[English] 日本語
Yorodumi
- PDB-6lfj: Crystal structure of mouse DCAR2 CRD domain complex with IPM2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lfj
TitleCrystal structure of mouse DCAR2 CRD domain complex with IPM2
ComponentsC-type lectin domain family 4, member b1
KeywordsSUGAR BINDING PROTEIN / C-type lectin
Function / homology
Function and homology information


antifungal innate immune response / positive regulation of release of sequestered calcium ion into cytosol / signaling receptor activity / carbohydrate binding / external side of plasma membrane / metal ion binding
Similarity search - Function
CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1-PHOSPHATE / alpha-D-mannopyranose / C-type lectin domain family 4, member b1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsOmahdi, Z. / Horikawa, Y. / Toyonaga, K. / Kakuta, Y. / Yamasaki, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR.
Authors: Omahdi, Z. / Horikawa, Y. / Nagae, M. / Toyonaga, K. / Imamura, A. / Takato, K. / Teramoto, T. / Ishida, H. / Kakuta, Y. / Yamasaki, S.
History
DepositionDec 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: C-type lectin domain family 4, member b1
B: C-type lectin domain family 4, member b1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,13310
Polymers31,7142
Non-polymers1,4198
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-10 kcal/mol
Surface area13990 Å2
Unit cell
Length a, b, c (Å)65.689, 72.564, 100.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 5 molecules AB

#1: Protein C-type lectin domain family 4, member b1 / Dendritic cell immuno-activating receptor beta isoform


Mass: 15856.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clec4b1, Clec4b, Dcar / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D8Q7
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 295 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Chemical ChemComp-IPD / D-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H11O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→48.7 Å / Num. obs: 80659 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.99 / Net I/σ(I): 5.6
Reflection shellResolution: 1.84→1.94 Å / Num. unique obs: 13015 / CC1/2: 0.5

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KZR

6kzr


Resolution: 1.84→48.7 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 3784 4.69 %
Rwork0.1772 76858 -
obs0.1782 80642 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.11 Å2 / Biso mean: 35.4228 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 1.84→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 86 290 2552
Biso mean--73.37 45.61 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.860.32541370.30262822295998
1.86-1.880.33621410.309828272968100
1.88-1.910.26671400.278728402980100
1.91-1.940.29911390.278928602999100
1.94-1.970.2891430.282128923035100
1.97-20.28811390.273328602999100
2-2.030.26971430.243128432986100
2.03-2.060.2641360.239228582994100
2.06-2.10.21571420.232328032945100
2.1-2.140.23611390.219428963035100
2.14-2.190.24761460.215628563002100
2.19-2.230.23821360.214428222958100
2.23-2.290.22671380.20772821295999
2.29-2.340.22721430.206228783021100
2.34-2.410.21461400.200528162956100
2.41-2.480.24971410.19528492990100
2.48-2.560.2281410.18128472988100
2.56-2.650.18421400.17128673007100
2.65-2.750.20431400.179528643004100
2.75-2.880.17131400.164128422982100
2.88-3.030.17071410.163528352976100
3.03-3.220.19171360.157128372973100
3.22-3.470.18211430.146428643007100
3.47-3.820.18191380.137728452983100
3.82-4.370.13061410.12752836297799
4.37-5.510.15481410.12512841298299
5.51-48.70.17071400.17362837297799
Refinement TLS params.Method: refined / Origin x: -5.4323 Å / Origin y: 24.7554 Å / Origin z: -13.1159 Å
111213212223313233
T0.1608 Å2-0.0009 Å2-0.0009 Å2-0.1842 Å2-0.0106 Å2--0.1747 Å2
L0.4346 °20.1489 °2-0.3377 °2-1.3876 °2-0.9274 °2--1.3087 °2
S0.0048 Å °0.0259 Å °0.0411 Å °0.0648 Å °0.0594 Å °0.0579 Å °-0.0777 Å °-0.0775 Å °-0.0645 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA75 - 207
2X-RAY DIFFRACTION1allB76 - 207
3X-RAY DIFFRACTION1allCC1
4X-RAY DIFFRACTION1allCa2
5X-RAY DIFFRACTION1allDD401
6X-RAY DIFFRACTION1allDa402
7X-RAY DIFFRACTION1allEE302
8X-RAY DIFFRACTION1allSS1 - 296

+
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