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- PDB-4mt8: Structure of the ERS1 dimerization and histidine phosphotransfer ... -

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Basic information

Entry
Database: PDB / ID: 4mt8
TitleStructure of the ERS1 dimerization and histidine phosphotransfer domain from Arabidopsis thaliana
ComponentsEthylene response sensor 1
KeywordsTRANSFERASE / Four helix bundle / Histidine kinase / CTR1 / ER Membrane
Function / homology
Function and homology information


ethylene binding / negative regulation of ethylene-activated signaling pathway / ethylene-activated signaling pathway / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum ...ethylene binding / negative regulation of ethylene-activated signaling pathway / ethylene-activated signaling pathway / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ethylene response sensor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMayerhofer, H. / Mueller-Dieckmann, J.
CitationJournal: J Biol Chem / Year: 2015
Title: Structural model of the cytosolic domain of the plant ethylene receptor 1 (ETR1).
Authors: Hubert Mayerhofer / Saravanan Panneerselvam / Heidi Kaljunen / Anne Tuukkanen / Haydyn D T Mertens / Jochen Mueller-Dieckmann /
Abstract: Ethylene initiates important aspects of plant growth and development through disulfide-linked receptor dimers located in the endoplasmic reticulum. The receptors feature a small transmembrane, ...Ethylene initiates important aspects of plant growth and development through disulfide-linked receptor dimers located in the endoplasmic reticulum. The receptors feature a small transmembrane, ethylene binding domain followed by a large cytosolic domain, which serves as a scaffold for the assembly of large molecular weight complexes of different ethylene receptors and other cellular participants of the ethylene signaling pathway. Here we report the crystallographic structures of the ethylene receptor 1 (ETR1) catalytic ATP-binding and the ethylene response sensor 1 dimerization histidine phosphotransfer (DHp) domains and the solution structure of the entire cytosolic domain of ETR1, all from Arabidopsis thaliana. The isolated dimeric ethylene response sensor 1 DHp domain is asymmetric, the result of different helical bending angles close to the conserved His residue. The structures of the catalytic ATP-binding, DHp, and receiver domains of ethylene receptors and of a homologous, but dissimilar, GAF domain were refined against experimental small angle x-ray scattering data, leading to a structural model of the entire cytosolic domain of the ethylene receptor 1. The model illustrates that the cytosolic domain is shaped like a dumbbell and that the receiver domain is flexible and assumes a position different from those observed in prokaryotic histidine kinases. Furthermore the cytosolic domain of ETR1 plays a key role, interacting with all other receptors and several participants of the ethylene signaling pathway. Our model, therefore, provides the first step toward a detailed understanding of the molecular mechanics of this important signal transduction process in plants.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethylene response sensor 1
B: Ethylene response sensor 1


Theoretical massNumber of molelcules
Total (without water)22,9082
Polymers22,9082
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-48 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.042, 98.747, 77.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

DetailsAsymmetric dimer

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Components

#1: Protein Ethylene response sensor 1 / AtERS1 / Protein ERS1


Mass: 11454.065 Da / Num. of mol.: 2
Fragment: dimerization and histidine phosphotransfer domain residues 308-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g40940, ERS, ERS1, T20B5.14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q38846, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.18 M l-proline, 0.1 M HEPES pH 7.5, 9% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.923 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2011
RadiationMonochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 1.9→49.3 Å / Num. all: 23082 / Num. obs: 22944 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 43.7 Å2 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→2 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXmodel building
PHENIX(phenix.refine: dev_1092)refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.3 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1159 5.06 %Random
Rwork0.1948 ---
obs0.1964 22919 99.8 %-
all-22964 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 0 84 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181578
X-RAY DIFFRACTIONf_angle_d1.5092129
X-RAY DIFFRACTIONf_dihedral_angle_d15.07608
X-RAY DIFFRACTIONf_chiral_restr0.088258
X-RAY DIFFRACTIONf_plane_restr0.008275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.98650.31311470.27162679X-RAY DIFFRACTION100
1.9865-2.09120.26981600.23022663X-RAY DIFFRACTION100
2.0912-2.22220.28111480.2022690X-RAY DIFFRACTION100
2.2222-2.39380.2321470.1872695X-RAY DIFFRACTION100
2.3938-2.63470.20751400.17432692X-RAY DIFFRACTION100
2.6347-3.01590.19981380.17952739X-RAY DIFFRACTION100
3.0159-3.79950.1941360.19672764X-RAY DIFFRACTION100
3.7995-49.39020.23911430.19492838X-RAY DIFFRACTION99
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)
10.5752-2.106-0.14156.5341.20391.1574-0.0383-0.06820.29660.30410.1013-0.5585-0.3507-0.1492-0.15730.26260.00150.13150.27570.02750.329723.463630.533314.6731
22.001-1.58330.13342.6298-0.18393.08490.11780.01940.06-0.2130.1673-0.30590.00110.2441-0.23690.08790.0051-0.00860.2340.01450.140933.02040.35646.1868
30.6637-1.15070.31637.32430.35110.38530.18560.03450.5082-1.08750.3351-0.0118-0.7419-0.0315-0.35440.7370.06670.43150.32990.02130.620621.484242.55716.55
41.8633-0.56230.46032.6188-0.18693.20810.2415-0.1871-0.1973-0.18760.13530.55580.1362-0.2818-0.26350.0807-0.05330.00330.25710.050.211824.2287-0.856911.6704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 406 )
3X-RAY DIFFRACTION3chain 'B' and (resid 312 through 350 )
4X-RAY DIFFRACTION4chain 'B' and (resid 351 through 407 )

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