[English] 日本語
Yorodumi
- PDB-7v3b: Crystal structure of NP exonuclease C409A-PCMPS complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v3b
TitleCrystal structure of NP exonuclease C409A-PCMPS complex
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / DEDDh exonuclease / NP exonuclease / anti-viral drug / PCMPS / PCMB
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 / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / ribonucleoprotein complex ...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 / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / identical protein 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 / WD40 repeat
Similarity search - Domain/homology
PARA-MERCURY-BENZENESULFONIC ACID / Nucleoprotein
Similarity search - Component
Biological speciesLassa virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHsiao, Y.Y. / Huang, K.W.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST103-2311-B-009-001-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST108-2636-B-009-004 Taiwan
CitationJournal: Jacs Au / Year: 2021
Title: Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites.
Authors: Huang, K.W. / Chen, J.W. / Hua, T.Y. / Chu, Y.Y. / Chiu, T.Y. / Liu, J.Y. / Tu, C.I. / Hsu, K.C. / Kao, Y.T. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionAug 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8607
Polymers55,3232
Non-polymers5375
Water5,242291
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1094
Polymers27,6621
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7513
Polymers27,6621
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.703, 58.897, 69.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 27661.574 Da / Num. of mol.: 2 / Mutation: C409A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
Strain: Mouse/Sierra Leone/Josiah/1976 / Production host: Escherichia coli (E. coli)
References: UniProt: P13699, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PMB / PARA-MERCURY-BENZENESULFONIC ACID


Mass: 357.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5HgO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350, 2 mM Sodium p-chloromercuriphenylsulphonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99258 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99258 Å / Relative weight: 1
ReflectionResolution: 1.795→30 Å / Num. obs: 47519 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 25.39 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 1.011 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8610.40.49746540.9370.1590.5220.37699.8
1.86-1.9410.80.36546800.9690.1150.3830.41799.8
1.94-2.0310.90.25346870.9850.0790.2650.47599.9
2.03-2.1311.10.18947120.9910.0580.1980.53699.9
2.13-2.2711.30.13647020.9950.0420.1430.645100
2.27-2.4411.50.10147340.9970.0310.1060.736100
2.44-2.6911.50.08347560.9980.0250.0870.928100
2.69-3.0811.50.07147570.9980.0220.0741.512100
3.08-3.8811.40.0548170.9990.0150.0531.97899.8
3.88-3011.10.0450200.9990.0120.0422.28899.4

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD
Starting model: 4G9Z

4g9z


Resolution: 1.8→29.829 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 21.19
RfactorNum. reflection% reflection
Rfree0.2184 3682 7.76 %
Rwork0.186 --
obs0.1885 47464 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.22 Å2 / Biso mean: 34.2104 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 1.8→29.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 15 291 3552
Biso mean--30.13 39.68 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.81830.30151410.2388154194
1.8183-1.84330.25991310.22861663100
1.8433-1.86960.25841200.21951687100
1.8696-1.89750.25921640.20671636100
1.8975-1.92710.23161330.2071669100
1.9271-1.95870.26961390.1941675100
1.9587-1.99250.22441390.1931644100
1.9925-2.02870.22181610.18381679100
2.0287-2.06770.2081290.19071665100
2.0677-2.10990.20711330.18451690100
2.1099-2.15580.19621090.18941698100
2.1558-2.20590.21181470.18451653100
2.2059-2.26110.2211560.18631665100
2.2611-2.32220.20611500.18741667100
2.3222-2.39050.22071390.19121695100
2.3905-2.46760.24531340.19511690100
2.4676-2.55570.26231500.19751678100
2.5557-2.6580.23521510.19551683100
2.658-2.77890.24411390.19911697100
2.7789-2.92530.25381440.20171690100
2.9253-3.10840.2311140.20271715100
3.1084-3.34810.25311480.19331697100
3.3481-3.68450.18411610.18041701100
3.6845-4.21640.19011420.1561729100
4.2164-5.30730.18991540.16521746100
5.3073-29.8290.20581540.1825182999
Refinement TLS params.Method: refined / Origin x: 25.7411 Å / Origin y: 29.5448 Å / Origin z: 30.2572 Å
111213212223313233
T0.2069 Å20.0124 Å2-0.0042 Å2-0.1476 Å2-0.002 Å2--0.1272 Å2
L2.2293 °20.7004 °2-0.0333 °2-0.2406 °2-0.0196 °2--0.0421 °2
S0.0324 Å °-0.0167 Å °0.042 Å °0.0128 Å °-0.0044 Å °0.0027 Å °-0.0018 Å °0.0073 Å °-0.0285 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA363 - 569
2X-RAY DIFFRACTION1allB363 - 569
3X-RAY DIFFRACTION1allD1 - 3
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allS1 - 357

+
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