[English] 日本語
Yorodumi
- EMDB-72752: 2.62A cryo-EM structure of RNA-directed RNA polymerase L of Crime... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72752
Title2.62A cryo-EM structure of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Map data2.62 A Cryo-EM map of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Sample
  • Complex: RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
KeywordsCrimean-Congo hemorrhagic fever virus / L protein / RNA-dependent RNA polymerase / PA-like / PB1-like / PB2-like / viral replication / VIRAL PROTEIN / TRANSFERASE
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / Hydrolases; Acting on ester bonds / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / Hydrolases; Acting on ester bonds / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, nairovirus / : / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus ...RNA-directed RNA polymerase, nairovirus / : / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU-like cysteine protease / OTU domain / OTU domain profile. / 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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsLiu B / Wang D / Yang G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 2.62A cryo-EM structure of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Authors: Liu B / Wang D / Yang G
History
DepositionSep 17, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72752.png

Downloads & links

-
Map

FileDownload / File: emd_72752.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2.62 A Cryo-EM map of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 384 pix.
= 339.968 Å		0.89 Å/pix.
x 384 pix.
= 339.968 Å		0.89 Å/pix.
x 384 pix.
= 339.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.30845895 - 0.6976058
Average (Standard dev.)-0.00015868146 (±0.012152841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: 2.62 A Cryo-EM sharpened map of RNA-directed RNA...

Fileemd_72752_additional_1.map
Annotation2.62 A Cryo-EM sharpened map of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_72752_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_72752_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever ...

EntireName: RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Components
  • Complex: RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION

-
Supramolecule #1: RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever ...

SupramoleculeName: RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus / Strain: IbAr10200
Molecular weightTheoretical: 450 KDa

