3WRY | pdb_00003wry

Crystal structure of helicase complex 2

PDB DOI: https://doi.org/10.2210/pdb3WRY/pdb

Classification: TRANSFERASE
Organism(s): Solanum lycopersicum, Tobacco mosaic virus strain tomato/L
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-02-27 Released: 2014-08-13
Deposition Author(s): Matsumura, H., Katoh, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.248 (Depositor), 0.240 (DCC)
R-Value Work:
0.202 (Depositor), 0.190 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1

Ishibashi, K., Kezuka, Y., Kobayashi, C., Kato, M., Inoue, T., Nonaka, T., Ishikawa, M., Matsumura, H., Katoh, E.

(2014) Proc Natl Acad Sci U S A 111: E3486-E3495

PubMed: 25092327 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.1407888111
Primary Citation of Related Structures:
3WRV, 3WRW, 3WRX, 3WRY

PubMed Abstract:
The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.

Organizational Affiliation

Plant-Microbe Interactions Research Unit and.

Macromolecule Content

Total Structure Weight: 195.52 kDa
Atom Count: 13,940
Modelled Residue Count: 1,705
Deposited Residue Count: 1,764
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tm-1 protein	A, B	431	Solanum lycopersicum	Mutation(s): 1 Gene Names: Tm-1
UniProt
Find proteins for A7M6E7 (Solanum lycopersicum) Explore A7M6E7 Go to UniProtKB: A7M6E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7M6E7
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase large subunit	C, D	451	Tobacco mosaic virus strain tomato/L	Mutation(s): 0 EC: 2.1.1 (PDB Primary Data), 2.7.7 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P03587 (Tomato mosaic virus (strain L)) Explore P03587 Go to UniProtKB: P03587
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03587
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	F [auth A], J [auth C], L [auth D], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248 (Depositor), 0.240 (DCC)
R-Value Work: 0.202 (Depositor), 0.190 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.981	α = 90
b = 133.55	β = 90
c = 195.786	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Matsumura, H.

Katoh, E.

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 1.1: 2016-11-16
Changes: Database references
Version 1.2: 2017-11-08
Changes: Source and taxonomy, Structure summary
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations