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- PDB-4v2e: FLRT3 LRR domain -

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Basic information

Entry
Database: PDB / ID: 4v2e
TitleFLRT3 LRR domain
ComponentsFIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 3
KeywordsSIGNALING PROTEIN / LEUCINE-RICH REPEAT / LRR / UNC5
Function / homology
Function and homology information


proepicardium cell migration involved in pericardium morphogenesis / Downstream signaling of activated FGFR1 / head development / synaptic membrane adhesion / growth cone membrane / cell-cell adhesion via plasma-membrane adhesion molecules / embryonic morphogenesis / fibroblast growth factor receptor binding / chemorepellent activity / positive regulation of synapse assembly ...proepicardium cell migration involved in pericardium morphogenesis / Downstream signaling of activated FGFR1 / head development / synaptic membrane adhesion / growth cone membrane / cell-cell adhesion via plasma-membrane adhesion molecules / embryonic morphogenesis / fibroblast growth factor receptor binding / chemorepellent activity / positive regulation of synapse assembly / neuron projection extension / response to axon injury / fibroblast growth factor receptor signaling pathway / axon terminus / axonal growth cone / synapse assembly / synaptic membrane / axon guidance / synapse organization / neuron projection development / cell-cell junction / cell junction / heart development / postsynaptic membrane / postsynaptic density / focal adhesion / glutamatergic synapse / endoplasmic reticulum membrane / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / Fibronectin type III / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat transmembrane protein FLRT3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. ...Seiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R.
CitationJournal: Neuron / Year: 2014
Title: Flrt Structure: Balancing Repulsion and Cell Adhesion in Cortical and Vascular Development.
Authors: Seiradake, E. / Del Toro, D. / Nagel, D. / Cop, F. / Hartl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R.
History
DepositionOct 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 3
B: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)75,1162
Polymers75,1162
Non-polymers00
Water0
1
A: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)37,5581
Polymers37,5581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)37,5581
Polymers37,5581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.810, 61.970, 92.970
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 3 / FLRT3


Mass: 37557.832 Da / Num. of mol.: 2 / Fragment: LRR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BGT1
Sequence detailsCONTAINS C-TERMINAL HIS TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.5→57 Å / Num. obs: 63975 / % possible obs: 90.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 35.05 Å2 / Rmerge(I) obs: 0.46 / Net I/σ(I): 3.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.98 / % possible all: 89.2

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V2D

4v2d


Resolution: 2.5→57.38 Å / Cor.coef. Fo:Fc: 0.6342 / Cor.coef. Fo:Fc free: 0.6285 / SU R Cruickshank DPI: 5.742 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.005 / SU Rfree Blow DPI: 0.435 / SU Rfree Cruickshank DPI: 0.452
RfactorNum. reflection% reflectionSelection details
Rfree0.3514 1051 5.1 %RANDOM
Rwork0.3448 ---
obs0.3451 20595 90.24 %-
Displacement parametersBiso mean: 40.66 Å2
Baniso -1Baniso -2Baniso -3
1-10.9764 Å20 Å210.6175 Å2
2--11.0812 Å20 Å2
3----22.0576 Å2
Refine analyzeLuzzati coordinate error obs: 1.212 Å
Refinement stepCycle: LAST / Resolution: 2.5→57.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 0 0 5118
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085224HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.97108HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1844SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes740HARMONIC5
X-RAY DIFFRACTIONt_it5224HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.19
X-RAY DIFFRACTIONt_other_torsion20.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion678SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5335SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3089 163 5.58 %
Rwork0.3021 2756 -
all0.3025 2919 -
obs--90.24 %
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)
10.0858-0.09320.60482.004-0.78351.1672-0.0012-0.001-0.0191-0.0032-0.007-0.030.0090.0190.00820.0264-0.0174-0.06680.0006-0.0017-0.022418.1201-0.15142.5557
2-0.02310.1190.90921.96570.41121.0381-0.00220.01430.00910.00250.0011-0.01960.00160.02250.0010.03040.0198-0.0767-0.0051-0.0033-0.039946.858-3.19064.7798

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