[English] 日本語
Yorodumi
- PDB-5u4w: Cryo-EM Structure of Immature Zika Virus -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5u4w
TitleCryo-EM Structure of Immature Zika Virus
DescriptorE protein, pr domain, Protein E, M protein
KeywordsVIRUS / immature Zika virus / viral protein
Specimen sourceZika virus / virus / ZIKV / ジカウイルス
MethodElectron microscopy (9.1 A resolution / Single particle)
AuthorsMangala Prasad, V. / Miller, A.S. / Klose, T. / Sirohi, D. / Buda, G. / Jiang, W. / Kuhn, R.J. / Rossmann, M.G.
CitationNat. Struct. Mol. Biol., 2017, 24, 184-186

Nat. Struct. Mol. Biol., 2017, 24, 184-186 StrPapers
Structure of the immature Zika virus at 9 Å resolution.
Vidya Mangala Prasad / Andrew S Miller / Thomas Klose / Devika Sirohi / Geeta Buda / Wen Jiang / Richard J Kuhn / Michael G Rossmann

DateDeposition: Dec 6, 2016 / Release: Jan 11, 2017 / Last modification: Feb 22, 2017

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8508
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: E protein
B: pr domain
C: E protein
D: pr domain
E: E protein
F: pr domain
G: Protein E
H: M protein
I: Protein E
J: M protein
K: Protein E
L: M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,55330
Polyers200,81812
Non-polymers3,73518
Water0
#1
A: E protein
B: pr domain
C: E protein
D: pr domain
E: E protein
F: pr domain
G: Protein E
H: M protein
I: Protein E
J: M protein
K: Protein E
L: M protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)12,273,1881800
Polyers12,049,062720
Non-polymers224,1261080
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: E protein
B: pr domain
C: E protein
D: pr domain
E: E protein
F: pr domain
G: Protein E
H: M protein
I: Protein E
J: M protein
K: Protein E
L: M protein
hetero molecules
x 5


  • icosahedral pentamer
  • 1.02 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,022,766150
Polyers1,004,08960
Non-polymers18,67790
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: E protein
B: pr domain
C: E protein
D: pr domain
E: E protein
F: pr domain
G: Protein E
H: M protein
I: Protein E
J: M protein
K: Protein E
L: M protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.23 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,227,319180
Polyers1,204,90672
Non-polymers22,413108
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

-
Components

-
Polypeptide(L) , 4 types, 12 molecules ACEBDFGIKHJL

#1: Polypeptide(L)E protein


Mass: 44801.410 Da / Num. of mol.: 3 / Source: (gene. exp.) Zika virus
#2: Polypeptide(L)pr domain


Mass: 9261.531 Da / Num. of mol.: 3 / Source: (gene. exp.) Zika virus
#3: Polypeptide(L)Protein E


Mass: 6892.228 Da / Num. of mol.: 3 / Fragment: transmembrane domain (UNP residues 726-791) / Source: (natural) Zika virus / References: UniProt: A0A1B2ZC85
#4: Polypeptide(L)M protein


Mass: 5984.065 Da / Num. of mol.: 3 / Fragment: transmembrane domain (UNP residues 238-290) / Source: (natural) Zika virus / References: UniProt: A0A142I5B9

-
Non-polymers , 2 types, 18 molecules

#5: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 12 / Formula: C8H15NO6
#6: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6 / Formula: C6H12O6

-
Details

Sequence detailsThe sample was from Zika virus, but the modeled sequences for chains A, B, C, D, E, and F are from Dengue virus.

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

-
Sample preparation

Component
IDNameTypeAssembly id
1Zika virusVIRUS1
2Transmembrane domainsCOMPLEX1
Details of the virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch. / Grid type: Ultrathin carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD

-
Processing

3D reconstructionResolution: 9.1 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9315
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more