[English] 日本語
Yorodumi
- EMDB-9907: RdRp complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9907
TitleRdRp complex
Map dataNone
Sample
  • Virus: Cypovirus (cytoplasmic polyhedrosis viruses)
    • Protein or peptide: x 5 types
    • RNA: x 2 types
  • Ligand: x 5 types
KeywordsCypovirus / Transcription / RNA-dependent RNA polymerase / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid / viral genome replication / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
: / : / CPV, RNA-directed RNA polymerase, N-terminal / CPV, RNA-directed RNA polymerase, central polymerase domain / CPV, RNA-directed RNA polymerase, C-terminal / : / CPV Capsid shell protein VP1, small protrusion domain / : / Inner layer core protein VP1-like, C-terminal / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile.
Similarity search - Domain/homology
Viral structural protein 4 / RNA-directed RNA polymerase / VP1 / Inner capsid protein VP1
Similarity search - Component
Biological speciesCypovirus 1 / Cypovirus (cytoplasmic polyhedrosis viruses)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi XW
CitationJournal: J Mol Biol / Year: 2020
Title: Structure of RdRps Within a Transcribing dsRNA Virus Provides Insights Into the Mechanisms of RNA Synthesis.
Authors: Xiaowu Li / Li Wang / Xurong Wang / Wenyuan Chen / Tao Yang / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
Abstract: RNA-dependent RNA polymerases (RdRps) catalyze RNA synthesis of RNA viruses. During initiation of RNA synthesis, the RdRp catalyzes the formation of the first dinucleotide, acting as primer for ...RNA-dependent RNA polymerases (RdRps) catalyze RNA synthesis of RNA viruses. During initiation of RNA synthesis, the RdRp catalyzes the formation of the first dinucleotide, acting as primer for subsequent processive RNA elongation. Here, we present the structure of the RdRp complexes in the dinucleotide primed state in situ within a transcribing cypovirus under near physiological conditions using cryo-electron microscopy. The 3' end of RNA templates, paired RNA dinucleotide primer, incoming nucleotide, and catalytic divalent cations in the RdRp were resolved at 3.8 Å resolution. The end of the RNA template and the dinucleotide is buttressed by the aromatic tyrosine in a loop from the RdRp bracelet domain. Our structure reveals the interactions between the nucleotide substrates and the conserved residues during the RdRp initiation, and the coordinated structural changes preceding the elongation stage. In addition, it provides the direct evidence for existence of the slow step of the dinucleotide primed state in the viral RdRp transcription.
History
DepositionMay 16, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6k32
  • Surface level: 25
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k32
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9907.png

Downloads & links

-
Map

FileDownload / File: emd_9907.map.gz / Format: CCP4 / Size: 43.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 225 pix.
= 285.75 Å		1.27 Å/pix.
x 225 pix.
= 285.75 Å		1.27 Å/pix.
x 225 pix.
= 285.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 25.0 / Movie #1: 25
Minimum - Maximum-93.427059999999997 - 161.941570000000013
Average (Standard dev.)2.236893 (±16.143709999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-348-310-253
Dimensions225225225
Spacing225225225
CellA=B=C: 285.75 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z225225225
origin x/y/z0.0000.0000.000
length x/y/z285.750285.750285.750
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS-310-348-253
NC/NR/NS225225225
D min/max/mean-93.427161.9422.237

-
Supplemental data

-
Sample components

+
Entire : Cypovirus

EntireName: Cypovirus (cytoplasmic polyhedrosis viruses)
Components
  • Virus: Cypovirus (cytoplasmic polyhedrosis viruses)
    • Protein or peptide: RNA-dependent RNA polymerase
    • Protein or peptide: Viral structural protein 4
    • RNA: RNA (5'-R(P*UP*UP*AP*CP*U)-3')
    • RNA: RNA (5'-D(*(3PO))-R(*AP*G)-3'
    • Protein or peptide: VP1
    • Protein or peptide: VP1
    • Protein or peptide: VP1
  • Ligand: MAGNESIUM ION
  • Ligand: 7-METHYLGUANOSINE
  • Ligand: DIPHOSPHATE
  • Ligand: 2'-O-methyladenosine 5'-(dihydrogen phosphate)
  • Ligand: URIDINE 5'-TRIPHOSPHATE

+
Supramolecule #1: Cypovirus

SupramoleculeName: Cypovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / NCBI-ID: 10981 / Sci species name: Cypovirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

