[English] 日本語
Yorodumi
- PDB-5ffl: Crystal structure of mouse CD300lf at 1.6 Angstroms resolution. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ffl
TitleCrystal structure of mouse CD300lf at 1.6 Angstroms resolution.
ComponentsCD300 antigen-like family member F
KeywordsIMMUNE SYSTEM / CD300LF / CD300f / CLM-1 / CLM1 / IREM-1 / IREM1 / IgSF13 / LMIR3 / NKIR / inhibitory receptor / Ig superfamily / CD300 molecule-like family member f / immunoglobulin superfamily member / cell surface receptor
Function / homology
Function and homology information


interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding ...interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding / osteoclast differentiation / transmembrane signaling receptor activity / virus receptor activity / plasma membrane
Similarity search - Function
SHP2-interacting transmembrane adaptor protein, SIT / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CMRF35-like molecule 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.602 Å
AuthorsNelson, C.A. / Fremont, D.H.
CitationJournal: Science / Year: 2016
Title: Discovery of a proteinaceous cellular receptor for a norovirus.
Authors: Orchard, R.C. / Wilen, C.B. / Doench, J.G. / Baldridge, M.T. / McCune, B.T. / Lee, Y.C. / Lee, S. / Pruett-Miller, S.M. / Nelson, C.A. / Fremont, D.H. / Virgin, H.W.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD300 antigen-like family member F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2845
Polymers12,7861
Non-polymers4984
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-16 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.633, 53.347, 70.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody CD300 antigen-like family member F


Mass: 12786.489 Da / Num. of mol.: 1 / Fragment: RANKL RESIDUES 156-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q6SJQ7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Fragment: OPG RESIDUES 22-197 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 50 mM sodium chloride, 120 mM Tris-HCL at pH 7.25

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 13686 / % possible obs: 95.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 28.94 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.029 / Net I/av σ(I): 22.813 / Net I/σ(I): 24.8 / Num. measured all: 74844
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-IDRejects% possible all
1.6-1.670.49715340.9941088.3
1.67-1.760.35617331.0161098
1.76-1.870.24817251.0521099.1
1.87-2.020.16217431.0571098.4
2.02-2.220.11917311.041097.6
2.22-2.540.08517271.0681096.6
2.54-3.20.05817381.061096
3.2-200.0417550.9461091

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å19.19 Å
Translation2 Å19.19 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XED

1xed


Resolution: 1.602→19.191 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 1364 9.99 %Random selection
Rwork0.1595 12290 --
obs0.1631 13654 95.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.93 Å2 / Biso mean: 36.8227 Å2 / Biso min: 22.28 Å2
Refinement stepCycle: final / Resolution: 1.602→19.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 77 112 1081
Biso mean--54.27 39.64 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008941
X-RAY DIFFRACTIONf_angle_d1.1021275
X-RAY DIFFRACTIONf_chiral_restr0.068136
X-RAY DIFFRACTIONf_plane_restr0.006159
X-RAY DIFFRACTIONf_dihedral_angle_d15.073571
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6018-1.6590.36581180.31241064118284
1.659-1.72540.32971360.26011234137097
1.7254-1.80390.28681390.22481245138499
1.8039-1.89890.22591380.17571244138299
1.8989-2.01780.221400.16531254139498
2.0178-2.17340.21021380.15231238137698
2.1734-2.39170.20351370.16671247138497
2.3917-2.7370.20851410.15881259140097
2.737-3.4450.18551380.15511249138795
3.445-19.19260.16111390.14221256139591

+
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://pdbjlvh1.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