[English] 日本語
Yorodumi
- PDB-4o6i: 2.0A crystal structure of Lymphocytic Choriomeningitis Virus Nucl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o6i
Title2.0A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal Domain
ComponentsNucleoprotein
KeywordsHYDROLASE / Exoribonuclease / Ribonucleoprotein
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / metal ion binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain
Similarity search - Domain/homology
IMIDAZOLE / Nucleoprotein
Similarity search - Component
Biological speciesLymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWest, B.R. / Hastie, K.M. / Saphire, E.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the LCMV nucleoprotein provides a template for understanding arenavirus replication and immunosuppression.
Authors: West, B.R. / Hastie, K.M. / Saphire, E.O.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,67116
Polymers52,8002
Non-polymers87014
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-12 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.962, 89.962, 145.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 26400.145 Da / Num. of mol.: 2 / Fragment: C-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis virus / Strain: Armstrong / Gene: N / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: P09992
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 277 K / Method: eppendorf crystallization / pH: 8
Details: 10 mM TRIS, 300 mM NaCl, protein concentration at 1.15 mg/mL, pH 8, Eppendorf Crystallization, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→38.955 Å / Num. all: 45091 / Num. obs: 45091 / % possible obs: 100 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9

-
Processing

Software
NameClassification
JBluIce-EPICSdata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q7C

3q7c


Resolution: 2→38.955 Å / SU ML: 0.25 / σ(F): 1.39 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2274 5.06 %RANDOM
Rwork0.2086 ---
all0.2095 45091 --
obs0.2095 44967 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 54 142 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043333
X-RAY DIFFRACTIONf_angle_d0.6394474
X-RAY DIFFRACTIONf_dihedral_angle_d12.251226
X-RAY DIFFRACTIONf_chiral_restr0.028486
X-RAY DIFFRACTIONf_plane_restr0.002588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.35431560.35952624X-RAY DIFFRACTION100
2.0435-2.0910.35561490.32742683X-RAY DIFFRACTION100
2.091-2.14330.34431480.31562650X-RAY DIFFRACTION100
2.1433-2.20130.32591510.28652651X-RAY DIFFRACTION100
2.2013-2.2660.32681430.28312641X-RAY DIFFRACTION100
2.266-2.33920.26721340.26752673X-RAY DIFFRACTION100
2.3392-2.42270.31771400.26762657X-RAY DIFFRACTION100
2.4227-2.51970.28561250.26722685X-RAY DIFFRACTION99
2.5197-2.63440.33461470.29272686X-RAY DIFFRACTION100
2.6344-2.77320.30051440.28312635X-RAY DIFFRACTION100
2.7732-2.94690.33341390.29062683X-RAY DIFFRACTION100
2.9469-3.17440.27621470.26472684X-RAY DIFFRACTION100
3.1744-3.49360.24571410.21872673X-RAY DIFFRACTION100
3.4936-3.99870.22171270.18922691X-RAY DIFFRACTION100
3.9987-5.03630.16741440.15492695X-RAY DIFFRACTION100
5.0363-38.96210.16391390.16462682X-RAY DIFFRACTION99

+
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