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- PDB-5xjx: Pre-formed plant receptor ERL1-TMM complex -

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Basic information

Entry
Database: PDB / ID: 5xjx
TitlePre-formed plant receptor ERL1-TMM complex
Components
  • LRR receptor-like serine/threonine-protein kinase ERL1
  • Protein TOO MANY MOUTHS
KeywordsTRANSFERASE/MEMBRANE PROTEIN / receptor like kinase / receptor like protein / pre-formed complexe / TRANSFERASE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


regulation of antifungal innate immune response / trichome morphogenesis / stomatal complex morphogenesis / stomatal complex formation / stomatal complex patterning / cellular response to abscisic acid stimulus / plant ovule development / embryo sac development / asymmetric cell division / response to abscisic acid ...regulation of antifungal innate immune response / trichome morphogenesis / stomatal complex morphogenesis / stomatal complex formation / stomatal complex patterning / cellular response to abscisic acid stimulus / plant ovule development / embryo sac development / asymmetric cell division / response to abscisic acid / receptor serine/threonine kinase binding / defense response to fungus / peptide binding / non-specific serine/threonine protein kinase / phosphorylation / signaling receptor binding / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / ATP binding / membrane / plasma membrane
Similarity search - Function
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 ...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 TOO MANY MOUTHS
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.055 Å
AuthorsChai, J. / Lin, G. / Zhang, L. / Han, Z. / Yang, X. / Liu, W. / Qi, Y. / Chang, J. / Li, E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31421001 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 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Protein TOO MANY MOUTHS
K: LRR receptor-like serine/threonine-protein kinase ERL1
F: Protein TOO MANY MOUTHS
D: Protein TOO MANY MOUTHS
L: Protein TOO MANY MOUTHS
H: Protein TOO MANY MOUTHS
J: Protein TOO MANY MOUTHS
G: LRR receptor-like serine/threonine-protein kinase ERL1
A: LRR receptor-like serine/threonine-protein kinase ERL1
I: LRR receptor-like serine/threonine-protein kinase ERL1
B: LRR receptor-like serine/threonine-protein kinase ERL1
E: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)647,89612
Polymers647,89612
Non-polymers00
Water0
1
C: Protein TOO MANY MOUTHS
A: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)107,9832
Polymers107,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: LRR receptor-like serine/threonine-protein kinase ERL1
L: Protein TOO MANY MOUTHS


Theoretical massNumber of molelcules
Total (without water)107,9832
Polymers107,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Protein TOO MANY MOUTHS
E: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)107,9832
Polymers107,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein TOO MANY MOUTHS
B: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)107,9832
Polymers107,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Protein TOO MANY MOUTHS
G: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)107,9832
Polymers107,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: Protein TOO MANY MOUTHS
I: LRR receptor-like serine/threonine-protein kinase ERL1


Theoretical massNumber of molelcules
Total (without water)107,9832
Polymers107,9832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.172, 114.395, 191.952
Angle α, β, γ (deg.)89.57, 90.46, 59.86
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.: 6
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
LRR receptor-like serine/threonine-protein kinase ERL1 / Protein ERECTA-like kinase 1


Mass: 60516.891 Da / Num. of mol.: 6
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

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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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4% v/v Tacsimate pH 6.0, 10% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: MAC Science DIP-320 / Detector: IMAGE PLATE / Date: Oct 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 158048 / % possible obs: 98.5 % / Redundancy: 3 % / Net I/σ(I): 14
Reflection shellResolution: 3.0553→3.0901 Å

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Processing

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

4mn8


Resolution: 3.055→43.249 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.3
RfactorNum. reflection% reflection
Rfree0.2761 7885 4.99 %
Rwork0.2536 --
obs0.2547 157985 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.055→43.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41970 0 0 0 41970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342792
X-RAY DIFFRACTIONf_angle_d0.70258206
X-RAY DIFFRACTIONf_dihedral_angle_d15.58825938
X-RAY DIFFRACTIONf_chiral_restr0.0456786
X-RAY DIFFRACTIONf_plane_restr0.0057602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0553-3.09010.37761780.35663753X-RAY DIFFRACTION72
3.0901-3.12640.36482670.34134971X-RAY DIFFRACTION98
3.1264-3.16450.34322810.32935016X-RAY DIFFRACTION98
3.1645-3.20460.34772540.33215074X-RAY DIFFRACTION99
3.2046-3.24670.35612580.32795058X-RAY DIFFRACTION98
3.2467-3.29120.35562650.32885094X-RAY DIFFRACTION99
3.2912-3.33820.36762460.33425035X-RAY DIFFRACTION99
3.3382-3.3880.36332510.32835126X-RAY DIFFRACTION99
3.388-3.44090.35682820.31845003X-RAY DIFFRACTION99
3.4409-3.49730.34262430.31225079X-RAY DIFFRACTION98
3.4973-3.55760.30962830.29085048X-RAY DIFFRACTION99
3.5576-3.62220.28972680.2765039X-RAY DIFFRACTION99
3.6222-3.69190.28162670.26845091X-RAY DIFFRACTION98
3.6919-3.76720.27722860.27094974X-RAY DIFFRACTION98
3.7672-3.8490.29712820.25895074X-RAY DIFFRACTION99
3.849-3.93850.26412960.24895034X-RAY DIFFRACTION99
3.9385-4.03690.28722800.24285014X-RAY DIFFRACTION99
4.0369-4.1460.30122380.24115125X-RAY DIFFRACTION99
4.146-4.26790.26792570.22585082X-RAY DIFFRACTION99
4.2679-4.40550.23942710.22075028X-RAY DIFFRACTION99
4.4055-4.56280.22652890.21755052X-RAY DIFFRACTION99
4.5628-4.74530.24682690.22545011X-RAY DIFFRACTION99
4.7453-4.9610.24292650.22375093X-RAY DIFFRACTION99
4.961-5.22210.2522600.22055085X-RAY DIFFRACTION99
5.2221-5.54870.27072480.23475038X-RAY DIFFRACTION99
5.5487-5.97610.29652600.27775039X-RAY DIFFRACTION98
5.9761-6.57560.28622530.25115073X-RAY DIFFRACTION98
6.5756-7.52280.21162460.21815002X-RAY DIFFRACTION97
7.5228-9.46150.26852660.23755066X-RAY DIFFRACTION99
9.4615-43.25360.21082760.2034923X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -50.2109 Å / Origin y: 67.4422 Å / Origin z: -126.1754 Å
111213212223313233
T0.4269 Å20.0762 Å20.012 Å2-0.3084 Å2-0.0089 Å2--0.3332 Å2
L-0.0051 °20.0142 °20.0311 °2-0.0322 °20.0014 °2--0.0689 °2
S-0.0119 Å °0.0162 Å °-0.003 Å °-0.0046 Å °-0.0024 Å °0.0016 Å °0.0262 Å °0.0453 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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