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- EMDB-6969: Structure of RNA polymerase complex and genome within a dsRNA vir... -

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Basic information

Entry
Database: EMDB / ID: EMD-6969
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Map dataIcosahedral capsid of aquareovirus
Sample
  • Virus: Grass carp reovirus
    • Protein or peptide: Outer capsid VP7
    • Protein or peptide: N-terminus of outer capsid protein VP5
    • Protein or peptide: C-terminus of outer capsid protein VP5
    • Protein or peptide: Core protein VP6
    • Protein or peptide: VP1
    • Protein or peptide: VP3
  • Ligand: MYRISTIC ACID
Function / homology
Function and homology information


host cell surface binding / viral inner capsid / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...host cell surface binding / viral inner capsid / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase / hydrolase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Outer capsid protein VP7 / Outer capsid protein VP7 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family ...Outer capsid protein VP7 / Outer capsid protein VP7 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer capsid VP7 / Core protein VP6 / Putative outer capsid VP4 / RNA helicase / VP1
Similarity search - Component
Biological speciesGrass carp reovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu H / Fang Q / Cheng L
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.
Authors: Xurong Wang / Fuxian Zhang / Rui Su / Xiaowu Li / Wenyuan Chen / Qingxiu Chen / Tao Yang / Jiawei Wang / Hongrong Liu / Qin Fang / Lingpeng Cheng /
Abstract: Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together ...Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.
History
DepositionMay 12, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseJul 4, 2018-
UpdateJul 25, 2018-
Current statusJul 25, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zvt
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5zvt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6969.png

Downloads & links

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Map

FileDownload / File: emd_6969.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral capsid of aquareovirus
Voxel sizeX=Y=Z: 0.932 Å
Density
Contour LevelBy AUTHOR: 9. / Movie #1: 9
Minimum - Maximum-88.945359999999994 - 134.412659999999988
Average (Standard dev.)0.6796208 (±8.760672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-450-450-450
Dimensions900900900
Spacing900900900
CellA=B=C: 838.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9320.9320.932
M x/y/z900900900
origin x/y/z0.0000.0000.000
length x/y/z838.800838.800838.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-450-450-450
NC/NR/NS900900900
D min/max/mean-88.945134.4130.680

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Supplemental data

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Mask #1

Fileemd_6969_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Grass carp reovirus

EntireName: Grass carp reovirus
Components
  • Virus: Grass carp reovirus
    • Protein or peptide: Outer capsid VP7
    • Protein or peptide: N-terminus of outer capsid protein VP5
    • Protein or peptide: C-terminus of outer capsid protein VP5
    • Protein or peptide: Core protein VP6
    • Protein or peptide: VP1
    • Protein or peptide: VP3
  • Ligand: MYRISTIC ACID

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Supramolecule #1: Grass carp reovirus

SupramoleculeName: Grass carp reovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / NCBI-ID: 128987 / Sci species name: Grass carp reovirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Ctenopharyngodon idella (grass carp)

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Macromolecule #1: Outer capsid VP7

MacromoleculeName: Outer capsid VP7 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 29.844648 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MPLHMIPQVA HAMVRAAAAG RLTLYTRTRT ETTNFDHAEY VTCGRYTICA FCLTTLAPHA NVKTIQDSHA CSRQPNEAIR SLVEVSDKA QTALVGSRTV DYHELDVKAG FVAPTADETI APSKDIVELP FRTCDLDDSS ATACVRNHCQ AGHDGVIHLP I LSGDFKLP ...String:
MPLHMIPQVA HAMVRAAAAG RLTLYTRTRT ETTNFDHAEY VTCGRYTICA FCLTTLAPHA NVKTIQDSHA CSRQPNEAIR SLVEVSDKA QTALVGSRTV DYHELDVKAG FVAPTADETI APSKDIVELP FRTCDLDDSS ATACVRNHCQ AGHDGVIHLP I LSGDFKLP NEHPTKPLDD THPHDKVLTR CPKTGLLLVH DTHAHATAVV ATAATRAILM HDLLTSANAD DGHQARSACY GP AFNNLTF ACHSTCASDM AHFDCGQIVG LDLHVEPSD

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Macromolecule #2: N-terminus of outer capsid protein VP5

MacromoleculeName: N-terminus of outer capsid protein VP5 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 4.302686 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString:
MGNVQTSVNT YNITGDGNSF TPTSDMTSTA APAIDLKPGV LN

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Macromolecule #3: C-terminus of outer capsid protein VP5

