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COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A
by single particle (icosahedral) reconstruction, at 16 A resolution
#1: Biological unit as complete icosahedral assembly, Made by Jmol
#2: Biological unit as icosahedral pentamer, Made by Jmol
#3: Biological unit as icosahedral 23 hexamer, Made by Jmol
#4: Depositted structure unit, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-1057, Made by Jmol
#6: Superimposing with simplified surface model of EM map, EMDB-1058, Made by Jmol
#7: Superimposing with EM 3D map: EMDB-1057, Made by UCSF CHIMERA
#8: Superimposing with EM 3D map: EMDB-1058, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 1upn |
|---|---|
| Title | COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A |
| Descriptor | ECHOVIRUS 11 COAT PROTEIN VP1 ECHOVIRUS 11 COAT PROTEIN VP2 ECHOVIRUS 11 COAT PROTEIN VP3 ECHOVIRUS 11 COAT PROTEIN VP4 COMPLEMENT DECAY-ACCELERATING FACTOR |
| Keywords |  VIRUS/RECEPTOR, COMPLEX (VIRUS COAT-IMMUNE PROTEIN), ECHOVIRUS, PICORNAVIRUS, CD55, DAF, VIRUS-RECEPTOR COMPLEX, ICOSAHEDRAL VIRUS |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Sequence details | THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12 |
| Structure Visualization | |
| Movies |  Movie Page#1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-1057, Made by Jmol #6: Superimposing with simplified surface model of EM map, EMDB-1058, Made by Jmol #7: Superimposing with EM 3D map: EMDB-1057, Made by UCSF CHIMERA #8: Superimposing with EM 3D map: EMDB-1058, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | J.Biol.Chem., Vol. 279, Page: 8325 - , Year: 2004, |
|---|---|
| Title | The Structure of Echovirus Type 12 Bound to a Two-Domain Fragment of its Cellular Attachment Protein Decay-Accelerating Factor (Cd 55) |
| Authors | Bhella, D., Goodfellow, I.G., Roversi, P., Pettigrew, D., Chaudhry, Y., Evans, D.J., Lea, S.M. |
| Links | DOI: 10.1074/JBC.M311334200 |
 Components | |
| ID 1 : ECHOVIRUS 11 COAT PROTEIN VP1 | |
| Image |   |
|---|---|
| Description | ECHOVIRUS 11 COAT PROTEIN VP1 |
| Type | polypeptide(L) |
| Formula weight | 32786.949 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:12078Organism scientific: HUMAN ECHOVIRUS 11 Strain: GREGORY |
| Links | UniProt: Q8JKE8, Sequence view |
| ID 2 : ECHOVIRUS 11 COAT PROTEIN VP2 | |
| Image |   |
| Description | ECHOVIRUS 11 COAT PROTEIN VP2 |
| Type | polypeptide(L) |
| Formula weight | 29048.713 Da |
| Number of molecules | 1 |
| ID | 2 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:12078Organism scientific: HUMAN ECHOVIRUS 11 Strain: GREGORY |
| Links | UniProt: Q8JKE8, Sequence view |
| ID 3 : ECHOVIRUS 11 COAT PROTEIN VP3 | |
| Image |   |
| Description | ECHOVIRUS 11 COAT PROTEIN VP3 |
| Type | polypeptide(L) |
| Formula weight | 25897.541 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:12078Organism scientific: HUMAN ECHOVIRUS 11 Strain: GREGORY |
| Links | UniProt: Q8JKE8, Sequence view |
| ID 4 : ECHOVIRUS 11 COAT PROTEIN VP4 | |
| Image |   |
| Description | ECHOVIRUS 11 COAT PROTEIN VP4 |
| Type | polypeptide(L) |
| Formula weight | 7509.366 Da |
| Number of molecules | 1 |
| ID | 4 |
| 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 | Method: Isolated from a natural source NCBI taxonomy: ID:12078Organism scientific: HUMAN ECHOVIRUS 11 Strain: GREGORY |
| Links | UniProt: Q8JKE8, Sequence view |
| ID 5 : CD55 | |
| Image |   |
| Description | COMPLEMENT DECAY-ACCELERATING FACTOR |
| Type | polypeptide(L) |
| Formula weight | 14094.814 Da |
| Number of molecules | 1 |
| ID | 5 |
| Source | Method: Isolated from a genetically manipulated source Gene: HUMAN, ID:9606, HOMO SAPIENSHost: ID:562, ESCHERICHIA COLI
|
| Links | UniProt: P08174, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | ECHOVIRUS TYPE 12 |
| Buffer | |
| Name | AMMONIUM MOLYBDATE |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.4 |
| Sample concentration | 0.2 mg/ml |
| Sample support | |
| Details | HOLEY CARBON |
| Vitrification | |
| Details | LIQUID ETHANE |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: JEOL 1200 EX II |
|---|---|
| Date | 2002-07-15 |
| Details | PARTICLES SELECTED WITH X3D |
| Electron gun | |
| Electron source | LAB6 |
| Accelerating voltage | 120 kV |
| Illumination mode | LOW DOSE |
| Lens | |
| Magnification | Calibrated: 29200 X, Nominal: 30000 X |
| Cs | Nominal: 3.4 mm |
| Nominal defocus | Max: 2000 nm, Min: 300 nm |
| Specimen holder | |
| Temperature | 108 Kelvin |
| Detector | |
| Type | KODAK SO-163 FILM |
| Image scans | |
| Number digital images | 16 |
 Processing | |
| 2D projection selection | |
| Software name | MRC |
|---|---|
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| 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 |
| Method | POLAR FOURIER TRANSFORM |
| 3D fitting | |
| Refinement Protocol | X-RAY |
| Refinement Space | REAL |
| Target criteria | CORRELATION COEFFICIENTS |
| 3D fitting list | |
| 3D fitting id | 1 |
| Refine | |
| Refine id | ELECTRON MICROSCOPY |
| Ls d res high | 16.00 A |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| D res high | 16.00 |
| Total atoms | 7463 |
| Protein atoms | 7463 |
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