[English] 日本語
Yorodumi
- EMDB-62890: The apo structure (State 1) of African Swine Fever Virus DNA poly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62890
TitleThe apo structure (State 1) of African Swine Fever Virus DNA polymerase
Map dataUnsharpened map for ASFV DNA polymerase in apo state 1
Sample
  • Organelle or cellular component: ASFV DNA polymerase
    • Protein or peptide: DNA polymerase
KeywordsASFV / DNA polymerase / Virus / DNA BINDING PROTEIN
Function / homology
Function and homology information


viral DNA genome replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / DNA binding
Similarity search - Function
: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family ...: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesAsfarviridae (virus) / African swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsHu Z / Yan R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: iScience / Year: 2025
Title: The apo structure (State 1) of African Swine Fever Virus DNA polymerase
Authors: Yan R / Hu Z
History
DepositionDec 28, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62890.png

Downloads & links

-
Map

FileDownload / File: emd_62890.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map for ASFV DNA polymerase in apo state 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 248 pix.
= 205.096 Å		0.83 Å/pix.
x 248 pix.
= 205.096 Å		0.83 Å/pix.
x 248 pix.
= 205.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.641916 - 3.8149397
Average (Standard dev.)0.0003586748 (±0.081794806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions248248248
Spacing248248248
CellA=B=C: 205.09601 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map for ASFV DNA polymerase in apo state 1

Fileemd_62890_additional_1.map
AnnotationUnsharpened map for ASFV DNA polymerase in apo state 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62890_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62890_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ASFV DNA polymerase

EntireName: ASFV DNA polymerase
Components
  • Organelle or cellular component: ASFV DNA polymerase
    • Protein or peptide: DNA polymerase

-
Supramolecule #1: ASFV DNA polymerase

SupramoleculeName: ASFV DNA polymerase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Asfarviridae (virus)

-
Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 115.258234 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: MISIMDRSEI VARENPVITQ RVTNLLQTNA PLLFMPIDIH EVRYGAYTLF MYGSLENGYK AEVRIENIPV FFDVQIEFND TNQLFLKSL LTAENIVYER LETLTQRPVM GYREKEKEFA PYIRIFFKSL YERRKAITYL NNMGYNTAAD DTTCYYRMVS R ELKLPLTS ...String:
MISIMDRSEI VARENPVITQ RVTNLLQTNA PLLFMPIDIH EVRYGAYTLF MYGSLENGYK AEVRIENIPV FFDVQIEFND TNQLFLKSL LTAENIVYER LETLTQRPVM GYREKEKEFA PYIRIFFKSL YERRKAITYL NNMGYNTAAD DTTCYYRMVS R ELKLPLTS WIQLQHYSYE PRGLVHRFSV TPEDLVSYQN DGPTDHSIVM AYDIETYSPV KGTVPDPNQA NDVVFMICMR IF WIHSTEP LASTCITMAP CKKSSEWTTI LCSSEKNLLL SFAEQFSRWA PDICTGFNDS RYDWPFIVEK SMQHGILEEI FNK MSLFWH QKLDTILKCY YVKEKRVKIS AEKSIISSFL HTPGCLPIDV RNMCMQLYPK AEKTSLKAFL ENCGLDSKVD LPYH LMWKY YETRDSEKIA DVAYYCIIDA QRCQDLLVRH NVIPDRREVG ILSYTSLYDC IYYAGGHKVC NMLIAYAIHD EYGRI ACST IARGKREHGK YPGAFVIDPV KGLEQDKPTT GLDFASLYPS LIMAYNFSPE KFVASRDEAN SLMAKGESLH YVSFHF NNR LVEGWFVWHN NVPDKMGLYP KVLIDLLNKR TALKQELKKL GEKKECIHES HPGFKELQFR HAMVDAKQKA LKIFMNT FY GEAGNNLSPF FLLPLAGGVT SSGQYNLKLV YNFVINKGYG IKYGDTDSLY ITCPDSLYTE VTDAYLNSQK TIKHYEQL C HEKVLLSMKA MSTLCAEVNE YLRQDNGTSY LRMAYEEVLF PVCFTGKKKY YGIAHVNTPN FNTKELFIRG IDIIKQGQT KLTKTIGTRI MEESMKLRRP EDHRPPLIEI VKTVLKDAVV NMKQWNFEDF IQTDAWRPDK DNKAVQIFMS RMHARREQLK KHGAAASQF AEPEPGERFS YVIVEKQVQF DIQGHRTDSS RKGDKMEYVS EAKAKNLPID ILFYINNYVL GLCARFINEN E EFQPPDNV SNKDEYAQRR AKSYLQKFVQ SIHPK

UniProtKB: DNA polymerase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 2626 / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 277489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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