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- PDB-5cmp: human FLRT3 LRR domain -

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Basic information

Entry
Database: PDB / ID: 5cmp
Titlehuman FLRT3 LRR domain
ComponentsLeucine-rich repeat transmembrane protein FLRT3
KeywordsCELL ADHESION / LRR repeats
Function / homology
Function and homology information


proepicardium cell migration involved in pericardium morphogenesis / head development / synaptic membrane adhesion / growth cone membrane / : / fibroblast growth factor receptor binding / embryonic morphogenesis / Signaling by ROBO receptors / Downstream signaling of activated FGFR1 / chemorepellent activity ...proepicardium cell migration involved in pericardium morphogenesis / head development / synaptic membrane adhesion / growth cone membrane / : / fibroblast growth factor receptor binding / embryonic morphogenesis / Signaling by ROBO receptors / Downstream signaling of activated FGFR1 / chemorepellent activity / positive regulation of synapse assembly / neuron projection extension / fibroblast growth factor receptor signaling pathway / axonal growth cone / response to axon injury / synapse assembly / axon terminus / extracellular matrix / axon guidance / synaptic membrane / neuron projection development / cell-cell junction / cell junction / heart development / protein-macromolecule adaptor activity / postsynaptic membrane / focal adhesion / endoplasmic reticulum membrane / glutamatergic synapse / 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 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. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat transmembrane protein FLRT3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsLu, Y. / Salzman, G. / Arac, D.
CitationJournal: Structure / Year: 2015
Title: Structural Basis of Latrophilin-FLRT-UNC5 Interaction in Cell Adhesion.
Authors: Lu, Y.C. / Nazarko, O.V. / Sando, R. / Salzman, G.S. / Sudhof, T.C. / Arac, D.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat transmembrane protein FLRT3
B: Leucine-rich repeat transmembrane protein FLRT3
C: Leucine-rich repeat transmembrane protein FLRT3
D: Leucine-rich repeat transmembrane protein FLRT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,7348
Polymers151,8494
Non-polymers8854
Water1,08160
1
A: Leucine-rich repeat transmembrane protein FLRT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1832
Polymers37,9621
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine-rich repeat transmembrane protein FLRT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1832
Polymers37,9621
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leucine-rich repeat transmembrane protein FLRT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1832
Polymers37,9621
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leucine-rich repeat transmembrane protein FLRT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1832
Polymers37,9621
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.140, 106.581, 84.152
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Leucine-rich repeat transmembrane protein FLRT3 / Fibronectin-like domain-containing leucine-rich transmembrane protein 3


Mass: 37962.219 Da / Num. of mol.: 4 / Fragment: UNP residues 29-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLRT3, KIAA1469, UNQ856/PRO1865 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NZU0
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7 / Details: 0.1M Tris pH7, 50% (v/v) PEG200

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96638 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96638 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 39415 / % possible obs: 95.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 8.765
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.647 / % possible all: 73.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2E

