[English] 日本語
Yorodumi
- EMDB-38746: ASFV RNAP M1249L C-tail occupied complex1 (MCOC1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38746
TitleASFV RNAP M1249L C-tail occupied complex1 (MCOC1)
Map data
Sample
  • Complex: ASFV RNAP M1249L C-tail occupied complex1 (MCOC1)
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsASFV / RNAP / M1249L C-tail occupied complex1 (MCOC1) / TRANSCRIPTION
Function / homology
Function and homology information


viral transcription / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / virion component / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / host cell cytoplasm ...viral transcription / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / virion component / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / host cell cytoplasm / transcription by RNA polymerase II / protein dimerization activity / DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. ...RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
C122R / DNA-directed RNA polymerase RPB5 homolog / DNA-directed RNA polymerase RPB10 homolog / C147L / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase RPB3-11 homolog / D339L / M1249L / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsZhu GL / Zhu Y / Zhu ZX / Sun F / Zheng HX
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFD1800100 China
Ministry of Science and Technology (MoST, China)2021YFD1801300 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of RNA polymerase complexes in African swine fever virus.
Authors: Guoliang Zhu / Fei Xi / Wuxia Zeng / Yifei Zhao / Weijun Cao / Chen Liu / Fan Yang / Yi Ru / Shuqi Xiao / Shilei Zhang / Huanan Liu / Hong Tian / Fayu Yang / Biao Lu / Shukai Sun / Haiyang ...Authors: Guoliang Zhu / Fei Xi / Wuxia Zeng / Yifei Zhao / Weijun Cao / Chen Liu / Fan Yang / Yi Ru / Shuqi Xiao / Shilei Zhang / Huanan Liu / Hong Tian / Fayu Yang / Biao Lu / Shukai Sun / Haiyang Song / Bozhang Sun / Xiaoyi Zhao / Lijie Tang / Kangli Li / Jijun He / Jianhong Guo / Yun Zhu / Zixiang Zhu / Fei Sun / Haixue Zheng /
Abstract: African swine fever virus is highly contagious and causes a fatal infectious disease in pigs, resulting in a significant global impact on pork supply. The African swine fever virus RNA polymerase ...African swine fever virus is highly contagious and causes a fatal infectious disease in pigs, resulting in a significant global impact on pork supply. The African swine fever virus RNA polymerase serves as a crucial multifunctional protein complex responsible for genome transcription and regulation. Therefore, it is essential to investigate its structural and functional characteristics for the prevention and control of African swine fever. Here, we determine the structures of endogenous African swine fever virus RNA polymerase in both nucleic acid-free and elongation states. The African swine fever virus RNA polymerase shares similarities with the core of typical RNA polymerases, but possesses a distinct subunit M1249L. Notably, the dynamic binding mode of M1249L with RNA polymerase, along with the C-terminal tail insertion of M1249L in the active center of DNA-RNA scaffold binding, suggests the potential of M1249L to regulate RNA polymerase activity within cells. These results are important for understanding the transcription cycle of the African swine fever virus and for developing antiviral strategies.
History
DepositionJan 17, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38746.png

Downloads & links

-
Map

FileDownload / File: emd_38746.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.739599 - 3.3274553
Average (Standard dev.)0.0011496379 (±0.08406813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_38746_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38746_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38746_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : ASFV RNAP M1249L C-tail occupied complex1 (MCOC1)

EntireName: ASFV RNAP M1249L C-tail occupied complex1 (MCOC1)
Components
  • Complex: ASFV RNAP M1249L C-tail occupied complex1 (MCOC1)
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase RPB3-11 homolog
    • Protein or peptide: DNA-directed RNA polymerase RPB5 homolog
    • Protein or peptide: D339L
    • Protein or peptide: C122R
    • Protein or peptide: DNA-directed RNA polymerase RPB10 homolog
    • Protein or peptide: M1249L
    • Protein or peptide: C147L
    • Protein or peptide: DNA-directed RNA polymerase subunit
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: ASFV RNAP M1249L C-tail occupied complex1 (MCOC1)

