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- PDB-4v2c: mouse FLRT2 LRR domain in complex with rat Unc5D Ig1 domain -

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Basic information

Entry
Database: PDB / ID: 4v2c
Titlemouse FLRT2 LRR domain in complex with rat Unc5D Ig1 domain
Components
  • FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2
  • PROTEIN UNC5D
KeywordsAPOPTOSIS / UNC5 / UNCOORDINATED-5 / LEUCINE-RICH REPEAT
Function / homology
Function and homology information


cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / basement membrane organization / cell-cell adhesion via plasma-membrane adhesion molecules / regulation of neuron migration / fibroblast growth factor receptor binding / chemorepellent activity / pyramidal neuron differentiation / positive regulation of synapse assembly ...cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / basement membrane organization / cell-cell adhesion via plasma-membrane adhesion molecules / regulation of neuron migration / fibroblast growth factor receptor binding / chemorepellent activity / pyramidal neuron differentiation / positive regulation of synapse assembly / fibroblast growth factor receptor signaling pathway / heart morphogenesis / axon guidance / cell-cell junction / presynaptic membrane / postsynaptic membrane / neuron projection / focal adhesion / glutamatergic synapse / endoplasmic reticulum membrane / apoptotic process / cell surface / extracellular space / plasma membrane
Similarity search - Function
UNC5D, Death domain / UPA domain / Netrin receptor UNC5 / UPA domain / : / Leucine rich repeat C-terminal domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. ...UNC5D, Death domain / UPA domain / Netrin receptor UNC5 / UPA domain / : / Leucine rich repeat C-terminal domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Netrin receptor UNC5D / Leucine-rich repeat transmembrane protein FLRT2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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. / Haertl, 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 1.1Jul 22, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2
B: PROTEIN UNC5D
C: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2
D: PROTEIN UNC5D


Theoretical massNumber of molelcules
Total (without water)110,3324
Polymers110,3324
Non-polymers00
Water00
1
A: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2
B: PROTEIN UNC5D


Theoretical massNumber of molelcules
Total (without water)55,1662
Polymers55,1662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-0.9 kcal/mol
Surface area24980 Å2
MethodPQS
2
C: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2
D: PROTEIN UNC5D


Theoretical massNumber of molelcules
Total (without water)55,1662
Polymers55,1662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-0.1 kcal/mol
Surface area24850 Å2
MethodPQS
Unit cell
Length a, b, c (Å)180.140, 150.910, 67.220
Angle α, β, γ (deg.)90.00, 102.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2 / PROTEIN FLRT2


Mass: 37037.426 Da / Num. of mol.: 2 / Fragment: LRR DOMAIN, RESIDUES 35-362
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: Q8BLU0
#2: Protein PROTEIN UNC5D


Mass: 18128.379 Da / Num. of mol.: 2 / Fragment: IG1 DOMAIN, RESIDUES 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: F1LW30
Has protein modificationY
Sequence detailsN-TERMINUS IS CLEAVED DURING EXPRESSION. CONTAINS C- TERMINAL HIS TAG. N-TERMINUS IS CLEAVED. C- ...N-TERMINUS IS CLEAVED DURING EXPRESSION. CONTAINS C- TERMINAL HIS TAG. N-TERMINUS IS CLEAVED. C-TERMINUS CONTAINS A 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: 4.04 Å3/Da / Density % sol: 69.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4→87 Å / Num. obs: 102048 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 136.77 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.4
Reflection shellResolution: 4→4.1 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.87 / % possible all: 87.8

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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 4V2B

4v2b


Resolution: 4→87.84 Å / Cor.coef. Fo:Fc: 0.6709 / Cor.coef. Fo:Fc free: 0.6392 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.877
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.3349 746 5.06 %RANDOM
Rwork0.3183 ---
obs0.3191 14730 98.97 %-
Displacement parametersBiso mean: 111.61 Å2
Baniso -1Baniso -2Baniso -3
1-32.3669 Å20 Å2-47.0654 Å2
2---17.7106 Å20 Å2
3----14.6563 Å2
Refine analyzeLuzzati coordinate error obs: 1.593 Å
Refinement stepCycle: LAST / Resolution: 4→87.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 0 0 6854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087012HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.959526HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2458SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes996HARMONIC5
X-RAY DIFFRACTIONt_it7012HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.52
X-RAY DIFFRACTIONt_other_torsion18.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion902SEMIHARMONIC5
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_contact7373SEMIHARMONIC4
LS refinement shellResolution: 4→4.32 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2941 165 5.66 %
Rwork0.3009 2749 -
all0.3005 2914 -
obs--98.97 %
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)
18.5992-2.9582-1.78948.3154-0.11565.2766-0.01780.18320.10570.13850.09790.2628-0.2618-0.4236-0.0801-0.11530.1343-0.18330.0185-0.0045-0.0534222.0645-4.763479.312
25.47313.4825-2.42028.3154-2.19392.1035-0.0791-0.24090.0410.13890.13590.0330.1398-0.0404-0.05680.0421-0.09490.04650.02060.13430.1413211.3366-26.220288.6284
36.8836-0.21261.07616.3589-0.49685.3220.0222-0.10690.0351-0.1647-0.05390.23380.0413-0.33910.03170.22760.15570.0723-0.214-0.0191-0.0607223.90411.2822115.8733
48.9579-2.3336-0.85548.3154-2.47173.3845-0.04090.13060.085-0.14870.03660.04270.0231-0.03730.00430.19380.1465-0.00040.01020.04110.188212.525722.4062107.4049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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