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- PDB-6l0v: Structure of RLD2 BRX domain bound to LZY3 CCL motif -

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Basic information

Entry
Database: PDB / ID: 6l0v
TitleStructure of RLD2 BRX domain bound to LZY3 CCL motif
Components
  • NGR2
  • RLD2
KeywordsSIGNALING PROTEIN / gravitropism / gravitropic setpoint angle / auxin / BRX domain
Function / homology
Function and homology information


lateral root branching / gravitropism / regulation of growth / metal ion binding / nucleus
Similarity search - Function
Brevis radix (BRX) domain / Transcription factor BREVIS RADIX, N-terminal domain / LAZY family / Transcription factor regulating root and shoot growth via Pin3 / Transcription factor BRX N-terminal domain / BRX domain profile. / Pleckstrin homology domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 ...Brevis radix (BRX) domain / Transcription factor BREVIS RADIX, N-terminal domain / LAZY family / Transcription factor regulating root and shoot growth via Pin3 / Transcription factor BRX N-terminal domain / BRX domain profile. / Pleckstrin homology domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Regulator of chromosome condensation (RCC1) signature 2. / Zinc finger FYVE/FYVE-related type profile. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Pleckstrin homology domain / Zinc finger, FYVE/PHD-type / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Regulator of chromosome condensation (RCC1) family with FYVE zinc finger domain-containing protein / Protein LAZY 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.347 Å
AuthorsHirano, Y. / Futrutani, M. / Nishimura, T. / Taniguchi, M. / Morita, M.T. / Hakoshima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST JPMJCR14M5 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Polar recruitment of RLD by LAZY1-like protein during gravity signaling in root branch angle control.
Authors: Furutani, M. / Hirano, Y. / Nishimura, T. / Nakamura, M. / Taniguchi, M. / Suzuki, K. / Oshida, R. / Kondo, C. / Sun, S. / Kato, K. / Fukao, Y. / Hakoshima, T. / Morita, M.T.
History
DepositionSep 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RLD2
B: NGR2
C: RLD2
D: NGR2
E: RLD2
F: NGR2
G: RLD2
H: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,89514
Polymers37,3908
Non-polymers5056
Water5,116284
1
A: RLD2
B: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5164
Polymers9,3482
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-2 kcal/mol
Surface area5730 Å2
MethodPISA
2
C: RLD2
D: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4103
Polymers9,3482
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-5 kcal/mol
Surface area5230 Å2
MethodPISA
3
E: RLD2
F: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4724
Polymers9,3482
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-2 kcal/mol
Surface area4830 Å2
MethodPISA
4
G: RLD2
H: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4983
Polymers9,3482
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-6 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.673, 31.237, 128.871
Angle α, β, γ (deg.)90.00, 91.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein
RLD2 / Regulator of chromosome condensation (RCC1) family with FYVE zinc finger domain-containing protein


Mass: 7498.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g12350 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: F4K0X5
#2: Protein/peptide
NGR2 / LZY3


Mass: 1849.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NGR2, At1g72490, T10D10.4, T10D10_4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Star / References: UniProt: Q5XVG3

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Non-polymers , 4 types, 290 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: PEG 4000, sodium acetate, Tris-HCl buffer (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.347→50 Å / Num. obs: 75903 / % possible obs: 95.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.1
Reflection shellResolution: 1.347→1.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3518 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.347→42.942 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 3752 4.95 %Random Selection
Rwork0.177 ---
obs0.1781 75856 95.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.347→42.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 33 284 2874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082781
X-RAY DIFFRACTIONf_angle_d0.9153758
X-RAY DIFFRACTIONf_dihedral_angle_d4.6311508
X-RAY DIFFRACTIONf_chiral_restr0.082373
X-RAY DIFFRACTIONf_plane_restr0.007496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.347-1.3640.2981200.2472262X-RAY DIFFRACTION80
1.364-1.38190.25921310.22282552X-RAY DIFFRACTION93
1.3819-1.40090.24561380.20382545X-RAY DIFFRACTION91
1.4009-1.42090.20391470.18822479X-RAY DIFFRACTION90
1.4209-1.44210.24411280.17012603X-RAY DIFFRACTION93
1.4421-1.46460.22691370.16552653X-RAY DIFFRACTION97
1.4646-1.48860.16991510.15612659X-RAY DIFFRACTION94
1.4886-1.51430.17361370.14762623X-RAY DIFFRACTION96
1.5143-1.54180.18361440.14772735X-RAY DIFFRACTION97
1.5418-1.57150.18521290.1472686X-RAY DIFFRACTION96
1.5715-1.60360.18571520.14592700X-RAY DIFFRACTION98
1.6036-1.63850.19571380.1352691X-RAY DIFFRACTION95
1.6385-1.67660.18191150.13732565X-RAY DIFFRACTION93
1.6766-1.71850.1991200.14452740X-RAY DIFFRACTION97
1.7185-1.7650.18761470.15552750X-RAY DIFFRACTION98
1.765-1.81690.22241520.15192701X-RAY DIFFRACTION97
1.8169-1.87550.1581560.14842691X-RAY DIFFRACTION97
1.8755-1.94260.20411500.16132737X-RAY DIFFRACTION98
1.9426-2.02040.2041530.16312739X-RAY DIFFRACTION98
2.0204-2.11230.21361390.16512624X-RAY DIFFRACTION93
2.1123-2.22370.20571490.16762765X-RAY DIFFRACTION97
2.2237-2.3630.17231420.17032749X-RAY DIFFRACTION98
2.363-2.54540.19891460.17762743X-RAY DIFFRACTION98
2.5454-2.80150.21471590.19952787X-RAY DIFFRACTION97
2.8015-3.20680.24881060.19872688X-RAY DIFFRACTION93
3.2068-4.03970.20641220.19222797X-RAY DIFFRACTION97
4.0397-42.9420.17631440.18972840X-RAY DIFFRACTION95

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