[English] 日本語
Yorodumi
- EMDB-65296: Structure of Ebinur lake virus polymerase complexed with suramin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65296
TitleStructure of Ebinur lake virus polymerase complexed with suramin
Map data
Sample
  • Complex: Structure of Ebinur lake virus polymerase complexed with suramin
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID
KeywordsViral protein / polymerase / suramin
Function / homology
Function and homology information


host cell / RNA-directed RNA polymerase / nucleotide binding / viral RNA genome replication / hydrolase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
: / Virus, RNA-directed RNA polymerase L, thumb ring domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / : / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesPipistrellus nathusii (Nathusius's pipistrelle) / Ebinur lake virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsTang J / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for RNA synthesis and inhibition of the orthobunyavirus polymerase
Authors: Tang J / Deng Z
History
DepositionJul 8, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65296.png

Downloads & links

-
Map

FileDownload / File: emd_65296.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0780683 - 1.7913448
Average (Standard dev.)-0.00013458812 (±0.05157294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_65296_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65296_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of Ebinur lake virus polymerase complexed with suramin

EntireName: Structure of Ebinur lake virus polymerase complexed with suramin
Components
  • Complex: Structure of Ebinur lake virus polymerase complexed with suramin
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID

-
Supramolecule #1: Structure of Ebinur lake virus polymerase complexed with suramin

SupramoleculeName: Structure of Ebinur lake virus polymerase complexed with suramin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pipistrellus nathusii (Nathusius's pipistrelle)

-
Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Ebinur lake virus
Molecular weightTheoretical: 199.038438 KDa
Recombinant expressionOrganism: Pichia (fungus)
SequenceString: MEDPMYEQFL QRIQAVRTAT VAKDISADIL EARHDYFGRE LCRALDIEYR NNVLLDEIIL DVYPGVNLME YNVPHVTPAN YIWTGDMLL ILAYKVSVGH DSTEVTYKKY TTLILPVMQE IGINTEICII RANPVTNQIS IVGEQFKRLF PTIPVELNFA R FFELRKML ...String:
MEDPMYEQFL QRIQAVRTAT VAKDISADIL EARHDYFGRE LCRALDIEYR NNVLLDEIIL DVYPGVNLME YNVPHVTPAN YIWTGDMLL ILAYKVSVGH DSTEVTYKKY TTLILPVMQE IGINTEICII RANPVTNQIS IVGEQFKRLF PTIPVELNFA R FFELRKML LDKFADDEEF LMMIAHGDFT LTAPWCQDDT PELIDHPIYQ EFLGSMPPRF VSMFEEAMDF SAYNAERWNT LL YKIKNLT LEDYQDYLNI KSHNIFNMTG DFMKPTQDEI DIGWESMSKR ISQERELTTD INKQKPSIHF IWAQNKDRKL LNS TAKLVF LSNTLQSITE QSTWTDALKA IGVSMDIGNN IGLYENLCAE RKLIARSTGK KVNNKRLEAV KIGKALVLWE QQFI LANEL FKGQERQKFI KNFFGIGKHK TFKDKTSEDL DREKPKILDF NNTRVLMAAR TMVNKNKKFL SQDNTLEFDH PIIST YFDQ VREASIDTAQ VLKKISKTCF WQAITDISTL MRNILAVSQY NRHNTFRVAM CANDSIYGLV FPSSDIKTKR ATIVFC IVC MHNSRDDIMD AGALFTTLET KTKTFVSISK AIRLDKERCQ RIVSSPGLFI LSTLLLYNNN TEISLYDVMN FTFYTSL SI TKSMLSLTEP SRYMIMNSLA ISSHVRDYIA EKFSPYTKTL FSVYMVNLIK RGCATANEQS EKIQVRNIYL SDYDITQK G INDIRNLDSI WFPGKVNLKE YINQIYLPFY FNAKGLHEKH HVMIDLAKTV LEIEMNQRLD QLGIWSKNEK KQHVNLPIL VHSIAKSLIL DTSRHNHLRN RVESRNNFRR SISTISTFTS SKSCIKIGEF QDLKTKEFKA TKKMNEKINQ KFRLANPLFI DDKDADAEI MHCNYDQLKT KVPNYKDYIS VKVFDRLYEL YKTKELDDKP FIEQAMKMMK EHKEFNFTFF NKGQKTSKDR E IFVGEFEA KMCMYVVERI SKERCKLNED EMISEPGDTK LRILEKKAEE EIRYIVEKTK DSILKGDPAH ALKLEINADM SK WSAQDVF FKYFWLVAMD PILYPSEKKR ILYFMCNYMQ KNLILPDDLL SNIMDQRRPY ENDIILESTN GLAQNFVQIK RNW LQGNFN YMSSYVHSCA MLVYKDVAKE AVKLLDGNCL VNSMVHSDDN QTSLSIIQNK LKDNMIIEYV AKLFEAVCLA FGCQ ANMKK TYITHTCKEF VSLFNLHGEP LSIYGRFLLP SVGDCAYIGP YEDLASRLSA AQQSLKHGCP PSYVWVAISC SHWIT HFTY NMMHDQVNSP MQYLPFEDRF QVPTELNGYL SAPLYLIALI GIEADNLWFL LNILKKLVPL DKQKETIQTQ FTAIQD NIN KLTPSELFRL KLLRYLTLDT EITSDSNMGE TSDMRSRSLL TPRKFTTAGS LNKLVSYNDF KNAMNTNEFQ ENLEYME MN PELLVTKGEN KEQYINSILF RYNSKRFKES LSIQAPSQLF VEQILFSHKP IIDYSSIFDK LASMAETEII ENLPDIIG R VTYPQAYQMI TRDITQLPLD IDDIKIVFKY CVLNDPLIIT AANTSLLCVR GAPQDRTGLS ACQMPEFRNM KLIHHSPAL VLKAFSKGTV DIPGADPVEL EKDLLHLKEF VENTGIQEKI QMNIDNPPKH LQGTEVLIYK IRELTKLYQV CYDYVKSTEH KVKVFILPM KSYTSIEFCT LIQGNTISDS KWYTMH

UniProtKB: RNA-directed RNA polymerase L

-
Macromolecule #2: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-P...

MacromoleculeName: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID
type: ligand / ID: 2 / Number of copies: 2 / Formula: SVR
Molecular weightTheoretical: 1.29728 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 85378
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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