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- PDB-6l0w: Structure of RLD2 BRX domain bound to LZY3 CCL motif -

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Basic information

Entry
Database: PDB / ID: 6l0w
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 / nucleus / metal ion binding
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 ...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 / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / 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
CITRATE ANION / 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: 1.591 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 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3877
Polymers18,9474
Non-polymers4403
Water2,882160
1
A: RLD2
B: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6623
Polymers9,4732
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7 kcal/mol
Surface area5150 Å2
MethodPISA
2
C: RLD2
D: NGR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7254
Polymers9,4732
Non-polymers2512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5 kcal/mol
Surface area5130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.755, 55.658, 93.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 7624.250 Da / Num. of mol.: 2 / Mutation: V1057M
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): BL21star (DE3) / References: UniProt: F4K0X5
#2: Protein/peptide NGR2 / LZY3


Mass: 1849.131 Da / Num. of mol.: 2
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 (E. coli) / Strain (production host): BL21star (DE3) / References: UniProt: Q5XVG3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 4000, 0.05 M sodium citrate buffer (pH 6.5), 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9658 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9658 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 26622 / % possible obs: 98.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.4
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2261 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX1.13_2998: ???refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.591→47.763 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1281 4.82 %Random selection
Rwork0.1914 ---
obs0.193 26550 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.591→47.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 30 160 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071401
X-RAY DIFFRACTIONf_angle_d0.9721894
X-RAY DIFFRACTIONf_dihedral_angle_d12.571831
X-RAY DIFFRACTIONf_chiral_restr0.059187
X-RAY DIFFRACTIONf_plane_restr0.006251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.591-1.65450.25491290.21972521X-RAY DIFFRACTION90
1.6545-1.72980.20941300.19982693X-RAY DIFFRACTION95
1.7298-1.8210.20461340.19062781X-RAY DIFFRACTION98
1.821-1.93510.23961580.18892793X-RAY DIFFRACTION100
1.9351-2.08460.20321300.18722854X-RAY DIFFRACTION100
2.0846-2.29430.20891460.17922837X-RAY DIFFRACTION100
2.2943-2.62630.21731580.2052837X-RAY DIFFRACTION100
2.6263-3.30870.291300.20982926X-RAY DIFFRACTION100
3.3087-47.7630.20511660.17493027X-RAY DIFFRACTION100

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