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- PDB-5jfi: Crystal structure of a TDIF-TDR complex -

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Basic information

Entry
Database: PDB / ID: 5jfi
TitleCrystal structure of a TDIF-TDR complex
Components
  • CLE41
  • Leucine-rich repeat receptor-like protein kinase TDR
KeywordsSIGNALING PROTEIN / TDIF peptide / TDR receptor extracellular domain / LRR / glycosylation / hydroxylation
Function / homology
Function and homology information


procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / cell-cell signaling involved in cell fate commitment / phloem or xylem histogenesis / secondary shoot formation / apoplast / receptor serine/threonine kinase binding ...procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / cell-cell signaling involved in cell fate commitment / phloem or xylem histogenesis / secondary shoot formation / apoplast / receptor serine/threonine kinase binding / regulation of cell differentiation / non-specific serine/threonine protein kinase / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
CLAVATA3/ESR (CLE)-related protein 41/42/44 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / 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 ...CLAVATA3/ESR (CLE)-related protein 41/42/44 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / 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
CLE41 / CLAVATA3/ESR (CLE)-related protein 41 / Leucine-rich repeat receptor-like protein kinase TDR
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.749 Å
AuthorsXu, G. / Li, Z.
CitationJournal: To Be Published
Title: Crystal structure of a TDIF-TDR complex
Authors: Xu, G. / Li, Z.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat receptor-like protein kinase TDR
C: CLE41
B: Leucine-rich repeat receptor-like protein kinase TDR
D: CLE41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,63314
Polymers137,4214
Non-polymers2,21210
Water2,810156
1
A: Leucine-rich repeat receptor-like protein kinase TDR
C: CLE41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8167
Polymers68,7102
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint12 kcal/mol
Surface area24670 Å2
MethodPISA
2
B: Leucine-rich repeat receptor-like protein kinase TDR
D: CLE41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8167
Polymers68,7102
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint16 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.445, 92.445, 252.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Leucine-rich repeat receptor-like protein kinase TDR / Protein PHLOEM INTERCALATED WITH XYLEM / Tracheary element differentiation inhibitory factor ...Protein PHLOEM INTERCALATED WITH XYLEM / Tracheary element differentiation inhibitory factor receptor / TDIF receptor


Mass: 67429.945 Da / Num. of mol.: 2 / Fragment: UNP residues 30-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TDR, PXY, At5g61480, MCI2.4
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9FII5, non-specific serine/threonine protein kinase
#2: Protein/peptide CLE41


