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- PDB-9h6e: Complex of Histidine-containing phosphotransfer 1 (AHP1) and Resp... -

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Basic information

Entry
Database: PDB / ID: 9h6e
TitleComplex of Histidine-containing phosphotransfer 1 (AHP1) and Response regulator 1 (ARR1) from A. thaliana
Components
  • Histidine-containing phosphotransfer protein 1
  • Two-component response regulator ARR1
KeywordsSIGNALING PROTEIN / response regulator / histidine-containing phosphotransfer / cytokinin signaling / protein-protein complex
Function / homology
Function and homology information


cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / callus formation / regulation of anthocyanin metabolic process / primary root development / maintenance of shoot apical meristem identity / axillary shoot meristem initiation / shoot system development / regulation of root meristem growth ...cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / callus formation / regulation of anthocyanin metabolic process / primary root development / maintenance of shoot apical meristem identity / axillary shoot meristem initiation / shoot system development / regulation of root meristem growth / response to cytokinin / regulation of chlorophyll biosynthetic process / multidimensional cell growth / embryo sac development / cytokinin-activated signaling pathway / protein histidine kinase binding / histidine phosphotransfer kinase activity / root development / response to water deprivation / phosphorelay response regulator activity / phosphorelay signal transduction system / transcription cis-regulatory region binding / DNA-binding transcription factor activity / nucleus / cytoplasm / cytosol
Similarity search - Function
Response regulator B-type, plant / Two-component response regulator ARR-like / Myb domain, plants / Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Myb-type HTH DNA-binding domain profile. / Myb domain ...Response regulator B-type, plant / Two-component response regulator ARR-like / Myb domain, plants / Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
OXAMIC ACID / Two-component response regulator ARR1 / Histidine-containing phosphotransfer protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsTran, L.H. / Ruszkowski, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Front Plant Sci / Year: 2025
Title: ARR1 and AHP interactions in the multi-step phosphorelay system.
Authors: Tran, L.H. / Ruszkowski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Histidine-containing phosphotransfer protein 1
A: Histidine-containing phosphotransfer protein 1
D: Two-component response regulator ARR1
B: Two-component response regulator ARR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,83411
Polymers98,2854
Non-polymers5487
Water1629
1
C: Histidine-containing phosphotransfer protein 1
D: Two-component response regulator ARR1
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, ARR1 and AHP1 were purified separately. Then, they were mixed in with an excess of AHP1. The mixture was concentrated and run on Sixe-exclusion chromatography. There is a ...Evidence: gel filtration, ARR1 and AHP1 were purified separately. Then, they were mixed in with an excess of AHP1. The mixture was concentrated and run on Sixe-exclusion chromatography. There is a peak of the complex and a peak of excess AHP1
  • 49.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)49,3865
Polymers49,1432
Non-polymers2433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-2 kcal/mol
Surface area17060 Å2
MethodPISA
2
A: Histidine-containing phosphotransfer protein 1
B: Two-component response regulator ARR1
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, ARR1 and AHP1 were purified separately. Then, they were mixed in with an excess of AHP1. The mixture was concentrated and run on Sixe-exclusion chromatography. There is a ...Evidence: gel filtration, ARR1 and AHP1 were purified separately. Then, they were mixed in with an excess of AHP1. The mixture was concentrated and run on Sixe-exclusion chromatography. There is a peak of the complex and a peak of excess AHP1
  • 49.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)49,4486
Polymers49,1432
Non-polymers3054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-0 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.500, 132.574, 160.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules CADB

#1: Protein Histidine-containing phosphotransfer protein 1


Mass: 17905.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHP1, ATHP3, At3g21510, MIL23.8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZNV9
#2: Protein Two-component response regulator ARR1


Mass: 31237.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: at the N terminus, there are 6H tag, TEV cleavage site and SNA linker
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARR1, At3g16857, K20I9.9, MUH15.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q940D0

