OCA Atlas for 2Y26

2Y26

Virus

date

Dec 13, 2010

title

Transmission Defective Mutant Of Grapevine Fanleaf Virus

authors

P.Schellenberger, C.Sauter, B.Lorber, P.Bron, S.Trapani, M.Bergdo A.Marmonier, C.Schmitt-Keichinger, O.Lemaire, G.Demangeat, C.Ritzenthaler

compound

source

Molecule: Coat Protein
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Synonym: 2c-Cp, Rna2 Polyprotein Chain 3
Mutation: Yes

Organism_scientific: Grapevine Fanleaf Virus
Organism_taxid: 12274
Strain: Gflv-Td

symmetry

Space Group: P 21 3

R_factor

0.193

R_Free

0.210

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
408.000	408.000	408.000	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.70 Å

Gene
Ontology

Chain	Function	Process	Component
S, F, T, N, K, E, Q, M, C, L, A, J, O, P, B, H, D, R, I, G

Primary reference

Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus Transmission., Schellenberger P, Sauter C, Lorber B, Bron P, Trapani S, Bergdoll M, Marmonier A, Schmitt-Keichinger C, Lemaire O, Demangeat G, Ritzenthaler C, PLoS Pathog. 2011 May;7(5):e1002034. Epub 2011 May 19. PMID:21625570

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1584 Kb) [Save to disk]

Biological Unit Coordinates (2y26.pdb1.gz) 4691 Kb

CSU: Contacts of Structural Units for 2Y26

Structure Factors (5205 Kb)

Retrieve 2Y26 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2Y26 from S2C, [Save to disk]

Re-refined 2y26 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Y26 in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2Y26

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 2Y26, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2y26_H] [2y26_C] [2y26_Q] [2y26_P] [2y26_F] [2y26_L] [2y26_S] [2y26_I] [2y26_T] [2y26_M] [2y26_J] [2y26_A] [2y26_E] [2y26_R] [2y26_D] [2y26_B] [2y26_G] [2y26] [2y26_N] [2y26_O] [2y26_K]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 2Y26

Community annotation for 2Y26 at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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