[English] 日本語
Yorodumi
- PDB-9jkc: Crystal structure of Aspergillus fumigatus polymycovirus 1 ployme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jkc
TitleCrystal structure of Aspergillus fumigatus polymycovirus 1 ploymerase (residues 85-763) in its apo state
ComponentsRNA dependent RNA polymerase
KeywordsVIRAL PROTEIN / RNA virus / RNA-dependent RNA polymerase
Function / homology
Function and homology information


viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA dependent RNA polymerase
Similarity search - Component
Biological speciesAspergillus fumigatus tetramycovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsJia, H. / Cao, S. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
National Natural Science Foundation of China (NSFC)32300139 China
CitationJournal: Sci Adv / Year: 2025
Title: An evolutionarily unique viral RdRP suggests a common dual-function feature of the priming element.
Authors: Jia, H. / Liu, S. / Rao, G. / Liu, Q. / Wu, J. / Cao, S. / Gong, P.
History
DepositionSep 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
C: RNA dependent RNA polymerase
D: RNA dependent RNA polymerase
E: RNA dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)384,5665
Polymers384,5665
Non-polymers00
Water52229
1
A: RNA dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)76,9131
Polymers76,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)76,9131
Polymers76,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)76,9131
Polymers76,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)76,9131
Polymers76,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)76,9131
Polymers76,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)257.961, 182.916, 118.681
Angle α, β, γ (deg.)90.000, 103.790, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
RNA dependent RNA polymerase


Mass: 76913.234 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus tetramycovirus 1 / Gene: RdRP / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: A0A0H5BRR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: Tris pH 8.5, SOKALAN CP 42

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 72936 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.09 / Rrim(I) all: 0.168 / Χ2: 0.891 / Net I/σ(I): 8 / Num. measured all: 245809
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.523.20.49272730.750.3240.5920.82699.8
3.52-3.663.40.38572310.8410.2430.4570.8199.7
3.66-3.833.50.27972990.9180.1760.330.808100
3.83-4.033.40.21972960.9450.140.2610.88199.9
4.03-4.283.30.15672620.970.1030.1880.887100
4.28-4.613.50.12672850.9810.0790.1490.94100
4.61-5.083.40.09873270.9870.0620.1160.965100
5.08-5.813.30.10172970.9870.0650.1210.94499.9
5.81-7.313.40.07973330.9910.050.0941.022100
7.31-403.20.03973330.9970.0250.0460.82298.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cyro-EM structure of AfuPmV-1 N85

Resolution: 3.4→29.88 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 3723 5.11 %
Rwork0.1576 69154 -
obs0.1601 72877 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.86 Å2 / Biso mean: 47.7779 Å2 / Biso min: 18.06 Å2
Refinement stepCycle: final / Resolution: 3.4→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25253 0 0 29 25282
Biso mean---31.23 -
Num. residues----3292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.440.30991210.24452300242188
3.44-3.490.27831390.228425272666100
3.49-3.540.29971460.208625252671100
3.54-3.590.29121650.21112585275099
3.59-3.640.24711260.187925362662100
3.64-3.70.22851520.182425792731100
3.7-3.760.23751610.170425202681100
3.76-3.820.21741290.16525842713100
3.82-3.890.23331260.162525762702100
3.89-3.970.20941050.165126172722100
3.97-4.050.21461260.157525712697100
4.05-4.130.21661220.15425622684100
4.13-4.230.1931530.141925692722100
4.23-4.340.17991220.14625522674100
4.34-4.450.17561320.142426062738100
4.45-4.580.21081430.141525642707100
4.58-4.730.19041660.133625472713100
4.73-4.90.18271500.136125532703100
4.9-5.090.17671340.132226062740100
5.09-5.330.18641400.143325442684100
5.33-5.60.22441560.166725892745100
5.6-5.950.22671260.161225792705100
5.95-6.410.21271240.156626032727100
6.41-7.040.19981260.160826012727100
7.05-8.050.16971450.13925912736100
8.05-10.070.1451470.115725862733100
10.07-29.880.16841410.16222582272397

+
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