-
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: ubiquitinyl hydrolase 1
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus / Strain: IbAr10200
Molecular weightTheoretical: 448.527531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDFLRSLDWT QVIAGQYVSN PRFNISDYFE IVRQPGDGNC FYHSIAELTM PNKTDHSYHY IKRLTESAAR KYYQEEPEAR LVGLSLEDY LKRMLSDNEW GSTLEASMLA KEMGITIIIW TVAASDEVEA GIKFGDGDVF TAVNLLHSGQ THFDALRILP Q FETDTREA ...String:
MDFLRSLDWT QVIAGQYVSN PRFNISDYFE IVRQPGDGNC FYHSIAELTM PNKTDHSYHY IKRLTESAAR KYYQEEPEAR LVGLSLEDY LKRMLSDNEW GSTLEASMLA KEMGITIIIW TVAASDEVEA GIKFGDGDVF TAVNLLHSGQ THFDALRILP Q FETDTREA LSLMDRVIAV DQLTSSSSDE LQDYEDLALA LTSAEESNRR SSLDEVTLSK KQAEILRQKA SQLSKLVNKS QN IPTRVGR VLDCMFNCKL CVEISADTLI LRPESKEKIG EIMSLRQLGH KLLTRDKQIK QEFSRMKLYV TKDLLDHLDV GGL LRAAFP GTGIERHMQL LHSEMILDIC TVSLGVMLST FLYGSNNKNK KKFITNCLLS TALSGKKVYK VLGNLGNELL YKAP RKALA TVCSALFGKQ INKLQNCFRT ISPVSLLALR NLDFDCLSVQ DYNGMIENMS KLDNTDVEFN HREIADLNQL TSRLI TLRK EKDTDLLKQW FPESDLTRRS IRNAANAEEF VISEFFKKKD IMKFISTSGR AMSAGKIGNV LSYAHNLYLS KSSLNM TSE DISQLLIEIK RLYALQEDSE VEPIAIICDG IESNMKQLFA ILPPDCAREC EVLFDDIRNS PTHSTAWKHA LRLKGTA YE GLFANCYGWQ YIPEDIKPSL TMLIQTLFPD KFEDFLDRTQ LHPEFRDLTP DFSLTQKVHF KRNQIPSVEN VQISIDAT L PESVEAVPVT ERKMFPLPET PLSEVHSIER IMENFTRLMH GGRLSTKKRD GDPAEQGNQQ SITEHESSSI SAFKDYGER GIVEENHMKF SGEDQLETRQ LLLVEVGFQT DIDGKIRTDH KKWKDILKLL ELLGIKCSFI ACADCSSTPP DRWWITEDRV RVLKNSVSF LFNKLSRNSP TEVTDIVVGA ISTQKVRSYL KAGTATKTPV STKDVLETWE KMKEHILNRP TGLTLPTSLE Q AMRKGLVE GVVISKEGSE SCINMLKENL DRITDEFERT KFKHELTQNI TTSEKMLLSW LSEDIKSSRC GECLSNIKKA VD ETANLSE KIELLAYNLQ LTNHCSNCHP NGVNISNTSN VCKRCPKIEV VSHCENKGFE DSNECLTDLD RLVRLTLPGK TEK ERRVKR NVEYLIKLMM SMSGIDCIKY PTGQLITHGR VSAKHNDGNL KDRSDDDQRL AEKIDTVRKE LSESKLKDYS TYAR GVISN SLKNLSRQGK SKCSVPRSWL EKVLFDLKVP TKDEEVLINI RNSLKARSEF VRNNDKLLIR SKEELKKCFD VQSFK LKKN KQPVPFQVDC ILFKEVAAEC MKRYIGTPYE GIVDTLVSLI NVLTRFTWFQ EVVLYGKICE TFLRCCTEFN RSGVKL VKI RHCNINLSVK LPSNKKENML CCLYSGNMEL LQGPFYLNRR QAVLGSSYLY IVITLYIQVL QQYRCLEVIN SVSEKTL QD IENHSMTLLE DSFREITFAL EGRFEESYKI RTSRCRASGN FLNRSSRDHF ISVVSGLNLV YGFLIKDNLL ANSQQQNK Q LQMLRFGMLA GLSRLVCPNE LGKKFSTSCR RIEDNIARLY LQTSIYCSVR DVEDNVKHWK QRDLCPEVTI PCFTVYGTF VNSDRQLIFD IYNVHIYNKE MDNFDEGCIS VLEETAERHM LWELDLMNSL CSDEKKDTRT ARLLLGCPNV RKAANREGKK LLKLNSDTS TDTQSIASEV SDRRSYSSSK SRIRSIFGRY NSQKKPFELR SGLEVFNDPF NDYQQAITDI CQFSEYTPNK E SILKDCLQ IIRKNPSHTM GSFELIQAIS EFGMSKFPPE NIDKARRDPK NWVSISEVTE TTSIVASPRT HMMLKDCFKI IL GTENKKI VKMLRGKLKK LGAISTNIEI GKRDCLDLLS TVDGLTDQQK ENIVNGIFEP SKLSFYHWKE LVKKNIDEVL LTE DGNLIF CWLKTISSSV KGSLKKRLKF MNIHSPELMP ENCLFSSEEF NELIKLKKLL LNEQQDEQEL KQDLLISSWI KCIT ACKDF ASINDKIQKF IYHLSEELYD IRLQHLELSK LKQEHPSVSF TKEEVLIKRL EKNFLKQHNL EIMETVNLVF FAALS APWC LHYKALESYL VRHPEILDCG SKEDCKLTLL DLSVSKLLVC LYQKDDEELI NSSSLKLGFL VKYVVTLFTS NGEPFS LSL NDGGLDLDLH KTTDEKLLHQ TKIVFAKIGL SGNSYDFIWT TQMIANSNFN VCKRLTGRST GERLPRSVRS KVIYEMV KL VGETGMAILQ QLAFAQALNY EHRFYAVLAP KAQLGGARDL LVQETGTKVM HATTEMFSRN LLKTTSDDGL TNPHLKET I LNVGLDCLAN MRNLDGKPIS EGSNLVNFYK VICISGDNTK WGPIHCCSFF SGMMQQVLKN VPDWCSFYKL TFIKNLCRQ VEIPAGSIKK ILNVLRYRLC SKGGVEQHSE EDLRRLLTDN LDSWDGNDTV KFLVTTYISK GLMALNSYNH MGQGIHHATS SVLTSLAAV LFEELAIFYL KRSLPQTTVH VEHAGSSDDY AKCIVVTGIL SKELYSQYDE TFWKHACRLK NFTAAVQRCC Q MKDSAKTL VSDCFLEFYS EFMMGYRVTP AVIKFMFTGL INSSVTSPQS LMQACQVSSQ QAMYNSVPLV TNTAFTLLRQ QI FFNHVED FIRRYGILTL GTLSPFGRLF VPTYSGLVSS AVALEDAEVI ARAAQTLQMN SVSIQSSSLT TLDSLGRSRT SST AEDSSS VSDTTAASHD SGSSSSSFSF ELNRPLSETE LQFIKALSSL KSTQACEVIQ NRITGLYCNS NEGPLDRHNV IYSS RMADS CDWLKDGKRR GNLELANRIQ SVLCILIAGY YRSFGGEGTE KQVKASLNRD DNKIIEDPMI QLIPEKLRRE LERLG VSRM EVDELMPSIS PDDTLAQLVA KKLISLNVST EEYSAEVSRL KQTLTARNVL HGLAGGIKEL SLPIYTIFMK SYFFKD NVF LSLTDRWSTK HSTNYRDSCG KQLKGRIITK YTHWLDTFLG CSVSINRHTT VKEPSLFNPN IRCVNLITFE DGLRELS VI QSHLKVFENE FTNLNLQFSD PNRQKLRIVE SRPAESELEA NRAVIVKTKL FSATEQVRLS NNPAVVMGYL LDESAISE V KPTKVDFSNL LKDRFKIMQF FPSVFTLIKM LTDESSDSEK SGLSPDLQQV ARYSNHLTLL SRMIQQAKPT VTVFYMLKG NLMNTEPTVA ELVSYGIKEG RFFRLSDTGV DASTYSVKYW KILHCISAIG CLPLSQADKS SLLMSFLNWR VNMDIRTSDC PLSSHEASI LSEFDGQVIA NILASELSSV KRDSEREGLT DLLDYLNSPT ELLKKKPYLG TTCKFNTWGD SNRSGKFTYS S RSGESIGI FIAGKLHIHL SSESVALLCE TERQVLSWMS KRRTEVITKE QHQLFLSLLP QSHECLQKHK DGSALSVIPD SS NPRLLKF VPLKKGLAVV KIKKQILTVK KQVVFDAESE PRLQWGHGCL SIVYDETDTQ TTYHENLLKV KHLVDCSTDR KKL LPQSVF SDSKVVLSRI KFKTELLLNS LTLLHCFLKH APSDAIMEVE SKSSLLHKYL KSGGVRQRNT EVLFREKLNK VVIK DNLEQ GVEEEIEFCN NLTKTVSENP LPLSCWSEVQ NYIEDIGFNN VLVNIDRNTV KSELLWKFTL DTNVSTTSTI KDVRT LVSY VSTETIPKFL LAFLLYEEVL MNLINQCKAV KELINSTGLS DLELESLLTL CAFYFQSECS KRDGPRCSFA ALLSLI HED WQRIGKNILV RANNELGDVS LKVNIVLVPL KDMSKPKSER VVMARRSLNH ALSLMFLDEM SLPELKSLSV NCKMGNF EG QECFEFTILK DNSARLDYNK LIDHCVDMEK KREAVRAVED LILMLTGRAV KPSAVTQFVH GDEQCQEQIS LDDLMAND T VTDFPDREAE ALKTGNLGFN WDSD

UniProtKB: RNA-directed RNA polymerase L

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 63.0 K / Max: 77.0 K
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8574 / Average exposure time: 1.7 sec. / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4409446
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 485017
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 59.61
Output model

PDB-9ybm:
2.62A cryo-EM structure of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)

+
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