SupramoleculeName: ASFV RNAP M1249L C-tail occupied complex1 (MCOC1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: African swine fever virus

+
Macromolecule #1: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 139.203438 KDa
SequenceString: ITYGPIETVD NEELTEADML SFISAAVNST GLIGYNIKSF DDLMDNGIPQ IVKQMFNVDI TYKDQRDHTE IDKLRESVQI QFNFTDVNI ERPQHRNYSQ GNKINLLPNK ARLCGLSYSG PVNLAAEVIL TAHYSNGRQE VKRASIPPFQ VSTFPIMRGS N RCHTHHLS ...String:
ITYGPIETVD NEELTEADML SFISAAVNST GLIGYNIKSF DDLMDNGIPQ IVKQMFNVDI TYKDQRDHTE IDKLRESVQI QFNFTDVNI ERPQHRNYSQ GNKINLLPNK ARLCGLSYSG PVNLAAEVIL TAHYSNGRQE VKRASIPPFQ VSTFPIMRGS N RCHTHHLS KTAKKEIGED PNEPGGYFIA RGGEWVVDLL ENIRFNTLHI HYHTMQQGNN EIIRGEFISQ PGGAFENSSQ II IRYMTTG AITIEINSTK FSKLRIPWYL IFRMFGMTGD DSIIEQVVFD LESNSLVNTF MIEILEKSIH VLDPIFQPVQ HEL NREKII QFLSEKVSKF VSNPSAYKSD ENAVQYLNER QLTILDKILL PHMGQTADTR VRKLRFLGLL IHKILLVIMN VFPP TDRDS YRTKRVHGSG VSLAKAFKAI FNTSVIAPII NGFKELLKQT AFEELTQRNI IEAFSAALSK NTASDLNRSM EQSII SGNK TIMVRQRPIV NRVSTQSLER KNLLNTISAL RTVNTHNTTN ASKQTERADM MRRVHASYPG YICVAQSADT GEKVGM SKQ LAITANVCTA GEVLSLKQRL LSDPAIQQLA DVSNKDIVRK GLARVFINGE WIGCCTNAFE LAQRYRMLRR EGKVVHP HT TIYWDSMVDE VEFWLDVGRL TRPLLIVDNN IEKYNQACYK AAEARKKGDK DWEKHKIPFI QNTRFTPQMA KDILAGTL T LEDLVAQGIC EFITPEEAEN CLVAFSIIEL RKHKHDVTRR FTHVDVPQAI LGLAALVSPY ANCTQPARVT YETNQGRQT GGWYCFSWPY RVDMNRFFQF YNEMPLVKTI AHNYVIPNGL NTIVAYMIYG GYNQEDSVIV SQSFIDRGGF AGTFYREEKV ELESDIESF GKPDPLITKN LKPGANYEKL VDGFVPVGTV VKKGDIIIGK VAKIRGEKDE LNKYIDRSVM YGFDEPAVVD A VMRPHGPN DEIFGLMRLR YERNLNIGDK MSSRSGNKGI AALALPTSDM PFTEDGLQPD LIVNPHSHPS RMTNGQMIET TV GLANALQ GVVTDGTAFL PINVQLLSER LAQEGLRFNG CQKMFNGQTG EYFDAAIFIG PTYHQRLQKF VLDDRYAVAS YGP TDALTG QPLDGKRSHG GLRLGEMEHW VLTAQGAMQT IIEKSHDDSD GCISYICRNC GEPAIYNASH PIYKCMNCDV QADI GMVDS RRSSIVFQHE MRAANVNITS VLSPRVFQPA

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #2: DNA-directed RNA polymerase RPB3-11 homolog

