[English] 日本語
Yorodumi
- PDB-8jah: Crystal structure of human CLEC12A C-type lectin domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jah
TitleCrystal structure of human CLEC12A C-type lectin domain
ComponentsC-type lectin domain family 12 member A
KeywordsSTRUCTURAL PROTEIN / Receptor
Function / homology
Function and homology information


negative regulation of dendritic cell differentiation / negative regulation of natural killer cell activation / negative regulation of immune response / signaling receptor regulator activity / negative regulation of neutrophil activation / pattern recognition receptor activity / tertiary granule membrane / positive regulation of type I interferon production / specific granule membrane / negative regulation of inflammatory response ...negative regulation of dendritic cell differentiation / negative regulation of natural killer cell activation / negative regulation of immune response / signaling receptor regulator activity / negative regulation of neutrophil activation / pattern recognition receptor activity / tertiary granule membrane / positive regulation of type I interferon production / specific granule membrane / negative regulation of inflammatory response / transmembrane signaling receptor activity / carbohydrate binding / Neutrophil degranulation / signal transduction / plasma membrane
Similarity search - Function
C-type lectin domain family 12 member A/B / Natural killer cell receptor-like, C-type lectin-like domain / 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
: / C-type lectin domain family 12 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLei, Q. / Tang, H. / Dong, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171254 China
National Natural Science Foundation of China (NSFC)32201007 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Mechanistic insights into the C-type lectin receptor CLEC12A-mediated immune recognition of monosodium urate crystal.
Authors: Tang, H. / Xiao, Y. / Qian, L. / Wang, Z. / Lu, M. / Yao, N. / Zhou, T. / Tian, F. / Cao, L. / Zheng, P. / Dong, X.
History
DepositionMay 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-type lectin domain family 12 member A
B: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2265
Polymers28,9952
Non-polymers2313
Water1,20767
1
A: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6333
Polymers14,4981
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5942
Polymers14,4981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.012, 50.012, 367.627
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein C-type lectin domain family 12 member A / C-type lectin-like molecule 1 / CLL-1 / Dendritic cell-associated lectin 2 / DCAL-2 / Myeloid ...C-type lectin-like molecule 1 / CLL-1 / Dendritic cell-associated lectin 2 / DCAL-2 / Myeloid inhibitory C-type lectin-like receptor / MICL


Mass: 14497.507 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC12A, CLL1, DCAL2, MICL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5QGZ9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M Potassium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationMonochromator: PILATUS XXX, S/N XX-XXX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.58→43.01 Å / Num. obs: 8840 / % possible obs: 92.38 % / Redundancy: 13.4 % / Biso Wilson estimate: 43.56 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 13.357
Reflection shellResolution: 2.58→2.67 Å / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.462 / Num. unique obs: 751

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→43.01 Å / SU ML: 0.2701 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 24.5232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 419 4.74 %
Rwork0.2049 8421 -
obs0.2076 8840 92.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.82 Å2
Refinement stepCycle: LAST / Resolution: 2.58→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 11 67 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282086
X-RAY DIFFRACTIONf_angle_d0.58682820
X-RAY DIFFRACTIONf_chiral_restr0.0411284
X-RAY DIFFRACTIONf_plane_restr0.0041356
X-RAY DIFFRACTIONf_dihedral_angle_d5.0546276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.950.33061160.25142543X-RAY DIFFRACTION86.61
2.95-3.720.2821430.21732744X-RAY DIFFRACTION92.8
3.72-43.010.23461600.18653134X-RAY DIFFRACTION96.88

+
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