[English] 日本語
Yorodumi
- PDB-1upn: COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1upn
TitleCOMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A
DescriptorECHOVIRUS 11 COAT PROTEIN VP1
ECHOVIRUS 11 COAT PROTEIN VP2
ECHOVIRUS 11 COAT PROTEIN VP3
ECHOVIRUS 11 COAT PROTEIN VP4
COMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsVIRUS/RECEPTOR / COMPLEX (VIRUS COAT-IMMUNE PROTEIN) / ECHOVIRUS / PICORNAVIRUS / CD55 / DAF / VIRUS-RECEPTOR COMPLEX / ICOSAHEDRAL VIRUS
Specimen sourceHomo sapiens / human
HUMAN ECHOVIRUS 11 / virus
MethodElectron microscopy (16 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsBhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M.
CitationJ. Biol. Chem., 2004, 279, 8325-8332

J. Biol. Chem., 2004, 279, 8325-8332 StrPapers
The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea

DateDeposition: Oct 8, 2003 / Release: Jan 7, 2004 / Last modification: Feb 24, 2009
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
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-1057
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1058
  • 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: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)109,3375
Polyers109,3375
Non-polymers00
Water0
#1
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 60


Theoretical massNumber of molelcules
Total (without water)6,560,243300
Polyers6,560,243300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 5


  • icosahedral pentamer
  • 547 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)546,68725
Polyers546,68725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 6


  • icosahedral 23 hexamer
  • 656 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)656,02430
Polyers656,02430
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


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

-
Components

#1: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP1


Mass: 32786.949 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP2


Mass: 29048.713 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP3


Mass: 25897.541 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP4


Mass: 7509.366 Da / Num. of mol.: 1
Details: STRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057
Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)COMPLEMENT DECAY-ACCELERATING FACTOR / CD55


Mass: 14094.814 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P08174

Cellular component

Molecular function

Biological process

  • CD4-positive, alpha-beta T cell cytokine production (GO: 0035743)
  • complement activation, classical pathway (GO: 0006958)
  • ER to Golgi vesicle-mediated transport (GO: 0006888)
  • innate immune response (GO: 0045087)
  • negative regulation of complement activation (GO: 0045916)
  • positive regulation of CD4-positive, alpha-beta T cell activation (GO: 2000516)
  • positive regulation of CD4-positive, alpha-beta T cell proliferation (GO: 2000563)
  • positive regulation of cytosolic calcium ion concentration (GO: 0007204)
  • regulation of complement activation (GO: 0030449)
  • regulation of lipopolysaccharide-mediated signaling pathway (GO: 0031664)
  • respiratory burst (GO: 0045730)
Sequence detailsTHE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenName: ECHOVIRUS TYPE 12 / Aggregation state: PARTICLE
Buffer solutionName: AMMONIUM MOLYBDATE
Sample preparationpH: 7.4 / Sample conc.: 0.2 mg/ml
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: LIQUID ETHANE
Crystal grow
*PLUS
Temp unit: unknown / Method: electron microscopy / Details: electron microscopy

-
Electron microscopy imaging

MicroscopyMicroscope model: JEOL 1200 EX II / Date: Jul 15, 2002 / Details: PARTICLES SELECTED WITH X3D
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: LOW DOSE
Electron lensNominal magnification: 30000 X / Calibrated magnification: 29200 X / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm / Cs: 3.4 mm
Specimen holderTemperature: 108 K
CameraType: KODAK SO-163 FILM
EM image scansNumber digital images: 16
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: MRC
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: POLAR FOURIER TRANSFORM
Details: MAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 WAS INTRODUCED BY RIGID-BODY REFINEMENT OF DOMAIN 4 KEEPING 3 FIXED
Atomic model buildingRef protocol: X-RAY / Ref space: REAL / Target criteria: CORRELATION COEFFICIENTS
Atomic model buildingPDB-ID: 1UPN
Least-squares processHighest resolution: 16 A
Refine hist #LASTHighest resolution: 16 A
Number of atoms included #LASTProtein: 7463 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7463

+
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