MacromoleculeName: C-terminus of outer capsid protein VP5 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 64.362086 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: PTGKLWRPVG TSVATIDSLA IVSDRFGQYS FVNEGMRETF SKALFDINMW QPLFQATKTG CGPIVLSSFT TTTSGYVGAT AGDALDNPV TNGVFISTVQ IMNLQRTIAA RMRDVALWQK HLDTAMTMLT PDISAGSASC NWKSLLAFAK DILPLDNLCL T YPNEFYNV ...String:
PTGKLWRPVG TSVATIDSLA IVSDRFGQYS FVNEGMRETF SKALFDINMW QPLFQATKTG CGPIVLSSFT TTTSGYVGAT AGDALDNPV TNGVFISTVQ IMNLQRTIAA RMRDVALWQK HLDTAMTMLT PDISAGSASC NWKSLLAFAK DILPLDNLCL T YPNEFYNV AIHRYPALKP GNPDTKLPDA QAHPLGEVAG AFNAATSEVG SLVGSSSTLS QAISTMAGKD LDLIEADTPL PV SVFTPSL APRSYRPAFI KPEDAKWIAE FNNSSLIRKT LTYSGATYTV QLGPGPTRVI DMNAMIDSVL TLDVSGTILP YDT NPDLST SVPAFVLIQT SVPIQQVTTA ANITAITVVS AAGASAINLA INVRGQPRFN MLHLQATFER ETITGIPYIY GLGT FLIPS PTSSSNFSNP TLMDGLLTVT PVLLRETTYK GEVVDAIVPA TVMANQTSEE VASALANDAI VLVSNHLNKL ANVVG DAIP VASRTDDSAT SAIVSRLAVQ HKLSQVGQAS PTPPDYPLLW RRAKRAASMF VSNPSLALQV GIPVLTQSGM LSALTS GVG TALRTGSLGK GVTDASEKLR ARQSLTVAKQ AFFDQIGSLW PGK

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Macromolecule #4: Core protein VP6

MacromoleculeName: Core protein VP6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 44.606535 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MAQRQFFGLT YNFYGQPAPL FDLNDLQELA GCYARPWTSR FSHLAISTGS LPVWSARYPS VASRNIVVNT LLGAHLNPFA GGQITSHQG ITWRDPVLSS LAPVPAIQPP PVWAVAENVL LDSNNYPTYV LNLSSMWPIN QDVHIMTMWA LSDQGPIYHL E VPVDPMPA ...String:
MAQRQFFGLT YNFYGQPAPL FDLNDLQELA GCYARPWTSR FSHLAISTGS LPVWSARYPS VASRNIVVNT LLGAHLNPFA GGQITSHQG ITWRDPVLSS LAPVPAIQPP PVWAVAENVL LDSNNYPTYV LNLSSMWPIN QDVHIMTMWA LSDQGPIYHL E VPVDPMPA ATTAALMAYT GVPIAHLAQT AYRFAGQLPQ SPDSTMVSTI RWLSAIWFGS LTGRLNRSRT CNGFYFEFAK PA LNPDQAV LKWNDGARAA PPAAAQSSYI RCISPHWQHQ IVEVAGALMS QSVTAVTGLP ALIDEATLPA WSQGVANLTG NGQ GVVPCL DYNPVPMAAA RHLQWRQDGL ITAAQEAQLN NDYTAYALTI ERHLTAMLVA NPIAAGRMPI QPFNAADFGQ AGQT AAAVA LAQAMFV

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Macromolecule #5: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 141.512156 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MAAVFGIQLV PKLNTSTTRR TFLPLRFDLL LDRLQSTNLH GVLYRALDFN PVDRSATVIQ TYPPLNAWSP HHAFIENPLD YRDWTEFIH DRALAFVGVL TQRYPLTQNA QRYTNPLVLG AAFGDFLNAR SIDIFLDRLF YDPTQDSPIT AITKFPYQWT I DSNVTTDS ...String:
MAAVFGIQLV PKLNTSTTRR TFLPLRFDLL LDRLQSTNLH GVLYRALDFN PVDRSATVIQ TYPPLNAWSP HHAFIENPLD YRDWTEFIH DRALAFVGVL TQRYPLTQNA QRYTNPLVLG AAFGDFLNAR SIDIFLDRLF YDPTQDSPIT AITKFPYQWT I DSNVTTDS VRTSAGCKYI TLYGYDPSRP STPATYGKHR PTYATVFYYS TLPARSRLLA NLAAGPTVLE HFDSPTYGPH LL LPQTGDV LGYSSSLISQ AALLMVESVM DALRDNANAS ASTAVTRLDQ SYHPVTSFDP STFNTLLQRA TNLALLAVQG VQS ESAIPA IPTMSDVRSF VARLMAEGDP QQWFPYRVDQ ILYWPESPFV PPIGPFYAPF RPVNFPFTTG SYTVVPDASR PLRL LPQYR NATITVQQAD DAYEDTALSP LITTHGFCVT GGVFTSIYDI SGDPTAYPPA QLVDAPNDYF DRERMARRDL FRRLR APAD RSAIKDRAVF DFLASLVNPT TANPVLDTSF SMAYLGASSA HANADEPVIL ADIRSGSIPG LPIPRRIVQF GYDVVH GSL LDLSRAVPTG TFGLVYADLD QVEDAGTDMP AANRAAIAML GTALQMTTAG GVSVLKVNFP TRAFWTQVFN LYATHAT TL HLVKPTIVNS SEVFLVFGGR QSNGALRSTT ALQRALLSLY ARNAAIDRAV THIPFFGVPD DGTSDLGIDA VRLFDPMF S DAVANLPSNA LASLVSRVVP SSIMFTRVPS NGPVSTTIYG KRTFLSNRRR ARLRDVPMLI TTTLVHQRRF TTPPTFTLF SSEAVPVTTL VAAGYNSFIS EQTRNPNLAH LLDLGTGPEC RILSLIPPTL QVTMSDSRPC AELMASFDPA LTAYVQGDYS TAAFWNGIR CDSATAIFTI GAAAAAAGTD LIAFVQQLIP RIVAAGGTRM WLQLNTPLYE VSSLPDLIEI DLRDHVYRFN G GERVEPYA DPVPLQQAIA ALLPAAALSW HTLSPTCDWL PYIIGVGSPL NLSDINTAIS YSRLTPILHI DTTTPPLRVN PV PTPLNQQ CAIRITSLDP AAVLSVQHNG VEVIGGTPGN VISVAGAAAL QYILANQEFL LQFTPTLPGI FDVFLTTLGQ PPV PRGSFT ITPPPTTVAL NMPPPRQLDF TDVGNDARIT CDPYYQLAVC IFKDGQYVRV NPEKASVVTN APNRDLHFVL DLAD NHVLL YLCDVTPSGL GDRIAFPIVD IYRIAFPRNT PVRASLPYTG GGAHLTSGGN PFMSLTTPPA VLPAGVALAA LSTSV ATQY PTYTLPAGVY EYVIE