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Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.84 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mM Sodium formate, 20 mM ammonium acetate, 20 sodium citrate tribasic dihydrate, 20 mM potassium sodium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM Tris (base) BICINE pH 8.5, 20% ...Details: 20 mM Sodium formate, 20 mM ammonium acetate, 20 sodium citrate tribasic dihydrate, 20 mM potassium sodium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM Tris (base) BICINE pH 8.5, 20% glycerol, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9196 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.87→80.336 Å / Num. obs: 30328 / % possible obs: 72.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 94.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.5
Reflection shellResolution: 2.874→3.15 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1517 / CC1/2: 0.81 / % possible all: 15.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→42.25 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1031 3.4 %
Rwork0.1913 --
obs0.1926 30299 72.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5390 0 36 9 5435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.14
X-RAY DIFFRACTIONf_dihedral_angle_d16.3682109
X-RAY DIFFRACTIONf_chiral_restr0.06852
X-RAY DIFFRACTIONf_plane_restr0.008945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.020.3688180.3464494X-RAY DIFFRACTION9
3.03-3.210.3775580.31511654X-RAY DIFFRACTION29
3.21-3.460.33811360.28083876X-RAY DIFFRACTION68
3.46-3.810.28431990.24355645X-RAY DIFFRACTION98
3.81-4.360.22332030.17795762X-RAY DIFFRACTION100
4.36-5.490.2082040.17415815X-RAY DIFFRACTION100
5.49-42.250.20382130.17246022X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6262-5.091-2.39267.06050.8883.21830.6968-0.27810.5093-0.4873-0.3494-0.3336-0.1614-0.3983-0.32240.4495-0.07690.00040.7401-0.06510.630510.908529.380778.3152
21.76022.8822-2.14229.0842-1.91116.58220.1577-0.66250.7379-0.0388-0.00261.03850.4527-0.49-0.19970.4314-0.0796-0.08850.86650.08620.794215.384514.766586.0679
34.15121.3110.04674.4157-0.98442.71690.2248-0.8154-0.26560.4086-0.1853-0.82320.42380.4299-0.17360.57930.0601-0.14710.91070.0990.741136.87414.681891.6611
48.9406-1.27341.66585.3015-0.97233.89680.4634-0.71241.8550.0823-0.2587-0.9184-0.08780.0750.12850.3594-0.0328-0.09140.5463-0.04020.538729.450224.850986.6956
56.65085.03914.00343.95932.26369.9014-0.74160.21810.45341.85770.87162.38681.0013-0.3574-0.31390.83180.01910.06051.22990.07481.00833.779824.771386.282
62.6494-1.61473.84028.07811.1648.01990.8262-1.8411-0.38211.1248-0.61190.8492-0.1361-0.5698-0.13490.4074-0.04540.05550.744-0.05560.689-13.861728.99580.9318
71.5384-0.26240.98577.7542-0.10338.74390.16830.02070.1495-0.3694-0.2427-0.3146-0.54580.12620.00120.51230.0211-0.01360.6167-0.00350.8141-2.708127.58769.1798
83.96744.71131.48799.6602-1.583.89811.40041.5054-1.6638-2.0229-0.46681.94720.6328-0.1756-1.05590.86880.0831-0.30091.09-0.11811.4809-15.930126.173360.823
95.6455-5.03331.16738.5312-0.92974.25070.53980.4468-1.1899-0.8035-0.28110.3590.89940.2793-0.2730.5730.0069-0.07350.5543-0.12760.65027.925510.916767.0287
106.6041-4.5447-0.86054.67450.67582.2651-0.4839-0.7061-1.12780.38060.50730.78850.3623-0.4662-0.02880.4118-0.1482-0.05360.66970.01540.6885-3.863218.541375.4867
114.5351-0.93450.2754.0433-0.86224.380.1788-1.5108-0.04841.0164-0.24120.0450.54370.2474-0.1360.8994-0.0609-0.02121.12980.19830.723422.73750.5537101.9768
123.2593-1.151-0.87267.1254-0.89782.55830.1328-0.21-0.8119-0.3875-0.2315-0.39491.65890.39690.09791.45990.1985-0.10190.9630.28030.79628.2468-15.466593.237
135.8176-0.0813-2.63454.2316-0.36658.14130.49010.7265-0.6764-1.536-0.1075-0.00581.0027-0.0883-0.29871.02750.1573-0.19550.7326-0.2520.65923.782518.995446.6625
142.48261.10770.79242.6511-2.71634.68750.16460.45150.4833-1.1717-0.0869-0.6611-0.16831.2209-0.07121.2186-0.03690.31861.0771-0.26930.782217.002530.575841.6655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid -2 through 19 )
2X-RAY DIFFRACTION2chain 'C' and (resid 20 through 40 )
3X-RAY DIFFRACTION3chain 'C' and (resid 41 through 108 )
4X-RAY DIFFRACTION4chain 'C' and (resid 109 through 142 )
5X-RAY DIFFRACTION5chain 'C' and (resid 143 through 150 )
6X-RAY DIFFRACTION6chain 'A' and (resid 0 through 19 )
7X-RAY DIFFRACTION7chain 'A' and (resid 20 through 33 )
8X-RAY DIFFRACTION8chain 'A' and (resid 34 through 40 )
9X-RAY DIFFRACTION9chain 'A' and (resid 41 through 108 )
10X-RAY DIFFRACTION10chain 'A' and (resid 109 through 154 )
11X-RAY DIFFRACTION11chain 'D' and (resid 38 through 96 )
12X-RAY DIFFRACTION12chain 'D' and (resid 97 through 296 )
13X-RAY DIFFRACTION13chain 'B' and (resid 38 through 120 )
14X-RAY DIFFRACTION14chain 'B' and (resid 121 through 296 )

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