[English] 日本語
Yorodumi
- PDB-5cmp: human FLRT3 LRR domain -

+
Open data


ID or keywords:

Loading...

-
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 / embryonic morphogenesis / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / 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 / embryonic morphogenesis / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / Signaling by ROBO receptors / Downstream signaling of activated FGFR1 / 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 / extracellular matrix / synaptic membrane / axon guidance / neuron projection development / cell-cell junction / cell junction / protein-macromolecule adaptor activity / 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 / Fibronectin type III 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / N-Acetylglucosamine


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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more