+
Macromolecule #1: RNA-dependent RNA polymerase

MacromoleculeName: RNA-dependent RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 137.058922 KDa
Recombinant expressionOrganism: invertebrate environmental sample (environmental samples)
SequenceString: TKLHNTIFSE TRKFTRESFK EIEHLTARLA NDRVARHDFL FNTSIVLISD YSGEDSNGNQ LQATITIPNE IINPKEYDPS DYPLAEDES FFKQGHKYDY LVTFRAGSLT NTYEPKTKMY KLHAALDKLM HVKQRKSRFA DLWRELCAVI ASLDVWYQTT N YPLRTYVK ...String:
TKLHNTIFSE TRKFTRESFK EIEHLTARLA NDRVARHDFL FNTSIVLISD YSGEDSNGNQ LQATITIPNE IINPKEYDPS DYPLAEDES FFKQGHKYDY LVTFRAGSLT NTYEPKTKMY KLHAALDKLM HVKQRKSRFA DLWRELCAVI ASLDVWYQTT N YPLRTYVK LLFHKGDEFP FYESPSQDRI IFNDKSVASI LPTFVYTCCQ VGTAIMSGIL THVESIVAMN HFLHCAKDSY ID EKLKIKG IGRSWYQEAL HNVCQATVPV WSQFNEVIGH RTKSTSEPHF VSSTFISLRA KRAELLYPEF NAYINRAIQL SKT QNDVAN YYAACRAMTN DGTFLATLTE LSLDAAVFPR IEQHLVTRPA VLMSNTRHES LKQKYTNGVG SIAQSYLSSF TDEI AKRVN GRHHDEAWLN FLTTSSPGRK LTEIEKLEVG GDVAAWSNSR IVMQAVFARE YRTPERIFKS LKAPIKLVER QQSDR RQRA ISGLDNDRLF LSFMPYTIGK QIYELNDNAA QGKQAGNAFD IGEMLYWTSQ RNVLLSSIDV AGMDASVTTN TKDIYN TFV LDVASKCTVP RFGPYYAKNM EVFEAGNRQS QVRYVNAAWQ ACALEAANSQ TSTSYESEIF GQVKNAEGTY PSGRADT ST HHTVLLQGLV RGNELKRASD GKNSCLATIK ILGDDIMEIF QGSESDTYDH AVSNASILNE SGFATTAELS QNSIVLLQ Q LVVNGTFWGF ADRISLWTRE DTKDIGRLNL AMMELNALID DLVFRVRRPE GLKMLGFFCG AICLRRFTLS VDNKLYDST YNNLSKYMTL TKYDKNPDSD STLMSLILPL AWLFMPRGGE YPAYPFERRD GTFTEDESMF TARGAYKRRL LYDVSNIGEM IQQNSMALD DDLLHEYGFT GALLLIDLNI LDLIDEVKKE DISPVKVSEL ATSLEQLGKL GEREKSRRAA SDLKIRGHAL S NDIVYGYG LQEKIQKSAM ATKETTVQSK RVSSRLHDVI VAKTRDYKIS TIPADALHLH EFEVEDVTVD LLPHAKHTSY SS LAYNMSF GSDGWFAFAL LGGLDRSANL LRLDVASIRG NYHKFSYDDP VFKQGYKIYK SDATLLNDFF TAISAGPKEQ GIL LRAFAY YSLYGNVEYH YVLSPRQLFF LSDNPVSAER LVRIPPKYYV STQCRALYNI FSYLHILRSI ANNRGKRLKM VLHP GLIAY VRG

UniProtKB: RNA-directed RNA polymerase

+
Macromolecule #2: Viral structural protein 4

MacromoleculeName: Viral structural protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 63.379449 KDa
Recombinant expressionOrganism: invertebrate environmental sample (environmental samples)
SequenceString: FAIDPLKHSK LYEEYGLYLR PHQINQEIKP TTIKKKELAP TIRSIKYASL IHSMLAEHAA RHNGTLINPR MYADMITLGN TKVTVTKGT PKAQIDTLKM NGLTVVSKSR RNNKKKPVSD TTATIDENTN AIVTYKALTE MSTLIESFRL PSGLTLIIFD D EKYQSLIP ...String:
FAIDPLKHSK LYEEYGLYLR PHQINQEIKP TTIKKKELAP TIRSIKYASL IHSMLAEHAA RHNGTLINPR MYADMITLGN TKVTVTKGT PKAQIDTLKM NGLTVVSKSR RNNKKKPVSD TTATIDENTN AIVTYKALTE MSTLIESFRL PSGLTLIIFD D EKYQSLIP NYINQLIAYT QPHIIPTWQG IADFSDTYLR SYFKRPFELT ASNLAAPQKH NLSPMTRSIF NNTGREDAVI RK LYGYGEY VFIKYEGCLI TWTGIYGEVT MMVNLSKRDL GLDVGDDYLK EYKKLLFYGV ITDAIPSGIS TRSTIMKISP HKM MNPSGG ALAVLSKFLE AVVSTNVINA TLVVYAEKGA GKTSFLSTYA EQLSLASGQV VGHLSSDAYG RWLAKTKDIE EPSF AYDYV LSLDTDDNES YYEQKASELL MSHGISEVAQ YELLSVRKKI KMMDEMNEVL IAQLENADTH SERNFYYMVS TGKTT PRIL IVEGHFNAQD ATIARTDTTV LLRTINDTTQ AMRDRQRGGV VQLFLRDTYY RLLPALHTTV YPFEMLESIK RWKWV

UniProtKB: Viral structural protein 4

+
Macromolecule #5: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 136.769422 KDa
Recombinant expressionOrganism: invertebrate environmental sample (environmental samples)
SequenceString: VQSRTDVFNE QFANEALHPM TKVIFNGLDV NTEVQPLSDD FKQISDPKGY LTYSVKYEDQ FTKKDKLRAS EADDRIVGPT VNLFKYGAA VVNIDLNRDF FDTATGIDLT KGIPLVQDLL VPIGVTAGAE QSAEYVSGLL MVLFKVMTDN RLVIVGETTT P MSNTLSTV ...String:
VQSRTDVFNE QFANEALHPM TKVIFNGLDV NTEVQPLSDD FKQISDPKGY LTYSVKYEDQ FTKKDKLRAS EADDRIVGPT VNLFKYGAA VVNIDLNRDF FDTATGIDLT KGIPLVQDLL VPIGVTAGAE QSAEYVSGLL MVLFKVMTDN RLVIVGETTT P MSNTLSTV VNNVLRTTYH NNVGVNPALL RDFTQVNWLN RDITNMLQQA GTKYGLGLTE TRLDYVRLVK TIVGHALNID HF AASVLNI NLRALMEANV TADDRIKALQ AHSMISTQFH GPNQGALRPE LAFDHDHIIR CLMLAAANYP RLEGIIVQIN TGY VASANV IRPVSEKRYF PENLEQNQSA ARLVSAVKAR ASEADISSIH LAIAREVSPM FNVHELKKIA ESFEDPSSIV VVLE FILFA LFFPTEFNRI KGDIQNVLLL FFSRWYPVEY GIFIQRGATY TINAAGEFEF SGRNEKWDQS LYLSEHFPAL FSDVP LAGA NTIIAIMRLF TPQGFLRTDD LAIAANFPRA SRNPQTYIPY TNQRGTVTNE FASRFRTIVA TLANVVNERA VQDDMQ KAT RSCTKQWLRH LETQFDNIAV AHTDHLSVVY ATMSNFMLNF TNNFSGNHAT FKPDQYVITS PEGSYKPIIE RQGETVD GL TIIDTSIVWP ILCQCTYPLV RQSGKGVDAV SIMEEIVYPD PSTTLSQSLS VAQVLSKLTL PDAFINMILS GGDSVVMR T YQTEADDDLD EGIRMTTYDQ YLSHIRERLH ITNVPDPIYI TGASTPDQIA ASVQATHVAV VLYQSGVING SASTYLREN EVLVVMPDYY DVVSRFANAN LQMNNNRYHE SVLEIADIFD QADFIQTSDA VRQLRALMPT LSTSQIRHAI ERIAQITDVD STDYGKLTL RFLGTLTRSL KMQNAQIRRI RPDGTVLRYD DQIDIEAFRW SRYFLDELRL RRLSVGLRLI TNPRIARRFD G VRIMYLTD DDPDPDFVPD VPEGYVAVQY AHRLFSSSLA NKRNRVTYTH PPTGMAYPSP TGRPHVHMTI NERAGMSKLV AD NIIASVI KSNWVVDIHD IEYTAEVMTP SEGYTQHVDA ESIMTAPKGK LFHLQFMDGL LRPEPSAFDP PASGEDMRLI YPL QPISVA RSMRAIVNHN EVDRPRGAVA PSSYEMDTGT LSRNGDLLYS PVANGQVGIP KLEVDHISFS NVVSMMTANI RTGD DMAVE RVNPDDVRAI NIRNA

