[English] 日本語
Yorodumi
- EMDB-9393: Electron Cryo-Microscopy Of Chikungunya VLP -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-9393
TitleElectron Cryo-Microscopy Of Chikungunya VLP
Map data
SampleChikungunya virus:
virus / E1 glycoprotein / E2 glycoprotein / Capsid proteinCapsid / ligand
Function / homology
Function and homology information


ec:3.4.21.90: / T=4 icosahedral viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / serine-type endopeptidase activity / structural molecule activity ...ec:3.4.21.90: / T=4 icosahedral viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / serine-type endopeptidase activity / structural molecule activity / RNA binding / integral component of membrane
Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein, domain A / Immunoglobulin E-set / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Alphavirus E2 glycoprotein, domain B / Peptidase S1, PA clan ...Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein, domain A / Immunoglobulin E-set / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Alphavirus E2 glycoprotein, domain B / Peptidase S1, PA clan / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein
Structural polyprotein
Biological speciesChikungunya virus / Chikungunya virus (strain 37997)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsBasore K / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.
Authors: Katherine Basore / Arthur S Kim / Christopher A Nelson / Rong Zhang / Brittany K Smith / Carla Uranga / Lo Vang / Ming Cheng / Michael L Gross / Jonathan Smith / Michael S Diamond / Daved H Fremont /
Abstract: Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal ...Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal structure of Mxra8 and 4 to 5 Å resolution cryo-electron microscopy reconstructions of Mxra8 bound to chikungunya (CHIKV) virus-like particles and infectious virus. The Mxra8 ectodomain contains two strand-swapped Ig-like domains oriented in a unique disulfide-linked head-to-head arrangement. Mxra8 binds by wedging into a cleft created by two adjacent CHIKV E2-E1 heterodimers in one trimeric spike and engaging a neighboring spike. Two binding modes are observed with the fully mature VLP, with one Mxra8 binding with unique contacts. Only the high-affinity binding mode was observed in the complex with infectious CHIKV, as viral maturation and E3 occupancy appear to influence receptor binding-site usage. Our studies provide insight into how Mxra8 binds CHIKV and creates a path for developing alphavirus entry inhibitors.
Validation ReportPDB-ID: 6nk5

SummaryFull reportAbout validation report
DateDeposition: Jan 4, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: May 22, 2019 / Update: May 29, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6nk5
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6nk5
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_9393.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 600 pix.
= 841.8 Å
1.4 Å/pix.
x 600 pix.
= 841.8 Å
1.4 Å/pix.
x 600 pix.
= 841.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-3.4880087 - 6.02024
Average (Standard dev.)0.0462273 (±0.5697404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 841.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z841.800841.800841.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-3.4886.0200.046

-
Supplemental data

-
Sample components

+
Entire Chikungunya virus

EntireName: Chikungunya virus / Details: Produced by PaxVax Corporation, Redwood CA, USA. / Number of components: 5

+
Component #1: virus, Chikungunya virus

VirusName: Chikungunya virusChikungunya / Class: VIRUS-LIKE PARTICLE / Details: Produced by PaxVax Corporation, Redwood CA, USA. / Empty: Yes / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Chikungunya virus / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

+
Component #2: protein, E1 glycoprotein

ProteinName: E1 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.346715 kDa
SourceSpecies: Chikungunya virus (strain 37997) / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human)

+
Component #3: protein, E2 glycoprotein

ProteinName: E2 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 46.858312 kDa
SourceSpecies: Chikungunya virus (strain 37997) / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 16.458701 kDa
SourceSpecies: Chikungunya virus (strain 37997) / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human)

+
Component #5: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.33 mg/mL / pH: 7.2
Support film0.458 mbar.l/s O2 and 0.11 mbar.l/s H2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 8113
3D reconstructionSoftware: cisTEM / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 3N42, 3N42, 3J0C, 3J0C, 5H23
Chain ID: B, F, A, B, A
Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
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

+
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

Read more

-
Yorodumi

Thousand views of thousand structures

  • 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.

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

Read more