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Macromolecule #6: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Grass carp reovirus
Molecular weightTheoretical: 132.203312 KDa
Recombinant expressionOrganism: Ctenopharyngodon idella (grass carp)
SequenceString: MPRRSARKAQ SAIASPADTN VVPAKDAPTT NSPPSTTSPN QAAADANQQQ AGIVSSQSGP NAVGDSAPSS SVNNDGDIIT RPTSDSIAA VANATKPAAV VSDPQSMKVT PIVNPSSYVC NVCNARFSTM SALSEHLRSD HRDDASTLLA TPMINNAIRS F LTAWDDIR ...String:
MPRRSARKAQ SAIASPADTN VVPAKDAPTT NSPPSTTSPN QAAADANQQQ AGIVSSQSGP NAVGDSAPSS SVNNDGDIIT RPTSDSIAA VANATKPAAV VSDPQSMKVT PIVNPSSYVC NVCNARFSTM SALSEHLRSD HRDDASTLLA TPMINNAIRS F LTAWDDIR ILSPDVSSKS LSAYLDSAVA NGPELIIEDT GLCTSFMLLD NIPSAHLTKE LIGFTWFMQM YQMTPPLPEG AV NRIVCMT NWASLGDEGR GLEVRLPPPT DSSVHAYKTV LSRGYIDNAQ FNPLALRSNV LLMLLQFTLS NLKINKSSTF TSD VTTITS GRMIRAFEGR PELLALAYPG RAVLPTQTKN AQFLSTAIAD RIGRLDRANL IGGEVSAMVE CMELCDALTL HIRE TYIML LRSMHQDPTQ IVQIVNECAN NLLNSTIPIS LRPTILCPWF ASSEDLRLQQ VMHLVNISSN TAAALPLVEA LSTLL RSVT PLVLDPTVLT NAITTISEST TQTISPISEI LRLLQPMGND YAAFWKCIAS WAYNGLVTTV LSEDAFPDSS QSITHL PSM WKCLFLTLAG PMTSDPHSPV KVFMALANLL AQPEPIAIGV PGMHQTTPAS QFSHPGVWPP GFLNPQLINP QQAPLLR AF AEHIRANWPQ PSEFGYGSTL QGSANLFIPS NRMVYPWPNQ PLPRLTVAPT YDSAMSNWIS TTIAFFIRVV NSVNMTAT V NDLTRRTMTG VMTAMRQVKT MTPFYIQHMC PTELSVLASV TVTPPFQVPF TRLVQNDVIT NVLVARVDPA QRGDAAVDI RATHATFAAA LPVDPAAIVV AMLCGQTETN LIPSHHYGKA FAPLFASNAM FTRNQRAVIT REAFVCARSA VAQCQDAGFL VPRPLDALR QFDVTSAAAA EIMHAVNDAF KTAFDLDGAL LDGLALYGDP RIADLSAAYL QYGGNVVREH VPPGPSHIHR A LQQVESTF MAEMNLFNVA RGNLYLVQTA TNGNWSPMAP VAAPPFVRGG PNVRVVGRFG TIVPRPNGLE PQLIDDGNVP RD IAGDWVY PSDVLQVSVA VFRDYVWPMV KAGRTRVLVE LGHYVYTLHY YDPQISLDEA PILEEWLSKI NPAGIPPVPF CIP IPQVYP CITARRVHYA FTSENNNDSL FSTNAASIDT AFGENAAVSP LRWPGLVDPN YRVGTNDLPN RITLYNSLYR YNFT YPTLD GIMYVRSAT

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 10 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41000

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