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- PDB-8h2i: Near-atomic structure of five-fold averaged PBCV-1 capsid -

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Basic information

Entry
Database: PDB / ID: 8h2i
TitleNear-atomic structure of five-fold averaged PBCV-1 capsid
Components
  • MCPv1
  • MCPv2
  • MCPv3
  • MCPv4
  • MCPv5
  • Major capsid protein (MCP)
  • P11
  • P12
  • P13
  • P15
  • P16
  • P17
  • P18
  • P19
  • P1v1
  • P2
  • P20
  • P21
  • P22
  • P23
  • P3
  • P4
  • P5
  • P6
  • P8
  • P9
KeywordsVIRAL PROTEIN / giant virus / nucleocytoplasmic large DNA viruses (NCLDVs) / viral assembly / Paramecium bursaria chlorella virus 1 (PBCV-1) / chlorovirus / major capsid protein / minor capsid protein / VIRUS
Function / homology
Function and homology information


viral capsid / lipid binding / structural molecule activity / virion membrane / membrane
Similarity search - Function
Chlorovirus glycoprotein repeat / Domain of unknown function DUF5901 / Chlorovirus glycoprotein repeat / Family of unknown function (DUF5901) / Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) ...Chlorovirus glycoprotein repeat / Domain of unknown function DUF5901 / Chlorovirus glycoprotein repeat / Family of unknown function (DUF5901) / Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / Parallel beta-helix repeat / Parallel beta-helix repeats
Similarity search - Domain/homology
Major capsid protein VP54 / DUF5901 domain-containing protein / Capsid protein / Minor capsid protein P4 / Capsid protein / Minor capsid protein P8 / Major capsid protein / Peptidase G2 IMC autoproteolytic cleavage domain-containing protein / Minor capsid protein P12 / Minor capsid protein P6 ...Major capsid protein VP54 / DUF5901 domain-containing protein / Capsid protein / Minor capsid protein P4 / Capsid protein / Minor capsid protein P8 / Major capsid protein / Peptidase G2 IMC autoproteolytic cleavage domain-containing protein / Minor capsid protein P12 / Minor capsid protein P6 / Uncharacterized protein / Capsid protein / Uncharacterized protein / Minor capsid protein P2 / Minor capsid protein P11 / Capsid protein / Capsid protein / Chlorovirus glycoprotein repeat domain-containing protein / Chlorovirus glycoprotein repeat domain-containing protein / Chlorovirus glycoprotein repeat domain-containing protein / Minor capsid protein P9 / Minor capsid protein P13 / Uncharacterized protein / Uncharacterized protein / Minor capsid protein 3 / Minor capsid protein P5
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShao, Q. / Agarkova, I.V. / Noel, E.A. / Dunigan, D.D. / Liu, Y. / Wang, A. / Guo, M. / Xie, L. / Zhao, X. / Rossmann, M.G. ...Shao, Q. / Agarkova, I.V. / Noel, E.A. / Dunigan, D.D. / Liu, Y. / Wang, A. / Guo, M. / Xie, L. / Zhao, X. / Rossmann, M.G. / Van Etten, J.L. / Klose, T. / Fang, Q.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1736030 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2022
Title: Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1.
Authors: Qianqian Shao / Irina V Agarkova / Eric A Noel / David D Dunigan / Yunshu Liu / Aohan Wang / Mingcheng Guo / Linlin Xie / Xinyue Zhao / Michael G Rossmann / James L Van Etten / Thomas Klose / Qianglin Fang /