4v2e


Resolution: 2.601→45.022 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3003 2014 5.11 %
Rwork0.2323 --
obs0.2358 39415 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→45.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10339 0 55 60 10454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910619
X-RAY DIFFRACTIONf_angle_d1.16314436
X-RAY DIFFRACTIONf_dihedral_angle_d14.1174002
X-RAY DIFFRACTIONf_chiral_restr0.0531664
X-RAY DIFFRACTIONf_plane_restr0.0061877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6015-2.66650.4055740.28022038X-RAY DIFFRACTION72
2.6665-2.73860.37961240.28212262X-RAY DIFFRACTION81
2.7386-2.81920.36171440.29612446X-RAY DIFFRACTION88
2.8192-2.91020.38551130.29952687X-RAY DIFFRACTION95
2.9102-3.01420.39341640.28512741X-RAY DIFFRACTION99
3.0142-3.13480.40441340.29472808X-RAY DIFFRACTION100
3.1348-3.27750.32141540.2772778X-RAY DIFFRACTION100
3.2775-3.45020.35491230.27062844X-RAY DIFFRACTION100
3.4502-3.66630.3341580.25592779X-RAY DIFFRACTION100
3.6663-3.94920.3311530.21582794X-RAY DIFFRACTION100
3.9492-4.34630.25931650.20332799X-RAY DIFFRACTION100
4.3463-4.97460.24941670.1792778X-RAY DIFFRACTION100
4.9746-6.26480.26951870.20362795X-RAY DIFFRACTION100
6.2648-45.02880.20721540.18712852X-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)
11.4869-0.83910.08522.75751.0963.026-0.1283-0.2469-0.10760.78080.1149-0.75110.11250.6723-0.14160.55320.0169-0.14920.43840.01290.483316.1159-1.414139.2361
21.3285-0.2620.94673.06930.89994.35690.3279-0.0512-0.17660.0797-0.04770.11430.68050.1097-0.07120.5501-0.0545-0.09070.31050.03260.39969.0746-8.49833.8584
32.9297-0.08710.2841.54330.06132.82750.2643-0.2744-0.1470.13990.03370.15010.6603-0.2645-0.06590.44640.0791-0.05550.3220.04630.32563.7461-8.839626.2974
42.0671-1.77140.11683.4419-0.11813.3638-0.05250.05180.05730.1047-0.08180.21830.7667-0.3514-0.05840.6882-0.0889-0.07170.37430.01320.41951.5423-12.19717.3177
51.4133-0.2858-0.30012.5430.70613.22590.2136-0.0463-0.51440.3032-0.14250.25440.98660.06350.0930.5318-0.116-0.12430.23220.03280.46640.9103-13.67038.2317
61.7192-1.1393-0.59093.3528-1.18761.9648-0.02250.0605-0.0805-0.86010.08420.37610.1598-0.37110.02890.7523-0.1121-0.13390.29590.05340.32981.3704-12.82242.1925
70.5617-0.1124-0.64412.3772-0.97872.65560.06550.13850.0896-0.3378-0.02340.00370.00720.0216-0.11330.68990.0125-0.17180.2767-0.02930.32999.2371-8.0894-11.4326
81.67760.2818-0.21453.11620.73230.2201-0.37810.58620.06-0.61120.22420.4338-0.52050.06440.32511.1112-0.1418-0.03270.3676-0.01010.362421.3341-11.7247-24.6056
92.9924-0.1099-0.3493.1051.92042.6004-0.2519-0.41760.38940.4060.2307-0.2012-0.5080.3226-0.00330.65460.0658-0.07110.3689-0.030.369248.3846-5.260674.9083
103.4215-1.9477-0.01844.529-0.29493.34080.1476-0.1617-0.0472-0.26920.15210.4215-0.2247-0.01630.04180.5480.0367-0.11420.2340.05410.364639.3912-12.059960.0703
111.6263-0.7698-1.10310.8453-0.32273.787-0.06280.0056-0.0081-0.2231-0.00860.1488-0.002-0.43660.06330.49540.0045-0.12610.3628-0.01080.315640.4554-11.400540.0696
122.1685-0.0979-0.75642.7718-1.38990.8776-0.09530.17070.1762-0.2342-0.0151-0.29830.1943-0.06090.03990.594-0.0311-0.10790.33450.0670.291350.1163-7.117521.3571
131.4292.40020.1713.99340.46352.1471-0.34430.1555-0.9086-0.72990.089-0.77530.86790.4839-0.77630.9657-0.30990.07040.5423-0.23060.472818.873913.48694.3519
142.28140.4972-0.07193.08330.03062.7961-0.4950.7161-0.398-0.42590.3218-0.10390.00870.22280.12560.7035-0.15340.02950.5398-0.08120.307614.736820.33499.1105
152.6658-0.52830.07931.9566-0.50092.5242-0.24420.1377-0.08310.00270.0347-0.16410.0849-0.03230.14990.5938-0.143-0.00780.3284-0.03860.285511.103924.990114.8723
164.1821.5720.04594.3059-0.49091.5262-0.38750.01750.0979-0.48120.34260.4958-0.5251-0.11090.18350.3964-0.0602-0.05860.31670.02810.23774.994326.588619.6348
172.69732.03110.50743.83191.63743.1168-0.3093-0.0454-0.32370.00820.28470.2345-0.211-0.45250.15820.491-0.0063-0.05620.28070.04650.38227.08225.147428.3899
184.03641.4303-0.15345.7677-0.43163.44250.1618-0.09820.55280.1094-0.08510.19720.19880.09210.02520.37430.0612-0.06410.22-0.02650.19976.063728.933134.9881
191.40.66520.60541.3202-0.57473.47950.0794-0.0441-0.19210.33090.10040.21440.1554-0.1269-0.1280.49830.07550.01420.1911-0.00550.309110.75124.475950.2479
204.69041.13580.32096.28340.31831.3746-0.1338-0.22670.32550.35760.0953-0.36950.50730.27550.04040.69010.131-0.06370.26190.0190.353419.86518.099665.8226
213.909-0.1162-3.2582.315-0.88178.6026-0.3787-0.9539-0.0180.54170.2854-0.1217-0.1815-0.611-0.00290.67750.1331-0.080.795-0.01950.329825.306-33.111225.5176
221.099-1.30470.78251.60220.61256.49430.04190.1302-0.2346-0.30840.0412-0.06460.1493-0.1713-0.08140.5056-0.0373-0.00290.301-0.0350.323127.2459-30.8421-11.2456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 202 )
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 228 )
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 330 )
8X-RAY DIFFRACTION8chain 'A' and (resid 331 through 352 )
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 134 )
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 181 )
11X-RAY DIFFRACTION11chain 'B' and (resid 182 through 292 )
12X-RAY DIFFRACTION12chain 'B' and (resid 293 through 352 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 64 )
14X-RAY DIFFRACTION14chain 'C' and (resid 65 through 94 )
15X-RAY DIFFRACTION15chain 'C' and (resid 95 through 120 )
16X-RAY DIFFRACTION16chain 'C' and (resid 121 through 154 )
17X-RAY DIFFRACTION17chain 'C' and (resid 155 through 181 )
18X-RAY DIFFRACTION18chain 'C' and (resid 182 through 202 )
19X-RAY DIFFRACTION19chain 'C' and (resid 203 through 313 )
20X-RAY DIFFRACTION20chain 'C' and (resid 314 through 350 )
21X-RAY DIFFRACTION21chain 'D' and (resid 31 through 202 )
22X-RAY DIFFRACTION22chain 'D' and (resid 203 through 351 )

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