MacromoleculeName: DNA-directed RNA polymerase RPB3-11 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 41.418137 KDa
SequenceString: MEKIFQNVEI KPFLIDFSNL FIKNAAKKLF QLEEQLPLVP VNVVMDFKGI SRAAVHGLSR VLQDEIPNYM LDIKPGGYKI EDSTDLFMT EQFIRNRINF IPIYAKNETL VFALRSLNNS CEVKTIYSRD LIQVAGPKLK YPIFNPTFEI GFLQPGKSLI I EDIYIKKG ...String:
MEKIFQNVEI KPFLIDFSNL FIKNAAKKLF QLEEQLPLVP VNVVMDFKGI SRAAVHGLSR VLQDEIPNYM LDIKPGGYKI EDSTDLFMT EQFIRNRINF IPIYAKNETL VFALRSLNNS CEVKTIYSRD LIQVAGPKLK YPIFNPTFEI GFLQPGKSLI I EDIYIKKG IGRKHAAFNL AVKTHFSHLD IEQYPTDKKE YMALSGYKQS SMTSDPRHHR LGLCFPAVPL PHINQAVRTY LK NACRIII GRIQSIQKIY ENFEEPQPEL VLFSMDEEKT KAIITIKDET HTIGNLLKTY IYEMIPDISF VGYQCVPHKQ EMV LTIIHK ASQEDLITLL EKSIQNIIQT FQILEKNVDE LIA

UniProtKB: DNA-directed RNA polymerase RPB3-11 homolog

+
Macromolecule #3: DNA-directed RNA polymerase RPB5 homolog

MacromoleculeName: DNA-directed RNA polymerase RPB5 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 23.693711 KDa
SequenceString: MAMQKLFTYI YEFIEYRKMV LLEEKVPYDK FVQMVLNTGF FRINAETLNH GIVSVFIFGA NGKYVHHGGD MRTLLTNTLN EKKHYEELI LIVDKPVLSK KNILDIIVEQ RAANPTIVIN IYPYHLFCIN IPKVSAIPKH KLITQEEAQE FLGREYLQPQ D LMQISASD ...String:
MAMQKLFTYI YEFIEYRKMV LLEEKVPYDK FVQMVLNTGF FRINAETLNH GIVSVFIFGA NGKYVHHGGD MRTLLTNTLN EKKHYEELI LIVDKPVLSK KNILDIIVEQ RAANPTIVIN IYPYHLFCIN IPKVSAIPKH KLITQEEAQE FLGREYLQPQ D LMQISASD PPVVWLGGRP GDFVQIERPS ETAMHAVVIR FITKSKI

UniProtKB: DNA-directed RNA polymerase RPB5 homolog

+
Macromolecule #4: D339L

MacromoleculeName: D339L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 38.22798 KDa
SequenceString: MIDQKIFETT LNIDDPTNFC TNVEAHLLKE LENIYVGKCF KNSFILNITG VIQRSPCFIM RTNNSGRGYM HVRFSAVVSY LNAFDLIAA VKIIKNDSNI ILGESLLTEP VTIVIPSSES QNNVAEVGQI VPVQLANSSV YYIPGRQQAS ATGSIFIPKH T FSVYHVQE ...String:
MIDQKIFETT LNIDDPTNFC TNVEAHLLKE LENIYVGKCF KNSFILNITG VIQRSPCFIM RTNNSGRGYM HVRFSAVVSY LNAFDLIAA VKIIKNDSNI ILGESLLTEP VTIVIPSSES QNNVAEVGQI VPVQLANSSV YYIPGRQQAS ATGSIFIPKH T FSVYHVQE ELTQEQALNL TKLVNIIEML LESRSKKDFK QICFFEKLYY TYSISSDEIL DLKIWKGPKG KEMSRLKPCN VL SFLYDAL KNKNSSLGFW ARPPNLLKSS PLAYQQDQNS FNATELPIIC SAEVMFVTLL KEIINYLQFI NDLCDTFNNE QLI KRHENI WMLIEQRK

UniProtKB: D339L

+
Macromolecule #5: C122R

MacromoleculeName: C122R / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 11.831861 KDa
SequenceString:
MKICKACSSC MVRTYVDGNI IFRCSCGESV QGDSQNLLVS SKVYHTGEME DKYKIFIKNA PFDPTNCQIK KDCPNCHLDY LTQICIGSQ KIIILVCRCG YMSNRG

