[English] 日本語
Yorodumi
- PDB-6puv: Crystal Structure of the Carbohydrate Recognition Domain of the H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6puv
TitleCrystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin
ComponentsC-type lectin domain family 10 member A
KeywordsSIGNALING PROTEIN / C-TYPE LECTIN CRD
Function / homology
Function and homology information


fucose binding / pattern recognition receptor activity / Dectin-2 family / D-mannose binding / endocytosis / carbohydrate binding / adaptive immune response / immune response / external side of plasma membrane / innate immune response / plasma membrane
Similarity search - Function
Hepatic lectin, N-terminal domain / 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
C-type lectin domain family 10 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBirrane, G. / Murphy, P.V. / Gabba, A. / Luz, J.G.
Funding support Ireland, European Union, 4items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1398 Ireland
Science Foundation Ireland16/IA/4419 Ireland
European Regional Development Fund16/IA/4419European Union
Irish Research CouncilGOIPG/2016/858 Ireland
CitationJournal: Biochemistry / Year: 2021
Title: Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to GalNAc and the Tumor-Associated Tn Antigen.
Authors: Gabba, A. / Bogucka, A. / Luz, J.G. / Diniz, A. / Coelho, H. / Corzana, F. / Canada, F.J. / Marcelo, F. / Murphy, P.V. / Birrane, G.
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2May 19, 2021Group: 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 1.3Oct 11, 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
Revision 1.4Nov 20, 2024Group: Author supporting evidence / Structure summary
Category: pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_audit_support.country / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-type lectin domain family 10 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8822
Polymers14,8421
Non-polymers401
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.958, 42.701, 89.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein C-type lectin domain family 10 member A / C-type lectin superfamily member 14 / Macrophage lectin 2


Mass: 14842.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC10A, CLECSF13, CLECSF14, HML / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IUN9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 3000, 100mM Sodium citrate tribasic / PH range: 5.5 - 5.5

-
Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2019 / Details: BE CRL/SI ELLIPTICAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→45 Å / Num. obs: 34612 / % possible obs: 96.8 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rpim(I) all: 0.037 / Rsym value: 0.066 / Net I/σ(I): 14
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1714 / CC1/2: 0.824 / Rpim(I) all: 0.25 / Rsym value: 0.44 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DV8

1dv8


Resolution: 1.2→45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.189 -5 %Random selection
Rwork0.155 ---
obs-32165 99.3 %-
Refinement stepCycle: LAST / Resolution: 1.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 103 1105

+
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