[English] 日本語
Yorodumi
- PDB-3wh3: human Mincle, ligand free form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wh3
Titlehuman Mincle, ligand free form
ComponentsC-type lectin domain family 4 member E
KeywordsIMMUNE SYSTEM / c-type lectin / carbohydrate recognition / glycolipid binding / Plasmamembrane
Function / homology
Function and homology information


T cell differentiation involved in immune response / glycolipid binding / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / Dectin-2 family / phagocytic cup / cell projection / positive regulation of cytokine production ...T cell differentiation involved in immune response / glycolipid binding / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / Dectin-2 family / phagocytic cup / cell projection / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding / defense response to bacterium / external side of plasma membrane / innate immune response / calcium ion binding / membrane / plasma membrane
Similarity search - Function
: / CD209-like, C-type lectin-like domain / 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 ...: / CD209-like, C-type lectin-like domain / 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
C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsFurukawa, A. / Kamishikiryo, J. / Mori, D. / Toyonaga, K. / Okabe, Y. / Toji, A. / Kanda, R. / Miyake, Y. / Ose, T. / Yamasaki, S. / Maenaka, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL
Authors: Furukawa, A. / Kamishikiryo, J. / Mori, D. / Toyonaga, K. / Okabe, Y. / Toji, A. / Kanda, R. / Miyake, Y. / Ose, T. / Yamasaki, S. / Maenaka, K.
History
DepositionAug 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-type lectin domain family 4 member E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9583
Polymers16,8781
Non-polymers802
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.074, 49.074, 43.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein C-type lectin domain family 4 member E / C-type lectin superfamily member 9 / Macrophage-inducible C-type lectin


Mass: 16878.072 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 74-219 / Mutation: I99K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4E / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9ULY5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.77 Å3/Da / Density % sol: 30.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris propane, 0.2M potassium thiocyanate, 20%(w/v) PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2012 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→24.54 Å / Num. obs: 27209 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 5.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.7
Reflection shellResolution: 1.32→1.367 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2690 / % possible all: 98.53

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FM5

1fm5


Resolution: 1.32→24.537 Å / SU ML: 0.15 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 1381 5.08 %random
Rwork0.1373 ---
obs0.1391 27209 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.615 Å2
Refinement stepCycle: LAST / Resolution: 1.32→24.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 2 165 1227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061093
X-RAY DIFFRACTIONf_angle_d1.1331480
X-RAY DIFFRACTIONf_chiral_restr0.077154
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d10.538387
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 (%)
1.32-1.36720.31781430.2982547269099
1.3672-1.42190.2191270.166625952722100
1.4219-1.48660.1781360.115826232759100
1.4866-1.5650.16131290.118725472676100
1.565-1.6630.17611310.12225732704100
1.663-1.79140.15711440.111126172761100
1.7914-1.97160.14141430.11325932736100
1.9716-2.25670.13831390.122325812720100
2.2567-2.84250.16581370.146725842721100
2.8425-24.54120.18391520.146925682720100

+
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