6SAG: TMV with Ca2+ at low pH

Name: PDB 6SAG: Cryo-EM structure of TMV with Ca2+ at low pH
Published: 2019-09-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of TMV with Ca2+ at low pH. Determined by electron microscopy at 2.0 Å resolution. Released 18 Sept 2019.

Method: Electron microscopy
Resolution: 2.0 Å
Organisms: Tobacco mosaic virus (strain vulgare), Tobacco mosaic virus (vulgare)
Chains: 2
Atoms: 1,352
Mol. weight: 18.63 kDa
Ligands: MG, CA
Released: 18 Sept 2019

Explore 6SAG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SAG contains 8 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	7-13	7
β-strand	17-18	2	2
α-helix	20-30	11
α-helix	38-50	13
β-strand	53	1	2
α-helix	61-63	3
β-strand	68-70	3	2
α-helix	76-86	11
α-helix	92-96	5
α-helix	104-133	30
β-strand	138-139	2	2
α-helix	141-148	8
β-strand	152	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein	A	protein	159	Tobacco mosaic virus (strain vulgare)	P69687
RNA (5'-r(pgpap*a)-3')	R	RNA	3	Tobacco mosaic virus (vulgare)

Sequence of entity 1 (A), FASTA

>6SAG_1 Capsid protein (chains A)
XSYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVT
VRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATV
AIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPAT

Sequence of entity 2 (R), FASTA

>6SAG_2 RNA (5'-R(P*GP*AP*A)-3') (chains R)
GAA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
CA	Calcium ion	Ca	1

Primary citation

Elucidation of the viral disassembly switch of tobacco mosaic virus. Weis, F., Beckers, M., von der Hocht, I. et al. EMBO Rep (2019) 20:e48451-e48451. DOI 10.15252/embr.201948451 · PubMed

Other PDB entries of the same protein (UniProt P69687), best resolution first:

6SAE 1.9 Å, Cryo-EM structure of TMV in water
6R7M 1.92 Å, Tobacco Mosaic Virus (TMV)
6I5A 2.3 Å, Tobacco Mosaic Virus
6RLP 2.3 Å, Cryo-EM reconstruction of TMV coat protein
1EI7 2.45 Å, Tmv coat protein refined from the 4-layer aggregate
8EAW 2.8 Å, An asymmetric disk assembly formed by tandem dimers of the tobacco mosaic viral capsid…
2TMV 2.9 Å, Visualization of protein-nucleic acid interactions in a virus. Refined structure of…
6X0Q 3.0 Å, A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H coordinated with heme
6X0R 3.0 Å, A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H
3KML 3.01 Å, Circular Permutant of the Tobacco Mosaic Virus
4GQH 3.06 Å, The Conformations and Interactions of the Four-Layer Aggregate Revealed by X-ray…
3J06 3.3 Å, CryoEM Helical Reconstruction of TMV

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