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- EMDB-33591: Molecular architecture of the chikungunya virus replication complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33591
TitleMolecular architecture of the chikungunya virus replication complex
Map datamain map
Sample
  • Complex: Alphavirus Replication Complex
    • Complex: nsP1 dodecameric ring
      • Protein or peptide: mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)
    • Complex: nsP4 RdRp; docked within nsP1 central cavity
      • Protein or peptide: RNA-directed RNA polymerase nsP4
    • Complex: nsP2 helicase-protease; docked on top of viral complex with synthetic RNA bound
      • Protein or peptide: Protease nsP2
      • RNA: RNA (5'-R(P*CP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
Keywordsreplicase / replication complex / viral RNA replication / capping / helicase / protease / RNA-dependent RNA polymerase / RdRp / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase ...: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesChikungunya virus strain S27-African prototype / Onyong-nyong virus / in vitro transcription vector pT7-TP(deltai) (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTan YB / Luo D
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)T2EP30220-0020, 2021-T1-002-021 Singapore
CitationJournal: Sci Adv / Year: 2022
Title: Molecular architecture of the Chikungunya virus replication complex.
Authors: Yaw Bia Tan / David Chmielewski / Michelle Cheok Yien Law / Kuo Zhang / Yu He / Muyuan Chen / Jing Jin / Dahai Luo /
Abstract: To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we ...To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we determined both the high-resolution structure of the core RNA replicase of chikungunya virus and the native RC architecture in its cellular context at subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase, the viral polymerase nsP4, which is in complex with nsP2 helicase-protease, sits in the central pore of the membrane-anchored nsP1 RNA-capping ring. The addition of a large cytoplasmic ring next to the C terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses.
History
DepositionJun 10, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33591.png

Downloads & links

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Map

FileDownload / File: emd_33591.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.068
Minimum - Maximum-0.44719985 - 0.9924839
Average (Standard dev.)-0.00030544016 (±0.030233989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33591_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpen map

Fileemd_33591_additional_1.map
Annotationsharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B (coordinated to the same as main map)

Fileemd_33591_half_map_1.map
Annotationhalfmap B (coordinated to the same as main map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap A (coordinated to the same as main map)

Fileemd_33591_half_map_2.map
Annotationhalfmap A (coordinated to the same as main 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 : Alphavirus Replication Complex

EntireName: Alphavirus Replication Complex
Components
  • Complex: Alphavirus Replication Complex
    • Complex: nsP1 dodecameric ring
      • Protein or peptide: mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)
    • Complex: nsP4 RdRp; docked within nsP1 central cavity
      • Protein or peptide: RNA-directed RNA polymerase nsP4
    • Complex: nsP2 helicase-protease; docked on top of viral complex with synthetic RNA bound
      • Protein or peptide: Protease nsP2
      • RNA: RNA (5'-R(P*CP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Alphavirus Replication Complex

SupramoleculeName: Alphavirus Replication Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Assembled replication complex composed of all full-length viral protein - nsP1, nsP2 and nsP4 bound with RNA and NTP
Molecular weightTheoretical: 100 KDa

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Supramolecule #2: nsP1 dodecameric ring

SupramoleculeName: nsP1 dodecameric ring / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: 12-mer ring
Source (natural)Organism: Chikungunya virus strain S27-African prototype

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Supramolecule #3: nsP4 RdRp; docked within nsP1 central cavity

SupramoleculeName: nsP4 RdRp; docked within nsP1 central cavity / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: viral RdRp protein, single copy nsP4 slotted in the central pore of nsP1
Source (natural)Organism: Onyong-nyong virus

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Supramolecule #4: nsP2 helicase-protease; docked on top of viral complex with synth...

