[English] 日本語
Yorodumi
- PDB-9kpl: Crystal structure of T. rubripes Mincle with glucose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kpl
TitleCrystal structure of T. rubripes Mincle with glucose
ComponentsC-type lectin domain-containing protein
KeywordsIMMUNE SYSTEM / C-type lectin / ectodomain / Carbohydrate recognition doamin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / 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
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-D-glucopyranose / C-type lectin domain-containing protein
Similarity search - Component
Biological speciesTakifugu rubripes (torafugu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIto, T. / Nagae, M. / Yamasaki, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Immunogenetics / Year: 2025
Title: Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates.
Authors: Ito, T. / Guenther, C. / Ishikawa, E. / Yabuki, T. / Nagae, M. / Nakatani, Y. / Yamasaki, S.
History
DepositionNov 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-type lectin domain-containing protein
E: C-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70610
Polymers34,8252
Non-polymers8818
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-50 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.353, 69.860, 51.584
Angle α, β, γ (deg.)90.000, 115.774, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein C-type lectin domain-containing protein


Mass: 17412.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence matches with Gene ID 105419054 (XP_029706534.1)
Source: (gene. exp.) Takifugu rubripes (torafugu) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B5KEF3
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M tris (pH8.5), 0.2M sodium chloride, 25% (w/v) polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.02 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.8→46.45 Å / Num. obs: 28652 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.041 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.369 / Num. unique obs: 1716 / CC1/2: 0.874 / Rpim(I) all: 0.226 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.45 Å / SU ML: 0.1842 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 20.3472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2155 1386 4.84 %
Rwork0.1799 27241 -
obs0.1816 28627 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.91 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 52 181 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192451
X-RAY DIFFRACTIONf_angle_d1.53293325
X-RAY DIFFRACTIONf_chiral_restr0.1137334
X-RAY DIFFRACTIONf_plane_restr0.0115421
X-RAY DIFFRACTIONf_dihedral_angle_d7.5116330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.25231510.20542714X-RAY DIFFRACTION99.97
1.86-1.940.23511400.19872708X-RAY DIFFRACTION99.55
1.94-2.030.25431160.18132715X-RAY DIFFRACTION99.75
2.03-2.130.22151150.18632733X-RAY DIFFRACTION99.48
2.13-2.270.24421460.18172708X-RAY DIFFRACTION99.76
2.27-2.440.23411580.19032719X-RAY DIFFRACTION99.83
2.44-2.690.25171290.1892730X-RAY DIFFRACTION99.76
2.69-3.080.21541400.19412702X-RAY DIFFRACTION99.68
3.08-3.880.19441420.17222746X-RAY DIFFRACTION99.72
3.88-46.450.18331490.15812766X-RAY DIFFRACTION99.12

+
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