[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 Å resolution / Particle / 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 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Jan 25, 2017Structure modelDatabase references
1.2Feb 22, 2017Structure modelDatabase references
1.3Sep 13, 2017Structure modelAuthor supporting evidence / Data collectionem_image_scans / em_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

-
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

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)pr domain


Mass: 9261.531 Da / Num. of mol.: 3 / Source: (gene. exp.) Zika virus

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

-
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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Zika virusVIRUS1,2,3,40MULTIPLE SOURCES
2Transmembrane domainsCOMPLEX3,41NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1164320Zika virus
2264320Zika virus
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: prM-E glycoprotein / Diameter: 600 Å / Triangulation number (T number): 1
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1200mMsodium chlorideNaCl1
220mMTrisC4H11NO31
31mMEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Ultrathin carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 7.6 sec. / Electron dose: 4.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3341

-
Processing

EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
1EMAN2PARTICLE SELECTIONe2boxer.py1
2Leginon3.2IMAGE ACQUISITION1
4CTFFIND3.0CTF CORRECTION1
5jsprCTF CORRECTION1
8UCSF ChimeraMODEL FITTING1
10jsprINITIAL EULER ASSIGNMENT1
11jsprFINAL EULER ASSIGNMENT1
12RELIONCLASSIFICATION1
13jsprRECONSTRUCTION1
14UCSF ChimeraMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 14351
SymmetryPoint symmetry: I
3D reconstructionResolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9315 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
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)

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