SupramoleculeName: nsP2 helicase-protease; docked on top of viral complex with synthetic RNA bound
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 / Details: only helicase density was observed
Source (natural)Organism: Chikungunya virus strain S27-African prototype

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Macromolecule #1: mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)

MacromoleculeName: mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)
type: protein_or_peptide / ID: 1
Details: 1. affinity-tag (strepII-3XFLAG) insertion in between residue number 517-552; 2. replaced the last residue A535 with short peptide-tag NGL (corresponding to position 571-573)
Number of copies: 12 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Chikungunya virus strain S27-African prototype / Strain: S27-African prototype
Molecular weightTheoretical: 64.328938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDAANA RAFSHLAIKL IEQEIDPDST ILDIGSAPAR RMMSDRKYHC VCPMRSAED PERLANYARK LASAAGKVLD RNISGKIGDL QAVMAVPDTE TPTFCLHTDV SCRQRADVAI YQDVYAVHAP T SLYHQAIK ...String:
MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDAANA RAFSHLAIKL IEQEIDPDST ILDIGSAPAR RMMSDRKYHC VCPMRSAED PERLANYARK LASAAGKVLD RNISGKIGDL QAVMAVPDTE TPTFCLHTDV SCRQRADVAI YQDVYAVHAP T SLYHQAIK GVRLAYWVGF DTTPFMYNAM AGAYPSYSTN WADEQVLKAK NIGLCSTDLT EGRRGKLSIM RGKKLEPCDR VL FSVGSTL YPESRKLLKS WHLPSVFHLK GKLSFTCRCD TVVSCEGYVV KRITMSPGLY GKTTGYAVTH HADGFLMCKT TDT VDGERV SFSVCTYVPA TICDQMTGIL ATEVTPEDAQ KLLVGLNQRI VVNGRTQRNT NTMKNYMIPV VAQAFSKWAK ECRK DMEDE KLLGVRERTL TCCCLWAFKK QKTHTVYKRP DTQSIQKVQA EFDSFVVPSL WSSGLSIPLR TRIKWLLSKV PKTDL TPYS GDAQEARDAE KEAEEEREAE LTLEALPPLQ AAGGGGSWSH PQFEKMDYKD HDGDYKDHDI DYKDDDDKQE DVQVEI DVE QLEDRAGNGL

UniProtKB: Polyprotein P1234, Polyprotein P1234

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Macromolecule #2: RNA-directed RNA polymerase nsP4

MacromoleculeName: RNA-directed RNA polymerase nsP4 / type: protein_or_peptide / ID: 2
Details: Sourced from virus isolate cDNA, not available in uniprot database at the time of biocuration
Number of copies: 1 / Enantiomer: LEVO / EC number: polynucleotide adenylyltransferase
Source (natural)Organism: Onyong-nyong virus / Strain: Chad
Molecular weightTheoretical: 68.373281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YIFSSDTGQG HLQQKSVRQT TLPVNIVEEV HEEKCYPPKL DEIKEQLLLK RLQESASTAN RSRYQSRKVE NMKAMIIHRL KEGCRLYLA SDTPRVPSYR ITYPAPIYSP SINIKLSNPE TAVAVCNEFL ARNYPTVASY QVTDEYDAYL DMVDGSESCL D RATFNPSK ...String:
YIFSSDTGQG HLQQKSVRQT TLPVNIVEEV HEEKCYPPKL DEIKEQLLLK RLQESASTAN RSRYQSRKVE NMKAMIIHRL KEGCRLYLA SDTPRVPSYR ITYPAPIYSP SINIKLSNPE TAVAVCNEFL ARNYPTVASY QVTDEYDAYL DMVDGSESCL D RATFNPSK LRSYPKQHSY HAPTIRSAVP SPFQNTLQNV LAAATKRNCN VTQMRELPTM DSAAFNVECF KKYACNQEYW RE FASSPIR VTTENLTTYV TKLKGPKAAA LFAKTHNLLP LQEVPMDRFT MDMKRDVKVT PGTKHTEERP KVQVIQAAEP LAT AYLCGI HRELVRRLNA VLLPNVHTLF DMSAEDFDAI IATHFKPGDA VLETDIASFD KSQDDSLALT AMMLLEDLGV DQPI LDLIE AAFGEISSCH LPTGTRFKFG AMMKSGMFLT LFVNTLLNIT IASRVLEERL TTSACAAFIG DDNIIHGVVS DALMA ARCA TWMNMEVKII DAVVSVKAPY FCGGFILHDT VTGTACRVAD PLKRLFKLGK PLAAGDEQDE DRRRALADEV TRWQRT GLV TELERAVYSR YEVQGITAVI TSMATFASSK ENFKKLRGPV VTLYGGPK

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Macromolecule #3: Protease nsP2

MacromoleculeName: Protease nsP2 / type: protein_or_peptide / ID: 3
Details: helicase region is built on visible 3D electron density map but not protease region
Number of copies: 1 / Enantiomer: LEVO / EC number: polynucleotide 5'-phosphatase
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Molecular weightTheoretical: 89.59982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIIETPRGAI KVTAQPTDHV VGEYLVLSPQ TVLRSQKLSL IHALAEQVKT CTHSGRAGRY AVEAYDGRVL VPSGYAISPE DFQSLSESA TMVYNEREFV NRKLHHIAMH GPALNTDEES YELVRAERTE HEYVYDVDQR RCCKKEEAAG LVLVGDLTNP P YHEFAYEG ...String:
GIIETPRGAI KVTAQPTDHV VGEYLVLSPQ TVLRSQKLSL IHALAEQVKT CTHSGRAGRY AVEAYDGRVL VPSGYAISPE DFQSLSESA TMVYNEREFV NRKLHHIAMH GPALNTDEES YELVRAERTE HEYVYDVDQR RCCKKEEAAG LVLVGDLTNP P YHEFAYEG LKIRPACPYK IAVIGVFGVP GSGKSAIIKN LVTRQDLVTS GKKENCQEIT TDVMRQRGLE ISARTVDSLL LN GCNRPVD VLYVDEAFAC HSGTLLALIA LVRPRQKVVL CGDPKQCGFF NMMQMKVNYN HNICTQVYHK SISRRCTLPV TAI VSSLHY EGKMRTTNEY NKPIVVDTTG STKPDPGDLV LTCFRGWVKQ LQIDYRGHEV MTAAASQGLT RKGVYAVRQK VNEN PLYAS TSEHVNVLLT RTEGKLVWKT LSGDPWIKTL QNPPKGNFKA TIKEWEVEHA SIMAGICSHQ MTFDTFQNKA NVCWA KSLV PILETAGIKL NDRQWSQIIQ AFKEDKAYSP EVALNEICTR MYGVDLDSGL FSKPLVSVYY ADNHWDNRPG GKMFGF NPE AASILERKYP FTKGKWNINK QICVTTRRIE DFNPTTNIIP ANRRLPHSLV AEHRPVKGER MEWLVNKING HHVLLVS GC SLALPTKRVT WVAPLGVRGA DYTYNLELGL PATLGRYDLV VINIHTPFRI HHYQQCVDHA MKLQMLGGDS LRLLKPGG S LLIRAYGYAD RTSERVICVL GRKFRSSRAL KPPCVTSNTE MFFLFSNFDN GRRNFTTHVM NNQLNAAFVG QATRAGC

UniProtKB: Polyprotein P1234

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Macromolecule #4: RNA (5'-R(P*CP*CP*A)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*A)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: in vitro transcription vector pT7-TP(deltai) (others)
Molecular weightTheoretical: 894.612 Da
SequenceString:
CCA

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 12 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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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

Concentration10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.025 MolarHEPESHEPES
0.075 MolarNaClSodium Chloride
0.02 MolarKClPotassium Chloride
0.005 MolarMgOAcMagnesium Acetate
0.0025 MolarMnCl2Mangenese Chloride
0.005 MolarTCEPTCEP
1.25 %SucroseSucrose

Details: 25mM HEPES, 75mM NaCl, 20mM KCl, 5mM MgOAc, 2.5mM MnCl2, 5mM TCEP, 1.25% Sucrose, pH8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.45 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 273.15 K / Instrument: FEI VITROBOT MARK III / Details: wait 45s, blot 2s at force -2.
DetailsThe sample was in vitro reconstituted and purified via affinity pulldown and ion-exchanged.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 7865 / Average exposure time: 5.0 sec. / Average electron dose: 34.0 e/Å2 / Details: movie-mode at 40 FPS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 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

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Image processing

DetailsThe images were recorded in MRC non-gain normalized format.
Particle selectionNumber selected: 2261181
Details: template-based picking and neural-network trained TOPAZ picking
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dop

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Homogenous/Heterogenous Refinement / Number images used: 132510
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 95000 / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: 3D Classification / Details: the 6th class has the highest number of particles
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7dop


Chain - Residue range: 1-516 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsChimeraX was used to fit the 7DOP ring and built/refined using coot/phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 63.66 / Target criteria: Correlation Coefficient
Output model

PDB-7y38:
Molecular architecture of the chikungunya virus replication complex

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