UniProtKB: VP1

+
Macromolecule #6: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 135.002609 KDa
Recombinant expressionOrganism: invertebrate environmental sample (environmental samples)
SequenceString: ALHPMTKVIF NGLDVNTEVQ PLSDDFKQIS DPKGYLTYSV KYEDQFTKKD KLRASEADDR IVGPTVNLFK YGAAVVNIDL NRDFFDTAT GIDLTKGIPL VQDLLVPIGV TAGAEQSAEY VSGLLMVLFK VMTDNRLVIV GETTTPMSNT LSTVVNNVLR T TYHNNVGV ...String:
ALHPMTKVIF NGLDVNTEVQ PLSDDFKQIS DPKGYLTYSV KYEDQFTKKD KLRASEADDR IVGPTVNLFK YGAAVVNIDL NRDFFDTAT GIDLTKGIPL VQDLLVPIGV TAGAEQSAEY VSGLLMVLFK VMTDNRLVIV GETTTPMSNT LSTVVNNVLR T TYHNNVGV NPALLRDFTQ VNWLNRDITN MLQQAGTKYG LGLTETRLDY VRLVKTIVGH ALNIDHFAAS VLNINLRALM EA NVTADDR IKALQAHSMI STQFHGPNQG ALRPELAFDH DHIIRCLMLA AANYPRLEGI IVQINTGYVA SANVIRPVSE KRY FPENLE QNQSAARLVS AVKARASEAD ISSIHLAIAR EVSPMFNVHE LKKIAESFED PSSIVVVLEF ILFALFFPTE FNRI KGDIQ NVLLLFFSRW YPVEYGIFIQ RGATYTINAA GEFEFSGRNE KWDQSLYLSE HFPALFSDVP LAGANTIIAI MRLFT PQGF LRTDDLAIAA NFPRASRNPQ TYIPYTNQRG TVTNEFASRF RTIVATLANV VNERAVQDDM QKATRSCTKQ WLRHLE TQF DNIAVAHTDH LSVVYATMSN FMLNFTNNFS GNHATFKPDQ YVITSPEGSY KPIIERQGET VDGLTIIDTS IVWPILC QC TYPLVRQSGK GVDAVSIMEE IVYPDPSTTL SQSLSVAQVL SKLTLPDAFI NMILSGGDSV VMRTYQTEAD DDLDEGIR M TTYDQYLSHI RERLHITNVP DPIYITGAST PDQIAASVQA THVAVVLYQS GVINGSASTY LRENEVLVVM PDYYDVVSR FANANLQMNN NRYHESVLEI ADIFDQADFI QTSDAVRQLR ALMPTLSTSQ IRHAIERIAQ ITDVDSTDYG KLTLRFLGTL TRSLKMQNA QIRRIRPDGT VLRYDDQIDI EAFRWSRYFL DELRLRRLSV GLRLITNPRI ARRFDGVRIM YLTDDDPDPD F VPDVPEGY VAVQYAHRLF SSSLANKRNR VTYTHPPTGM AYPSPTGRPH VHMTINERAG MSKLVADNII ASVIKSNWVV DI HDIEYTA EVMTPSEGYT QHVDAESIMT APKGKLFHLQ FMDGLLRPEP SAFDPPASGE DMRLIYPLQP ISVARSMRAI VNH NEVDRP RGAVAPSSYE MDTGTLSRNG DLLYSPVANG QVGIPKLEVD HISFSNVVSM MTANIRTGDD MAVERVNPDD VRAI NIRNA