Abstract: Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play ...Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.
History
DepositionOct 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
aa: Major capsid protein (MCP)
ab: Major capsid protein (MCP)
ac: Major capsid protein (MCP)
ad: Major capsid protein (MCP)
ae: Major capsid protein (MCP)
af: Major capsid protein (MCP)
ag: Major capsid protein (MCP)
ah: Major capsid protein (MCP)
ai: Major capsid protein (MCP)
aj: Major capsid protein (MCP)
ak: Major capsid protein (MCP)
al: Major capsid protein (MCP)
am: Major capsid protein (MCP)
an: Major capsid protein (MCP)
ao: Major capsid protein (MCP)
ap: Major capsid protein (MCP)
aq: Major capsid protein (MCP)
ar: Major capsid protein (MCP)
as: Major capsid protein (MCP)
at: Major capsid protein (MCP)
au: Major capsid protein (MCP)
av: Major capsid protein (MCP)
aw: Major capsid protein (MCP)
ax: Major capsid protein (MCP)
ay: Major capsid protein (MCP)
az: Major capsid protein (MCP)
aA: Major capsid protein (MCP)
aB: Major capsid protein (MCP)
aC: Major capsid protein (MCP)
aD: Major capsid protein (MCP)
aE: Major capsid protein (MCP)
aF: Major capsid protein (MCP)
aG: Major capsid protein (MCP)
aH: Major capsid protein (MCP)
aI: Major capsid protein (MCP)
aJ: Major capsid protein (MCP)
aK: Major capsid protein (MCP)
aL: Major capsid protein (MCP)
aM: Major capsid protein (MCP)
aN: Major capsid protein (MCP)
aO: Major capsid protein (MCP)
aP: Major capsid protein (MCP)
aQ: Major capsid protein (MCP)
aR: Major capsid protein (MCP)
aS: Major capsid protein (MCP)
aT: Major capsid protein (MCP)
aU: Major capsid protein (MCP)
aV: Major capsid protein (MCP)
aW: Major capsid protein (MCP)
aX: Major capsid protein (MCP)
aY: Major capsid protein (MCP)
aZ: Major capsid protein (MCP)
ba: Major capsid protein (MCP)
bb: Major capsid protein (MCP)
bc: Major capsid protein (MCP)
bd: Major capsid protein (MCP)
be: Major capsid protein (MCP)
bf: Major capsid protein (MCP)
bg: Major capsid protein (MCP)
bh: Major capsid protein (MCP)
bi: Major capsid protein (MCP)
bj: Major capsid protein (MCP)
bk: Major capsid protein (MCP)
bl: Major capsid protein (MCP)
bm: Major capsid protein (MCP)
bn: Major capsid protein (MCP)
bo: Major capsid protein (MCP)
bp: Major capsid protein (MCP)
bq: Major capsid protein (MCP)
br: Major capsid protein (MCP)
bs: Major capsid protein (MCP)
bt: Major capsid protein (MCP)
bu: MCPv1
bv: MCPv1
bw: MCPv1
bx: MCPv1
by: MCPv1
bz: MCPv1
bA: MCPv1
bB: MCPv1
bC: MCPv2
bD: MCPv3
bE: MCPv4
bF: MCPv3
bG: P1v1
bH: P2
bI: P3
bJ: P3
bK: P3
bL: P4
bM: P4
bN: P4
bO: P4
bP: P5
bQ: P6
bR: P8
bS: P9
bT: P11
bU: P11
bV: P11
bW: P11
bX: P11
bY: P11
bZ: P11
ca: P11
cb: P11
cc: P11
cd: P11
ce: P11
cf: P12
cg: P13
ch: P15
ci: P16
cj: P17
ck: P17
cl: P17
cm: P17
cn: P18
co: P18
cp: P19
cq: P19
cr: P19
cs: P19
ct: P19
cu: P19
cv: P19
cw: P19
cx: P19
cy: P19
cz: P19
cA: P19
cB: P19
cC: P19
cD: P19
cE: P19
cF: P19
cG: P19
cH: P19
cI: P19
cJ: P19
cK: P19
cL: P19
cM: P19
cN: P19
cO: P20
cP: P21
cQ: P20
cR: MCPv5
cS: MCPv5
cT: MCPv5
cU: P22
cV: P22
cW: P22
cX: MCPv3
cY: MCPv4
cZ: MCPv3
da: P20
db: P21
dc: P20
dd: MCPv3
de: MCPv4
df: MCPv3
dg: P20
dh: P21
di: P20
dj: MCPv3
dk: MCPv3
dl: MCPv3
dm: P23
dn: P23
do: P23
dp: MCPv3
dq: MCPv4
dr: MCPv3
ds: P20
dt: P21
du: P20


