[English] 日本語
Yorodumi
- EMDB-39245: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39245
TitlepP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
Map data
Sample
  • Complex: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
    • Protein or peptide: DNA topoisomerase 2
    • DNA: DNA (20-mer)
    • DNA: DNA (8-mer)
    • DNA: DNA (12-mer)
  • Ligand: MAGNESIUM ION
  • Ligand: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide
KeywordsASFV / PROTEIN BINDING / ISOMERASE-DNA complex
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA ...C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Biological speciesAfrican swine fever virus pig/Kenya/KEN-50/1950
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsSun JQ / Liu RL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R.
Authors: Ruili Liu / Junqing Sun / Lian-Feng Li / Yingxian Cheng / Meilin Li / Lifeng Fu / Su Li / Guorui Peng / Yanjin Wang / Sheng Liu / Xiao Qu / Jiaqi Ran / Xiaomei Li / Erqi Pang / Hua-Ji Qiu / ...Authors: Ruili Liu / Junqing Sun / Lian-Feng Li / Yingxian Cheng / Meilin Li / Lifeng Fu / Su Li / Guorui Peng / Yanjin Wang / Sheng Liu / Xiao Qu / Jiaqi Ran / Xiaomei Li / Erqi Pang / Hua-Ji Qiu / Yanli Wang / Jianxun Qi / Han Wang / George Fu Gao /
Abstract: The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. ...The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.
History
DepositionFeb 26, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_39245.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.124
Minimum - Maximum-0.3787855 - 1.2228976
Average (Standard dev.)0.00020246819 (±0.037891146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain

EntireName: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
Components
  • Complex: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
    • Protein or peptide: DNA topoisomerase 2
    • DNA: DNA (20-mer)
    • DNA: DNA (8-mer)
    • DNA: DNA (12-mer)
  • Ligand: MAGNESIUM ION
  • Ligand: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide

-
Supramolecule #1: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain

SupramoleculeName: pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950

-
Macromolecule #1: DNA topoisomerase 2

MacromoleculeName: DNA topoisomerase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950
Molecular weightTheoretical: 135.859891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METFEISDFK EHAKKKSMWA GALNKVTISG LMGVFTEDED LMALPIHRDH CPALLKIFDE LIVNATDHER ACHNKTKKVT YIKISFDKG VFSCENDGPG IPIVKHEQAS LIAKRDVYVP EVASCYFLAG TNINKAKDCI KGGTNGVGLK LAMVHSQWAI L TTADGSQK ...String:
METFEISDFK EHAKKKSMWA GALNKVTISG LMGVFTEDED LMALPIHRDH CPALLKIFDE LIVNATDHER ACHNKTKKVT YIKISFDKG VFSCENDGPG IPIVKHEQAS LIAKRDVYVP EVASCYFLAG TNINKAKDCI KGGTNGVGLK LAMVHSQWAI L TTADGSQK YVQHINQRLD NIEPPTITPS REMFTRIELM PVYQELGYAQ PLSETEQADL SAWIYLRACQ CAAYVGKGTT IY YNDKPCS TSSVMALAKM YTLVTAPNST IYTATIKADA KPYSLHPLQV AAVVSPKFKK FEHVSIINGV NCVKGEHVTF LKK AINEMV VKKFQQTIKD KNRKTTLRDS CSNIFVVIVG SIPGIEWTGQ RKDELSIAEN VFKTHYSIPS SFLTSMTRSI VDIL LQSIS KKDNHKQIDV DKYTRARNAG GKKAQDCMLL AAEGDSALSL LRAGLTLGKS NPSGPSFDFC GMISLGGVIM NACKK VTNI TTDSGETIMV RNEQLTNNKV LQGIVQVLGL DFNCHYKTQE ERAKLRYGCI VACVDQDLDG CGKILGLLLA YFHLFW PQL IVHGFVKRLL TPLIRVYEKG NTVPVEFYYE QEFDAWAKKQ TSLANHTVKY YKGLAAHDTH EVKSMFKHFD KMVYTFT LD DSAKELFHIY FGGESELRKR ELCTGVVPLT ETQTQSIHSV RRIPCSLHLQ VDTKAYKLDA IERQIPNFLD GMTRARRK I LAGGLKCFAS NNRERKVFQF GGYVADHMFY HHGDMSLNTS IIKAAQYYPG SSHLYPVFIG IGSFGSRHLG GKDAGSPRY ISVQLASEFI KTMFPTEDSW LLPYVFEDGQ RAEPEYYVPV LPLAIMEYGA NPSEGWKYTT WARQLEDILA LVRAYVDKNN PKHELLHYA IDHKITVLPL RPSNYNFKGH LKRFGQYYYS YGTYVVSEQR NMITITELPL RVPTVAYIES IKKSSNRMAF I EEIVDYSS SETIEILVKL KPNSLSRIME EFKETEEQNS IENFLRLRNC LHSHLNFVKP KGGIIEFNSY YEILYAWLPY RR DLYQKRL MRERAVLKLR LIMETAIVRY INESADLNLS HYEDEKEAGR ILSEHGFPPL NQSLITSPEF ATIEELNQKA LQG CYTYIL SLQARELLIA AKTRRVEKIK KMQARLDKVE QLLQESPFPG ASVWLEEIDA VEKAIIKGRN TQWKFHHH

UniProtKB: DNA topoisomerase 2

-
Macromolecule #2: DNA (20-mer)

MacromoleculeName: DNA (20-mer) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950
Molecular weightTheoretical: 6.189014 KDa
SequenceString:
(DG)(DA)(DT)(DT)(DG)(DG)(DA)(DT)(DA)(DG) (DC)(DT)(DA)(DT)(DT)(DC)(DA)(DC)(DG)(DG)

-
Macromolecule #3: DNA (8-mer)

MacromoleculeName: DNA (8-mer) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950
Molecular weightTheoretical: 2.426617 KDa
SequenceString:
(DC)(DC)(DG)(DT)(DG)(DA)(DA)(DT)

-
Macromolecule #4: DNA (12-mer)

MacromoleculeName: DNA (12-mer) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus pig/Kenya/KEN-50/1950
Molecular weightTheoretical: 3.606381 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DA)(DT)(DC)(DC)(DA)(DA) (DT)(DC)

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide

MacromoleculeName: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide
type: ligand / ID: 6 / Number of copies: 2 / Formula: ASW
Molecular weightTheoretical: 393.459 Da
Chemical component information

ChemComp-ASW:
N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide / antineoplastic*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 8 / Details: 20mM NaCl,150mM Tris-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271076
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