[English] 日本語
Yorodumi
- PDB-4v2d: FLRT2 LRR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v2d
TitleFLRT2 LRR domain
ComponentsFIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2
KeywordsSIGNALING PROTEIN / LEUCINE-RICH REPEAT / UNC5
Function / homology
Function and homology information


cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / regulation of neuron migration / basement membrane organization / fibroblast growth factor receptor binding / chemorepellent activity / positive regulation of synapse assembly / fibroblast growth factor receptor signaling pathway / heart morphogenesis / axon guidance ...cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / regulation of neuron migration / basement membrane organization / fibroblast growth factor receptor binding / chemorepellent activity / positive regulation of synapse assembly / fibroblast growth factor receptor signaling pathway / heart morphogenesis / axon guidance / cell-cell junction / neuron projection / focal adhesion / synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / 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 C-terminal domain / 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 / Fibronectin type III domain / 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 FLRT2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBRONECTIN LEUCINE RICH TRANSMEMBRANE PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)36,8071
Polymers36,8071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.120, 41.450, 87.350
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 36807.207 Da / Num. of mol.: 1 / Fragment: LRR DOMAIN, UNP RESIDUES 36-381 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BLU0
Sequence detailsCONTAINS MUTATION E352A

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.14 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→42 Å / Num. obs: 26383 / % possible obs: 78.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 60.23 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.51 / % possible all: 33

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.57 Å / Cor.coef. Fo:Fc: 0.8354 / Cor.coef. Fo:Fc free: 0.7884 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.424
RfactorNum. reflection% reflectionSelection details
Rfree0.301 416 4.72 %RANDOM
Rwork0.2798 ---
obs0.2808 8815 79.07 %-
Displacement parametersBiso mean: 58.57 Å2
Baniso -1Baniso -2Baniso -3
1-11.748 Å20 Å2-3.8112 Å2
2---32.7722 Å20 Å2
3---21.0242 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 0 0 2559
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082613HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963553HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d918SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes371HARMONIC5
X-RAY DIFFRACTIONt_it2613HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.29
X-RAY DIFFRACTIONt_other_torsion19.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion339SEMIHARMONIC5
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_contact2665SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.79 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3532 65 4.88 %
Rwork0.2851 1268 -
all0.2881 1333 -
obs--79.07 %

+
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