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The pseudo-atomic structure of West Nile immature virus in complex with Fab fragments of the anti-fusion loop antibody E53
by single particle (icosahedral) reconstruction, at 15 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-5103, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-5103, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3ixx |
|---|---|
| Title | The pseudo-atomic structure of West Nile immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 |
| Descriptor | Envelope protein E Pre-membrane E53 Fab Fragment (chain H) E53 Fab Fragment (chain L) |
| Keywords |  VIRUS, West Nile Virus, WNV, immature, fusion loop, Fab, E53, ATP-binding, Envelope protein, Helicase, Hydrolase, Membrane, Nucleotide-binding, RNA replication, Transmembrane, Virion, Icosahedral virus |
| Authors | Cherrier, M.V., Kaufmann, B., Nybakken, G.E., Lok, S.M., Warren, J.T., Nelson, C.A., Kostyuchenko, V.A., Holdaway, H.A., Chipman, P.R., Kuhn, R.J., Diamond, M.S., Rossmann, M.G., Fremont, D.H. |
| Date | Deposition: 2009-02-26, Release: 2009-10-27 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| 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-5103, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5103, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | EMBO J., Vol. 28, Issue 20, Page 3269-76, Year 2009 |
|---|---|
| Title | Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody. |
| Authors | Mickaël V Cherrier, Bärbel Kaufmann, Grant E Nybakken, Shee-Mei Lok, Julia T Warren, Beverly R Chen, Christopher A Nelson, Victor A Kostyuchenko, Heather A Holdaway, Paul R Chipman, Richard J Kuhn, Michael S Diamond, Michael G Rossmann, Daved H Fremont Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA. |
| Keywords | Antibodies, Viral (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, Flavivirus (chemistry), Glycoproteins (chemistry), Models, Molecular, Protein Structure, Secondary, Viral Envelope Proteins (chemistry) |
| Links | DOI: 10.1038/emboj.2009.245, PubMed: 19713934, PMC: PMC2771083 |
 Components | |
| ID 1 : Envelope protein E | |
| Image |   |
|---|---|
| Description | Envelope protein E |
| Type | polymer |
| Fragment | West Nile Virus envelope protein |
| Formula weight | 43272.512 Da |
| Number of molecules | 3 |
| Source | Method: Isolated from a genetically manipulated source Gene: WNV, NY99, ID:11082, West Nile virus |
| Links | UniProt: Q9Q6P4, Sequence view |
| ID 2 : Peptide pr | |
| Image |   |
| Description | Peptide pr |
| Type | polymer |
| Fragment | West Nile Virus pr peptide |
| Formula weight | 8742.036 Da |
| Number of molecules | 3 |
| Source | Method: Isolated from a genetically manipulated source Gene: WNV, NY99, ID:11082, West Nile virus |
| Links | UniProt: Q9WHD2, Sequence view |
| ID 3 : E53 Fab Fragment (chain H) | |
| Image |   |
| Description | E53 Fab Fragment (chain H) |
| Type | polymer |
| Fragment | E53 Fab Fragment |
| Formula weight | 23630.650 Da |
| Number of molecules | 2 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:10090, Mus musculusHost: ID:562, Escherichia coli
|
| Links | Sequence view |
| ID 4 : E53 Fab Fragment (chain L) | |
| Image |   |
| Description | E53 Fab Fragment (chain L) |
| Type | polymer |
| Fragment | E53 Fab Fragment |
| Formula weight | 23588.275 Da |
| Number of molecules | 2 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:10090, Mus musculusHost: ID:562, Escherichia coli, DE3 |
| Links | Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Composition | T1 icosahedron with three E monomers and two Fab per asymmetric unit |
| Theoretical Mass | 24.5 |
| Name | Immature West Nile Virus complexed with E53 Fab |
| Num components | 2 |
| Entity assembly | |
| Name | Immature West Nile Virus |
| Type | VIRUS |
| Virus entity | |
| Empty | NO |
| Enveloped | YES |
| Ictvdb id | 00.026.0.01.051 |
| Virus host category | VERTEBRATES |
| Virus host species | Homo sapiens |
| Virus isolate | STRAIN |
| Virus type | VIRION |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| Details | 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
| Entity assembly id | 1 |
| pH | 8.0 |
| Vitrification | |
| Cryogen name | ETHANE |
| Instrument | Guillotine-style plunge freezeing device |
| Method | A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope. |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI/PHILIPS CM300FEG/T |
|---|---|
| Date | 08-JAN-08 / 25-MAR-08 |
| Details | low dose |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 12.0 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | calibrated: 47244 X, nominal: 45000 X |
| Cs | nominal: 2.0 mm |
| Astigmatism | live FFT |
| Detector distance | 0.0 |
| Nominal defocus | max: 2859 nm, min: 1193 nm |
| Specimen holder | |
| Specimen holder | model: GATAN LIQUID NITROGEN, type: EUCENTRIC |
| Tilt angle | min: -9999.0 degrees, max: -9999.0 degrees |
| Temperature | 98 Kelvin |
| Detector | |
| Type | Kodak SO163 |
 Processing | |
| 2D projection selection | |
| Software name | EMFIT |
|---|---|
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| Actual pixel size | 2.69 A/pix |
| CTF correction method | Each particle |
| Details | Final maps were calculated from two averaged datasets ( Details about the particle: 400 mesh copper grid ) |
| Magnification calibration | 47244 |
| Number of particles | 3927 |
| Resolution | 15.0 A |
| Resolution method | FSC at 0.5 cut-off |
| Software | Spider, XMIPP |
| 3D fitting | |
| Details | Each E molecule was divided into two rigid bodies, DI-DIII and DII-pr |
| Refinement Protocol | Rigid Body |
| Refinement Space | REAL |
| Software name | EMFIT |
| 3D fitting | |
| Details | a model for WNV pr was generated by SWISS-MODEL based on DENV pr structure |
| Refinement Protocol | Rigid Body |
| Refinement Space | REAL |
| Software name | EMFIT |
| Refine hist | |
| Total atoms | 2308 |
| Protein atoms | 2308 |
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