OCA Atlas for 3J9X

3J9X

Virus

date

Mar 21, 2015

title

A Virus That Infects A Hyperthermophile Encapsidates A-Form

authors

F.Dimaio, X.Yu, E.Rensen, M.Krupovic, D.Prangishvili, E.Egelman

compound

source

Molecule: Coat Protein
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R V, W, X, Y, Z, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6;

Organism_scientific: Sulfolobus Islandicus Rod-Shaped Virus
Organism_taxid: 157899

Molecule: Dna
Chain: 7, 8

Organism_scientific: Sulfolobus Islandicus Rod-Shaped Virus
Organism_taxid: 157899

symmetry

Space Group: P 1

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
1.000	1.000	1.000	90.00	90.00	90.00

method

Electron Microscopy

resolution

3.80 Å

Primary reference

Virology. A virus that infects a hyperthermophile encapsidates A-form DNA., DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D, Egelman EH, Science. 2015 May 22;348(6237):914-7. doi: 10.1126/science.aaa4181. PMID:25999507

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1198 Kb) [Save to disk]

Biological Unit Coordinates (3j9x.pdb1.gz) 1196 Kb

CSU: Contacts of Structural Units for 3J9X

Retrieve 3J9X in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3J9X from S2C, [Save to disk]

View 3J9X 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 3J9X

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 3J9X, from MSDmotif at EBI

Fold representative 3j9x from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3j9x_C] [3j9x_n] [3j9x_4] [3j9x_z] [3j9x_e] [3j9x_U] [3j9x_j] [3j9x_Q] [3j9x_b] [3j9x_S] [3j9x_V] [3j9x_w] [3j9x_P] [3j9x_R] [3j9x_3] [3j9x] [3j9x_B] [3j9x_p] [3j9x_F] [3j9x_2] [3j9x_G] [3j9x_J] [3j9x_l] [3j9x_f] [3j9x_d] [3j9x_O] [3j9x_i] [3j9x_1] [3j9x_E] [3j9x_s] [3j9x_v] [3j9x_M] [3j9x_X] [3j9x_W] [3j9x_h] [3j9x_6] [3j9x_g] [3j9x_5] [3j9x_T] [3j9x_q] [3j9x_x] [3j9x_u] [3j9x_L] [3j9x_a] [3j9x_H] [3j9x_Z] [3j9x_Y] [3j9x_k] [3j9x_c] [3j9x_m] [3j9x_8] [3j9x_N] [3j9x_K] [3j9x_t] [3j9x_D] [3j9x_o] [3j9x_A] [3j9x_I] [3j9x_r] [3j9x_7] [3j9x_y]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 3J9X

Community annotation for 3J9X at PDBWiki (http://pdbwiki.org)

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