9H6E | pdb_00009h6e

Complex of Histidine-containing phosphotransfer 1 (AHP1) and Response regulator 1 (ARR1) from A. thaliana

PDB DOI: https://doi.org/10.2210/pdb9H6E/pdb

Classification: SIGNALING PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-24 Released: 2025-03-26
Deposition Author(s): Tran, L.H., Ruszkowski, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.229 (Depositor), 0.231 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

ARR1 and AHP interactions in the multi-step phosphorelay system.

Tran, L.H., Ruszkowski, M.

(2025) Front Plant Sci 16: 1537021-1537021

PubMed: 40084109 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fpls.2025.1537021
Primary Citation Related Structures:
9H6E

PubMed Abstract:
Plants use multi-step phosphorelay (MSP) systems in response to exogenous and endogenous stimuli. Cytokinin and ethylene are among the factors that engage MSP signaling cascades but examples independent of phytohormones also exist. The MSP signaling involves four consecutive phosphorylation events at: (i) the kinase domain of the sensory histidine kinase, (ii) the receiver domain of the latter protein, (iii) the histidine-containing phosphotransfer protein, and (iv) the response regulator. In Arabidopsis thaliana , there are eight canonical histidine kinases, five histidine-containing phosphotransfer proteins (AHPs), one pseudo AHP, and 23 response regulators (ARRs). This redundancy suggests complex interactions between signaling pathways, including those involved in phytohormone cross-talk. To bring new insights at the molecular level, we investigated the structural and biophysical characteristics of the AHP1/ARR1 complex. ARR1, a type-B ARR, contains the GARP domain for DNA binding, in addition to the canonical receiver domain that mediates AHP1 interaction. We compared the ARR1 affinities across all five active AHPs and found a modest, two-fold higher affinity for AHP1. This result suggests that while ARR1 shows a slight preference for AHP1, it can also interact with AHP2-5, which potentially makes ARR1 a central node in signaling and a cross-talk modulator. In addition, we discuss the oligomerization state of AHP and related proteins utilizing all available experimental data to conclude that free AHPs are most likely monomeric.

Organizational Affiliation

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Macromolecule Content

Total Structure Weight: 98.83 kDa
Atom Count: 5,435
Modeled Residue Count: 672
Deposited Residue Count: 864
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine-containing phosphotransfer protein 1	A [auth C], B [auth A]	157	Arabidopsis thaliana	Mutation(s): 0 Gene Names: AHP1, ATHP3, At3g21510, MIL23.8
UniProt
Find proteins for Q9ZNV9 (Arabidopsis thaliana) Explore Q9ZNV9 Go to UniProtKB: Q9ZNV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZNV9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-component response regulator ARR1	C [auth D], D [auth B]	275	Arabidopsis thaliana	Mutation(s): 0 Gene Names: ARR1, At3g16857, K20I9.9, MUH15.1
UniProt
Find proteins for Q940D0 (Arabidopsis thaliana) Explore Q940D0 Go to UniProtKB: Q940D0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q940D0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth C]	G [auth C], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth A] Interactions & Density Focus chain G [auth C] Focus chain H [auth A]
OXM Query on OXM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain E [auth C] MOL2 format, chain I [auth A] MOL2 format, chain E [auth C] mmCIF format, chain I [auth A] mmCIF format, chain E [auth C]	E [auth C], I [auth A]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain I [auth A] Interactions & Density Focus chain E [auth C] Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain F [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth C]	F [auth C], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth C] Focus chain J [auth A] Focus chain K [auth A]