Theoretical massNumber of molelcules
Total (without water)9,133,989177
Polymers9,133,989177
Non-polymers00
Water00
1
aa: Major capsid protein (MCP)
ab: Major capsid protein (MCP)
ac: Major capsid protein (MCP)
ad: Major capsid protein (MCP)
ae: Major capsid protein (MCP)
af: Major capsid protein (MCP)
ag: Major capsid protein (MCP)
ah: Major capsid protein (MCP)
ai: Major capsid protein (MCP)
aj: Major capsid protein (MCP)
ak: Major capsid protein (MCP)
al: Major capsid protein (MCP)
am: Major capsid protein (MCP)
an: Major capsid protein (MCP)
ao: Major capsid protein (MCP)
ap: Major capsid protein (MCP)
aq: Major capsid protein (MCP)
ar: Major capsid protein (MCP)
as: Major capsid protein (MCP)
at: Major capsid protein (MCP)
au: Major capsid protein (MCP)
av: Major capsid protein (MCP)
aw: Major capsid protein (MCP)
ax: Major capsid protein (MCP)
ay: Major capsid protein (MCP)
az: Major capsid protein (MCP)
aA: Major capsid protein (MCP)
aB: Major capsid protein (MCP)
aC: Major capsid protein (MCP)
aD: Major capsid protein (MCP)
aE: Major capsid protein (MCP)
aF: Major capsid protein (MCP)
aG: Major capsid protein (MCP)
aH: Major capsid protein (MCP)
aI: Major capsid protein (MCP)
aJ: Major capsid protein (MCP)
aK: Major capsid protein (MCP)
aL: Major capsid protein (MCP)
aM: Major capsid protein (MCP)
aN: Major capsid protein (MCP)
aO: Major capsid protein (MCP)
aP: Major capsid protein (MCP)
aQ: Major capsid protein (MCP)
aR: Major capsid protein (MCP)
aS: Major capsid protein (MCP)
aT: Major capsid protein (MCP)
aU: Major capsid protein (MCP)
aV: Major capsid protein (MCP)
aW: Major capsid protein (MCP)
aX: Major capsid protein (MCP)
aY: Major capsid protein (MCP)
aZ: Major capsid protein (MCP)
ba: Major capsid protein (MCP)
bb: Major capsid protein (MCP)
bc: Major capsid protein (MCP)
bd: Major capsid protein (MCP)
be: Major capsid protein (MCP)
bf: Major capsid protein (MCP)
bg: Major capsid protein (MCP)
bh: Major capsid protein (MCP)
bi: Major capsid protein (MCP)
bj: Major capsid protein (MCP)
bk: Major capsid protein (MCP)
bl: Major capsid protein (MCP)
bm: Major capsid protein (MCP)
bn: Major capsid protein (MCP)
bo: Major capsid protein (MCP)
bp: Major capsid protein (MCP)
bq: Major capsid protein (MCP)
br: Major capsid protein (MCP)
bs: Major capsid protein (MCP)
bt: Major capsid protein (MCP)
bu: MCPv1
bv: MCPv1
bw: MCPv1
bx: MCPv1
by: MCPv1
bz: MCPv1
bA: MCPv1
bB: MCPv1
bC: MCPv2
bD: MCPv3
bE: MCPv4
bF: MCPv3
bG: P1v1
bH: P2
bI: P3
bJ: P3
bK: P3
bL: P4
bM: P4
bN: P4
bO: P4
bP: P5
bQ: P6
bR: P8
bS: P9
bT: P11
bU: P11
bV: P11
bW: P11
bX: P11
bY: P11
bZ: P11
ca: P11
cb: P11
cc: P11
cd: P11
ce: P11
cf: P12
cg: P13
ch: P15
ci: P16
cj: P17
ck: P17
cl: P17
cm: P17
cn: P18
co: P18
cp: P19
cq: P19
cr: P19
cs: P19
ct: P19
cu: P19
cv: P19
cw: P19
cx: P19
cy: P19
cz: P19
cA: P19
cB: P19
cC: P19
cD: P19
cE: P19
cF: P19
cG: P19
cH: P19
cI: P19
cJ: P19
cK: P19
cL: P19
cM: P19
cN: P19
cO: P20
cP: P21
cQ: P20
cR: MCPv5
cS: MCPv5
cT: MCPv5
cU: P22
cV: P22
cW: P22
cX: MCPv3
cY: MCPv4
cZ: MCPv3
da: P20
db: P21
dc: P20
dd: MCPv3
de: MCPv4
df: MCPv3
dg: P20
dh: P21
di: P20
dj: MCPv3
dk: MCPv3
dl: MCPv3
dm: P23
dn: P23
do: P23
dp: MCPv3
dq: MCPv4
dr: MCPv3
ds: P20
dt: P21
du: P20
x 5


