4NIA Virus Rna date Nov 05, 2013
title Satellite Tobacco Mosaic Virus Refined At Room Temperature T Resolution Using Ncs Restraints
authors S.B.Larson, J.S.Day, A.Mcpherson
compound source
Molecule: Coat Protein
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
Organism_scientific: Satellite Tobacco Mosaic Virus
Organism_common: Stmv
Organism_taxid: 12881

Molecule: Rna (5'-R(Papapapapapapapapapa)-3')
Chain: P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d
Other_details: Arbitrary Rna Adenine Nucleotide Decamer

Organism_scientific: Satellite Tobacco Mosaic Virus
Organism_common: Stmv
Organism_taxid: 12881

Molecule: Rna (5'-R(Pupupupupupupupupupu)-3')
Chain: e, f, g, h, I, j, k, l, m, n, o, p, q, r, s
Other_details: Arbitrary Rna Uridine Nucleotide Decamer

Organism_scientific: Satellite Tobacco Mosaic Virus
Organism_common: Stmv
Organism_taxid: 12881

Molecule: Rna (5'-R(Pupu)-3')
Chain: t, u, v, w, x, y, z, 1, 2, 3, 4, 5, 6, 7, 8
Other_details: Arbitrary Rna Uridine Nucleotide Dimer

Organism_scientific: Satellite Tobacco Mosaic Virus
Organism_common: Stmv
Organism_taxid: 12881
symmetry Space Group: I 2 2 2
R_factor 0.123 R_Free 0.156
crystal
cell
length a length b length c angle alpha angle beta angle gamma
174.268 191.774 202.503 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.82 Å
ligand MG, PO4, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, O, J, N, K, E, B, H, M, C, D, I, G, L


Primary referenceSatellite tobacco mosaic virus refined to 1.4 A resolution., Larson SB, Day JS, McPherson A, Acta Crystallogr D Biol Crystallogr. 2014 Sep 1;70(Pt 9):2316-30. doi:, 10.1107/S1399004714013789. Epub 2014 Aug 29. PMID:25195746
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (592 Kb) [Save to disk]
  • Biological Unit Coordinates (4nia.pdb1.gz) 2283 Kb
  • LPC: Ligand-Protein Contacts for 4NIA
  • CSU: Contacts of Structural Units for 4NIA
  • Structure Factors (4212 Kb)
  • Retrieve 4NIA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NIA from S2C, [Save to disk]
  • Re-refined 4nia structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NIA 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 4NIA
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NIA, from MSDmotif at EBI
  • Fold representative 4nia from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nia_S] [4nia_y] [4nia_B] [4nia_a] [4nia_7] [4nia_N] [4nia_4] [4nia_2] [4nia_d] [4nia_q] [4nia_W] [4nia_T] [4nia_Z] [4nia_C] [4nia_l] [4nia_c] [4nia_Y] [4nia_5] [4nia_z] [4nia_o] [4nia_k] [4nia_u] [4nia_R] [4nia_M] [4nia_r] [4nia_Q] [4nia_3] [4nia_j] [4nia_8] [4nia_s] [4nia_V] [4nia_6] [4nia_A] [4nia_b] [4nia_h] [4nia_I] [4nia_w] [4nia_i] [4nia_m] [4nia_H] [4nia_e] [4nia_G] [4nia_U] [4nia_p] [4nia_n] [4nia_F] [4nia_g] [4nia_t] [4nia_O] [4nia_L] [4nia_J] [4nia] [4nia_D] [4nia_X] [4nia_v] [4nia_E] [4nia_f] [4nia_P] [4nia_1] [4nia_x] [4nia_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4NIA
  • Community annotation for 4NIA at PDBWiki (http://pdbwiki.org)

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