UniProtKB: C122R

+
Macromolecule #6: DNA-directed RNA polymerase RPB10 homolog

MacromoleculeName: DNA-directed RNA polymerase RPB10 homolog / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 9.04079 KDa
SequenceString:
MLIPVVCFTC GFPIGTYAAI FDKARTEYIK TKMGGTLPQN IPLDASLQIE LKDLITALGI PMRVCCRTHL ITTLDYRKYY

UniProtKB: DNA-directed RNA polymerase RPB10 homolog

+
Macromolecule #7: M1249L

MacromoleculeName: M1249L / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 137.040656 KDa
SequenceString: KLPDLSMPIE AYIRQLLVDP DVVPIVSEKK KELRVRPSTR KEIFLINGTH LAVPAEAPIE IYGLKLRLKT FSPQCFMRMA EIGSFSPET LGYVASGANL TNFIRVFMKC VDQETWKKNG EGVVVTTKEN IIQFTHQYIE LYKFLRSGGH SWLINRLAEE M VHRKLDRE ...String:
KLPDLSMPIE AYIRQLLVDP DVVPIVSEKK KELRVRPSTR KEIFLINGTH LAVPAEAPIE IYGLKLRLKT FSPQCFMRMA EIGSFSPET LGYVASGANL TNFIRVFMKC VDQETWKKNG EGVVVTTKEN IIQFTHQYIE LYKFLRSGGH SWLINRLAEE M VHRKLDRE DQGSHISNIV ETEEIEPEEN IKRVIFFLKE LSTMYSVSPV FTSGYMPLLY DLYRAGYLEV LWNPVEQKFL QH AEQREKE QMILQQVDMK LTEVITQARQ YFKIMEEKIG RVQSDAIREI LTMEGKVDDP NSILQEVIKA CGKQEAELIT TEY LNIKKQ WELQEKNACA HLKLVKQLRS GLQYAELLKV LESIRVLYKE KNNTTNWNLC KACGFKLLCP HVDMLIQLQA AEAS YDTMR TKLMKFSGIN KEKENNQGLI YSYFCKICGE ELAHFIQEDR TADVGIIGDL NSKLRVFIWQ ETMKACTFIH FGKLV DVKQ FANIAVNVCL PLVYSIENIK KEEDYDPLTQ LYAVIYIYAY ILNLIYSSQK NKEFLTITIH GMKADSSLNA YVTFLL EKM MQQYSGIINQ LSEITDQWIA NNFREAFKKI IHQNGLQGLS VQDDTKVLLT EILLDPMYDY AATVARIDGS IPMHKPR TP KEAEYEFKTV IGRTPAELLS QKEFYDKIYT SKYRPDFTQL TRLNDIYFQE ESLRVWWGGR DEEKTSTLIY LRAYELFL K YLQNAPNFNS ELAEFKTYEN AYGEQKALLA QQGFYNIFDP NTGRADQRTR LFEYKRLPIS TLYDERGLPH KWTIYVYKA VDSSQKPAEI EVTRKDVIKK IDNHYALADL RCSVCHVLQH EVGQLNIKKV QTALKASLEF NTFYAFYESR CPKGGLHDFQ DKKCVKCGL FTYIIYDHLS QPELVHDYYN NYKDQYDKEK MSIRSIQIKK DMTTPSTETQ PKPPQEPWTF DYGKIIKTAK I LDISPAVI EAIGAMEGRS YADIREGQGA PPPPTSMDDP RLMAVDSAVR IFLYNYNCLR HVSTFNKPPI HVERLVKHLS YE EKEDLEK VLPNVVNEYH TTFKHLRVTD PASALLYSIE FLCISFLTLY EIKEPSWVVN IVREFALTEL NTIIQSEKLL SKP GAFNFM IFGEDFVCSG EDSSMDDISA YSSPGLFGED IIDRLDDPFS IEDVDISLDV LDNLAPQ

UniProtKB: M1249L

+
Macromolecule #8: C147L

MacromoleculeName: C147L / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 15.765938 KDa
SequenceString:
LIMDDLVEEY VETEEENLVD SEEESEDKDE IVESPSICEG FVQASSQTLV IIPDNERITS NVLTTFEATR LVAVRAQQLA INGSTMLKK KYSSPIDIAK QELFNRKIPL LVMRCIKVTP EGQKIVEIWN PREMGIPLLD