  • complete point assembly
  • Evidence: microscopy
  • 45.7 MDa, 885 polymers
Theoretical massNumber of molelcules
Total (without water)45,669,943885
Polymers45,669,943885
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C5 (5 fold cyclic))

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Components

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Protein , 26 types, 177 molecules aaabacadaeafagahaiajakalamanaoapaqarasatauavawaxayazaAaBaCaD...

#1: Protein ...
Major capsid protein (MCP) / Major capsid protein


Mass: 48199.625 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328
#2: Protein
MCPv1 / Major capsid protein variant 1 (MCPv1)


Mass: 58136.645 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41104
#3: Protein MCPv2 / Major capsid protein variant 2 (MCPv2)


Mass: 55733.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: M1I493
#4: Protein
MCPv3 / Major capsid protein variant 3 (MCPv3)


Mass: 45115.641 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89346
#5: Protein
MCPv4 / Major capsid protein variant 4 (MCPv4)


Mass: 45034.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89345
#6: Protein P1v1 / DUF5901 domain-containing protein / Penton protein variant 1 (P1v1)


Mass: 57555.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: M1I677
#7: Protein P2 / DUF5899 domain-containing protein


Mass: 63888.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84656
#8: Protein P3 / Reductive dehalogenase subunit A


Mass: 19116.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98573
#9: Protein
P4 / DUF2268 domain-containing protein


Mass: 20637.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41054
#10: Protein P5 / NADH-ubiquinone oxidoreductase subunit


Mass: 16455.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98576
#11: Protein P6 / PsbP domain-containing protein


Mass: 24036.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84523
#12: Protein P8 / Copine domain-containing protein


Mass: 19226.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41126
#13: Protein P9 / Transmembrane protein


Mass: 23407.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98459
#14: Protein
P11 / Secreted protein


Mass: 23322.656 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84666
#15: Protein P12


Mass: 17715.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84459
#16: Protein P13 / NVEALA family protein


Mass: 11070.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98473
#17: Protein P15 / Entry/fusion complex component


Mass: 18627.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98534
#18: Protein P16 / Glycine-rich protein


Mass: 9844.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98530
#19: Protein
P17


Mass: 9122.370 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84629
#20: Protein P18 / Transmembrane protein


Mass: 16497.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84533
#21: Protein ...
P19 / A2M domain-containing protein


Mass: 43094.387 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84602
#22: Protein
P20 / Peptidase S74 domain-containing protein


Mass: 137671.312 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89353
#23: Protein
P21


Mass: 141414.188 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89349
#24: Protein MCPv5 / Capsid protein


Mass: 45585.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41040
#25: Protein P22 / Peptidase_G2 domain-containing protein


Mass: 137927.828 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84443
#26: Protein P23 / Chlorovirus glycoprotein repeat domain-containing protein


Mass: 140121.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89360

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Paramecium bursaria Chlorella virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Paramecium bursaria Chlorella virus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 8 sec. / Electron dose: 24.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Gautomatchparticle selection
5CTFFIND4CTF correction
11RELIONinitial Euler assignment
12jsprfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56500 / Symmetry type: POINT

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  • 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

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