4V5W | pdb_00004v5w

Grapevine Fanleaf virus

• PDB DOI: https://doi.org/10.2210/pdb4V5W/pdb
• Entry: 4V5W supersedes: 2YI2, 2YI3, 2YI4

• Classification: VIRUS
• Organism(s): Grapevine fanleaf virus
• Mutation(s): No 


• Deposited: 2011-05-10 Released: 2014-07-09 
• Deposition Author(s): Schellenberger, P., Demangeat, G., Ritzenthaler, C., Lorber, B., Sauter, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.247 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination

Bonnefond, L., Schellenberger, P., Basquin, J., Demangeat, G., Ritzenthaler, C., Chenevert, R., Balg, C., Frugier, M., Rudinger-Thirion, J., Giege, R., Lorber, B., Sauter, C.

(2011) Cryst Growth Des 11: 4334

• DOI: https://doi.org/10.1021/CG101468P

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3,364.39 kDa 
• Atom Count: 237,060 
• Modeled Residue Count: 30,240 
• Deposited Residue Count: 30,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAT PROTEIN	A [auth AA], AA [auth BG], AB [auth CM], B [auth AB], BA [auth BH], BB [auth CN], C [auth AC], CA [auth BI], CB [auth CO], D [auth AD], DA [auth BJ], DB [auth CP], E [auth AE], EA [auth BK], EB [auth CQ], F [auth AF], FA [auth BL], FB [auth CR], G [auth AG], GA [auth BM], GB [auth CS], H [auth AH], HA [auth BN], HB [auth CT], I [auth AI], IA [auth BO], J [auth AJ], JA [auth BP], K [auth AK], KA [auth BQ], L [auth AL], LA [auth BR], M [auth AM], MA [auth BS], N [auth AN], NA [auth BT], O [auth AO], OA [auth CA], P [auth AP], PA [auth CB], Q [auth AQ], QA [auth CC], R [auth AR], RA [auth CD], S [auth AS], SA [auth CE], T [auth AT], TA [auth CF], U [auth BA], UA [auth CG], V [auth BB], VA [auth CH], W [auth BC], WA [auth CI], X [auth BD], XA [auth CJ], Y [auth BE], YA [auth CK], Z [auth BF], ZA [auth CL]	504	Grapevine fanleaf virus	Mutation(s): 0
UniProt
Find proteins for P18474 (Grapevine fanleaf virus) Explore P18474  Go to UniProtKB:  P18474

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.247 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 283.6	α = 90
b = 295.5	β = 91.6
c = 394.3	γ = 90

Software Package:

Software Name	Purpose
AMoRE	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Schellenberger, P., Demangeat, G., Ritzenthaler, C., Lorber, B., Sauter, C.
• This entry supersedes: 2YI2, 2YI3, 2YI4

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description