UniProtKB: VP1

+
Macromolecule #7: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 137.422234 KDa
Recombinant expressionOrganism: invertebrate environmental sample (environmental samples)
SequenceString: KKPPTVVQSR TDVFNEQFAN EALHPMTKVI FNGLDVNTEV QPLSDDFKQI SDPKGYLTYS VKYEDQFTKK DKLRASEADD RIVGPTVNL FKYGAAVVNI DLNRDFFDTA TGIDLTKGIP LVQDLLVPIG VTAGAEQSAE YVSGLLMVLF KVMTDNRLVI V GETTTPMS ...String:
KKPPTVVQSR TDVFNEQFAN EALHPMTKVI FNGLDVNTEV QPLSDDFKQI SDPKGYLTYS VKYEDQFTKK DKLRASEADD RIVGPTVNL FKYGAAVVNI DLNRDFFDTA TGIDLTKGIP LVQDLLVPIG VTAGAEQSAE YVSGLLMVLF KVMTDNRLVI V GETTTPMS NTLSTVVNNV LRTTYHNNVG VNPALLRDFT QVNWLNRDIT NMLQQAGTKY GLGLTETRLD YVRLVKTIVG HA LNIDHFA ASVLNINLRA LMEANVTADD RIKALQAHSM ISTQFHGPNQ GALRPELAFD HDHIIRCLML AAANYPRLEG IIV QINTGY VASANVIRPV SEKRYFPENL EQNQSAARLV SAVKARASEA DISSIHLAIA REVSPMFNVH ELKKIAESFE DPSS IVVVL EFILFALFFP TEFNRIKGDI QNVLLLFFSR WYPVEYGIFI QRGATYTINA AGEFEFSGRN EKWDQSLYLS EHFPA LFSD VPLAGANTII AIMRLFTPQG FLRTDDLAIA ANFPRASRNP QTYIPYTNQR GTVTNEFASR FRTIVATLAN VVNERA VQD DMQKATRSCT KQWLRHLETQ FDNIAVAHTD HLSVVYATMS NFMLNFTNNF SGNHATFKPD QYVITSPEGS YKPIIER QG ETVDGLTIID TSIVWPILCQ CTYPLVRQSG KGVDAVSIME EIVYPDPSTT LSQSLSVAQV LSKLTLPDAF INMILSGG D SVVMRTYQTE ADDDLDEGIR MTTYDQYLSH IRERLHITNV PDPIYITGAS TPDQIAASVQ ATHVAVVLYQ SGVINGSAS TYLRENEVLV VMPDYYDVVS RFANANLQMN NNRYHESVLE IADIFDQADF IQTSDAVRQL RALMPTLSTS QIRHAIERIA QITDVDSTD YGKLTLRFLG TLTRSLKMQN AQIRRIRPDG TVLRYDDQID IEAFRWSRYF LDELRLRRLS VGLRLITNPR I ARRFDGVR IMYLTDDDPD PDFVPDVPEG YVAVQYAHRL FSSSLANKRN RVTYTHPPTG MAYPSPTGRP HVHMTINERA GM SKLVADN IIASVIKSNW VVDIHDIEYT AEVMTPSEGY TQHVDAESIM TAPKGKLFHL QFMDGLLRPE PSAFDPPASG EDM RLIYPL QPISVARSMR AIVNHNEVDR PRGAVAPSSY EMDTGTLSRN GDLLYSPVAN GQVGIPKLEV DHISFSNVVS MMTA NIRTG DDMAVERVNP DDVRAINIRN A

UniProtKB: VP1

+
Macromolecule #3: RNA (5'-R(P*UP*UP*AP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*AP*CP*U)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 1.507928 KDa
SequenceString:
UUACU

+
Macromolecule #4: RNA (5'-D(*(3PO))-R(*AP*G)-3'

MacromoleculeName: RNA (5'-D(*(3PO))-R(*AP*G)-3' / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Cypovirus 1
Molecular weightTheoretical: 869.394 Da
SequenceString:
(3PO)AG

+
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #9: 7-METHYLGUANOSINE

MacromoleculeName: 7-METHYLGUANOSINE / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG7
Molecular weightTheoretical: 298.275 Da
Chemical component information

ChemComp-MG7:
7-METHYLGUANOSINE

+
Macromolecule #10: DIPHOSPHATE

MacromoleculeName: DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: DPO
Molecular weightTheoretical: 173.943 Da
Chemical component information

ChemComp-DPO:
DIPHOSPHATE

+
Macromolecule #11: 2'-O-methyladenosine 5'-(dihydrogen phosphate)

MacromoleculeName: 2'-O-methyladenosine 5'-(dihydrogen phosphate) / type: ligand / ID: 11 / Number of copies: 1 / Formula: A2M
Molecular weightTheoretical: 361.248 Da
Chemical component information

ChemComp-0AV:
2'-O-methyladenosine 5'-(dihydrogen phosphate)

+
Macromolecule #12: URIDINE 5'-TRIPHOSPHATE

MacromoleculeName: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: UTP
Molecular weightTheoretical: 484.141 Da
Chemical component information

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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