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- PDB-5xkj: Crystal structure of plant receptor ERL1-TMM in complexe with EPF2 -

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Basic information

Entry
Database: PDB / ID: 5xkj
TitleCrystal structure of plant receptor ERL1-TMM in complexe with EPF2
Components
  • LRR receptor-like serine/threonine-protein kinase ERL1
  • Protein EPIDERMAL PATTERNING FACTOR 2
  • Protein TOO MANY MOUTHS
KeywordsTRANSFERASE/MEMBRANE PROTEIN/HORMONE / stomata development ER / family TMM / peptide hormone EPFs / TRANSFERASE-MEMBRANE PROTEIN-HORMONE complex
Function / homology
Function and homology information


plant epidermis morphogenesis / negative regulation of stomatal complex development / guard cell differentiation / regulation of antifungal innate immune response / trichome morphogenesis / stomatal complex morphogenesis / stomatal complex formation / cellular response to abscisic acid stimulus / stomatal complex patterning / plant ovule development ...plant epidermis morphogenesis / negative regulation of stomatal complex development / guard cell differentiation / regulation of antifungal innate immune response / trichome morphogenesis / stomatal complex morphogenesis / stomatal complex formation / cellular response to abscisic acid stimulus / stomatal complex patterning / plant ovule development / embryo sac development / stomatal complex development / asymmetric cell division / response to abscisic acid / receptor serine/threonine kinase binding / defense response to fungus / peptide binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / signaling receptor binding / innate immune response / protein serine kinase activity / protein kinase binding / extracellular region / ATP binding / membrane / plasma membrane
Similarity search - Function
EPIDERMAL PATTERNING FACTOR-like protein / : / Epidermal patterning factor proteins / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype ...EPIDERMAL PATTERNING FACTOR-like protein / : / Epidermal patterning factor proteins / : / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
LRR receptor-like serine/threonine-protein kinase ERL1 / Protein EPIDERMAL PATTERNING FACTOR 2 / Protein TOO MANY MOUTHS
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.475 Å
AuthorsChai, J. / Lin, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31421001 China
Ministry of Science and Technology (China)2015CB910200 China
CitationJournal: Genes Dev. / Year: 2017
Title: A receptor-like protein acts as a specificity switch for the regulation of stomatal development.
Authors: Lin, G. / Zhang, L. / Han, Z. / Yang, X. / Liu, W. / Li, E. / Chang, J. / Qi, Y. / Shpak, E.D. / Chai, J.
History
DepositionMay 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protein TOO MANY MOUTHS
E: Protein EPIDERMAL PATTERNING FACTOR 2
A: LRR receptor-like serine/threonine-protein kinase ERL1
D: Protein TOO MANY MOUTHS
B: LRR receptor-like serine/threonine-protein kinase ERL1
F: Protein EPIDERMAL PATTERNING FACTOR 2


Theoretical massNumber of molelcules
Total (without water)227,1106
Polymers227,1106
Non-polymers00
Water00
1
C: Protein TOO MANY MOUTHS
E: Protein EPIDERMAL PATTERNING FACTOR 2
A: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)113,5553
Polymers113,5553
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-13 kcal/mol
Surface area35180 Å2
MethodPISA
2
D: Protein TOO MANY MOUTHS
B: LRR receptor-like serine/threonine-protein kinase ERL1
F: Protein EPIDERMAL PATTERNING FACTOR 2


Theoretical massNumber of molelcules
Total (without water)113,5553
Polymers113,5553
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-12 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.154, 65.601, 142.496
Angle α, β, γ (deg.)102.86, 97.60, 93.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein TOO MANY MOUTHS / Receptor-like protein 17 / AtRLP17


Mass: 47465.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TMM, RLP17, At1g80080, F18B13.16 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9SSD1
#2: Protein Protein EPIDERMAL PATTERNING FACTOR 2


Mass: 5669.548 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EPF2, At1g34245, F23M19 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8LC53
#3: Protein LRR receptor-like serine/threonine-protein kinase ERL1 / Protein ERECTA-like kinase 1


Mass: 60419.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ERL1, At5g62230, MMI9.14 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: C0LGW6, non-specific serine/threonine protein kinase
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 mM Ammonium citrate tribasic pH 7.0, 10% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 29462 / % possible obs: 93.8 % / Redundancy: 3 % / Net I/σ(I): 6.8
Reflection shellResolution: 3.4751→3.5993 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MN8

4mn8


Resolution: 3.475→46.186 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 1415 5.04 %
Rwork0.2543 --
obs0.2555 28075 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.475→46.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14174 0 0 0 14174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514444
X-RAY DIFFRACTIONf_angle_d0.8519628
X-RAY DIFFRACTIONf_dihedral_angle_d16.5948780
X-RAY DIFFRACTIONf_chiral_restr0.0482288
X-RAY DIFFRACTIONf_plane_restr0.0062556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4751-3.59930.30371200.29642336X-RAY DIFFRACTION83
3.5993-3.74330.31851550.27622652X-RAY DIFFRACTION96
3.7433-3.91360.32511380.2712712X-RAY DIFFRACTION95
3.9136-4.11980.28121540.25472693X-RAY DIFFRACTION95
4.1198-4.37780.2721480.23212687X-RAY DIFFRACTION95
4.3778-4.71550.27741260.23632731X-RAY DIFFRACTION96
4.7155-5.18940.27221230.22992715X-RAY DIFFRACTION97
5.1894-5.9390.32271510.27152755X-RAY DIFFRACTION97
5.939-7.47740.27891360.26992719X-RAY DIFFRACTION96
7.4774-46.19010.22231640.2462660X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -39.8 Å / Origin y: 3.0775 Å / Origin z: 94.4339 Å
111213212223313233
T0.3282 Å20.0094 Å2-0.0397 Å2-0.4599 Å2-0.0243 Å2--0.4787 Å2
L0.1451 °20.0835 °2-0.142 °2-0.1176 °2-0.165 °2--0.3947 °2
S0.0015 Å °0.0546 Å °0.0067 Å °0.0431 Å °0.0326 Å °0.0319 Å °-0.0266 Å °-0.0383 Å °-0.059 Å °
Refinement TLS groupSelection details: all

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