Mass: 1280.322 Da / Num. of mol.: 2 / Fragment: UNP residues 88-99 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178VDH8, UniProt: Q84W98*PLUS
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 200 mM MgSO4, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0422 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0422 Å / Relative weight: 1
ReflectionResolution: 2.749→46.223 Å / Num. obs: 54277 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 20.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.749→46.223 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1605 3.09 %
Rwork0.214 --
obs0.2156 52019 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.749→46.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9104 0 140 156 9400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129480
X-RAY DIFFRACTIONf_angle_d1.56212908
X-RAY DIFFRACTIONf_dihedral_angle_d14.6545556
X-RAY DIFFRACTIONf_chiral_restr0.0871478
X-RAY DIFFRACTIONf_plane_restr0.011668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.749-2.83780.36021060.30683777X-RAY DIFFRACTION77
2.8378-2.93920.34251430.27084134X-RAY DIFFRACTION87
2.9392-3.05680.36881300.25694426X-RAY DIFFRACTION91
3.0568-3.19590.28971600.24214601X-RAY DIFFRACTION95
3.1959-3.36440.30991640.24134654X-RAY DIFFRACTION97
3.3644-3.57510.31641560.22864725X-RAY DIFFRACTION98
3.5751-3.8510.23991500.18834815X-RAY DIFFRACTION99
3.851-4.23830.22981340.1814813X-RAY DIFFRACTION100
4.2383-4.8510.22411740.17064802X-RAY DIFFRACTION100
4.851-6.10950.28261490.20984827X-RAY DIFFRACTION100
6.1095-46.2290.24211390.23614840X-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)
10.9808-0.2114-0.41830.9611-0.75461.4448-0.0503-0.5480.6242-0.9192-0.2695-0.78680.75810.12180.3960.97470.1136-0.04530.41980.19070.684211.353622.1172-24.0321
22.099-0.778-0.48432.2115-1.91515.5098-0.06270.14220.321-0.47530.20720.52880.0978-0.6001-0.19160.6054-0.068-0.20560.40990.17680.6337-1.202315.9668-10.6386
32.68390.25630.36473.3753-0.14251.83540.0173-0.1364-0.0845-0.39240.26540.80160.2944-0.5893-0.2180.4541-0.0829-0.1690.59510.21170.5798-2.5609-0.41656.8807
43.7150.23961.77642.38780.45262.84820.1605-0.2522-0.60880.02680.0450.15470.3438-0.1334-0.22680.4548-0.0798-0.1450.46460.07490.470414.0328-12.367118.0975
53.88161.10261.12092.89420.58823.92260.18570.0491-0.68740.03490.168-0.41230.48210.3938-0.24030.43740.0208-0.09340.4711-0.03190.522135.8909-9.955626.0287
62.60511.24381.9212.96721.1453.6096-0.23850.13240.034-0.04530.2377-0.3173-0.13030.38480.05080.40310.0546-0.09590.6086-0.11280.517650.18927.065434.7607
72.11191.5358-0.02692.4031.74962.5075-0.0878-0.03030.10330.52560.6087-0.9437-1.19470.2254-0.23570.73090.109-0.2850.6462-0.15880.805449.72921.906844.0692
87.2554-1.76830.5489.8533-0.38023.9765-0.52330.187-0.21790.59990.1344-0.786-0.5926-0.62170.45380.287-0.1043-0.00190.5278-0.04150.441614.05935.66718.9876
91.0647-0.01531.69040.4685-0.16542.6677-0.1498-0.70750.20.1762-0.3289-0.1678-0.4954-0.71910.34380.52680.0878-0.12080.98960.03410.836968.3349-34.844523.1423
102.2309-0.76461.99171.5544-0.00165.32770.2187-0.6422-0.50730.0104-0.0773-0.22770.618-0.0091-0.14460.4064-0.0838-0.16270.6780.22140.676562.2087-47.38989.7002
112.8995-0.06620.44452.9958-0.96172.6480.273-0.3481-0.7469-0.32560.00620.14010.6884-0.1589-0.35820.5987-0.0742-0.20320.45430.1670.561945.8136-48.8018-7.8248
122.032-0.0154-0.63083.5273-1.31712.95490.07950.057-0.0828-0.19990.13570.47910.0606-0.4698-0.21010.4363-0.0806-0.09180.46590.13420.424233.8507-32.2073-19.0456
133.06171.507-0.32422.8937-0.58282.84070.07350.0030.36970.11060.15480.6809-0.2625-0.3916-0.20040.53780.04210.03950.41390.10150.503436.2378-10.3593-27.0028
143.1140.9564-0.7242.9504-2.44223.42380.30530.07140.40740.2135-0.17610.0886-0.3891-0.0083-0.14310.54320.04180.12720.3140.07110.447553.32153.9156-35.7032
152.26080.1621-1.4651.39471.42922.6830.5928-0.22880.55350.2412-0.3252-0.26770.21190.7927-0.04830.56080.13530.12490.58940.27690.745467.82723.1301-45.2151
169.8444-1.74312.88795.7199-2.8288.27820.17780.83450.95910.2017-0.6589-0.07520.30580.85660.5780.4187-0.09020.0360.357-0.00740.424551.8858-32.2203-9.9541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 40:100)
2X-RAY DIFFRACTION2chain A and (resseq 101:200)
3X-RAY DIFFRACTION3chain A and (resseq 201:300)
4X-RAY DIFFRACTION4chain A and (resseq 301:400)
5X-RAY DIFFRACTION5chain A and (resseq 401:500)
6X-RAY DIFFRACTION6chain A and (resseq 501:600)
7X-RAY DIFFRACTION7chain A and (resseq 601:625)
8X-RAY DIFFRACTION8chain C and (resseq 651:662)
9X-RAY DIFFRACTION9chain B and (resseq 40:100)
10X-RAY DIFFRACTION10chain B and (resseq 101:200)
11X-RAY DIFFRACTION11chain B and (resseq 201:300)
12X-RAY DIFFRACTION12chain B and (resseq 301:400)
13X-RAY DIFFRACTION13chain B and (resseq 401:500)
14X-RAY DIFFRACTION14chain B and (resseq 501:600)
15X-RAY DIFFRACTION15chain B and (resseq 601:625)
16X-RAY DIFFRACTION16chain D and (resseq 651:662)

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