2213-0.33330.3418-0.02920.0090.28450.1129-0.0599-0.09730.05530.0134-0.10080.0415-0.066338.977117.638333.2552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA-1 - 171
2X-RAY DIFFRACTION2Chain BB-2 - 191

+
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