UniProtKB: C147L

+
Macromolecule #9: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 162.830625 KDa
SequenceString: MEAGYAEIAA VQFNIAGDND HKRQGVMEVT ISNLFEGTLP AEGGIYDARM GTTDHHYKCI TCSHQRKQCM GHPGILQMHA PVLQPLFIA EIRRWLRVIC LNCGAPIVDL KRYEHLIRPK RLIEAASSQT EGKQCYVCKA VHPKIVKDSE DYFTFWADQQ G KIDKLYPQ ...String:
MEAGYAEIAA VQFNIAGDND HKRQGVMEVT ISNLFEGTLP AEGGIYDARM GTTDHHYKCI TCSHQRKQCM GHPGILQMHA PVLQPLFIA EIRRWLRVIC LNCGAPIVDL KRYEHLIRPK RLIEAASSQT EGKQCYVCKA VHPKIVKDSE DYFTFWADQQ G KIDKLYPQ IIREIFSRVT YDTVVKLGRS KNSHPEKLVL KAIQIPPISI RPGIRLGIGS GPQSFHDINN VIQYLVRKNL LI PKDLQIV RGQKIPLNID RNLQTIQQLY YNFLLDSVST TATQGGTGKR GIVMGARPAP SIMRRLPRKE GRIRKSLLGS QVW SISRST ICGNSDLHLD EVGYPISFAR TLQVAETVQH YNINRLMPYF LNGKRQYPGC SRVYKQITQS VHDIEGLKQD FRLE VGDIL YRDVVTGDVA FFNRQPSLER SSIGVHRIVV LENPKISTFQ MNVSACAWYN ADFDGDQMNL WVPWSVMSRV EAELL CSVR NWFISTKSSG PVNGQVQDST VGSFLLTRTN TPMGKNVMNK LHAMGLFQTT QTDPPCFANY SPTDLLDGKS VVSMLL RQT PINYQRAPTW YSEVYAPYMH YNKQDISTQI RNGELIEGVL DKKAVGAGSS GGIYHLISRR YGPQQALKMI FATQQLA LN YVRNAGFTVS TADMLLTPEA HQEVQEIINE LLLESEEINN RLLHGDIMPP IGLTTHDFYE KLQLNALKFP DRILKPIM N SINPETNGLF QMVATGAKGS NPNMIHIMAG IGQIEINTQR IQPQFSFGRT LVYYPRFALE AQAYGFICNS YIAGLTSPE FIFGEMNGRF DLINKALSTS STGYANRKAI FGLQSCIVDY YRRVSIDTRL VQQLYGEDGL DARQLETVRF ETIMLSDQEL EDKFKYTGI QSPLFEEEFS RLKKDRDKYR QIFLNVENFN FSQLLTDVRQ VPVNVASIVK NILLSSTSGV LPFDEKSILQ K YAMVKTFC KNLPYVFINN IQERLQTPIP VYLKRAASLM RMLIRIELAT VKTLNITCEQ MSAILDLIRL QYTQSLINYG EA VGILAAQ SVSEPLTQYM LDSHHRSVAG GTNKSGIVRP QEIFSAKPVE AEQSSEMLLR LKNPEVETNK TYAQEIANSI ELI TFERLI LQWHLLYETY SSTKKNVMYP DFASDVEWMT DFLENHPLLQ PPEDIANWCI RLELNKTTMI LKSISLESII NSLR AKHPN TYIMHSVENT ASGIPIIIRI YLRESAFRRS TNTRMATDEK IAVNVVDKLL NSTIRGIPGI KNANVVKLMR HRVDA QGKL VRLDNIYAIK TNGTNIFGAM LDDNIDPYTI VSSSIGDTME LYGIEAARQK IISEIRTVMG DKGPNHRHLL MYADLM TRT GQVTSLEKAG LNAREPSNVL LRMALSSPVQ VLTDAAVDSA VNPIYGIAAP TLMGSVPRIG TMYSDIIMDE KYITENY

UniProtKB: DNA-directed RNA polymerase subunit

+
Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372305
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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