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- PDB-6puv: Crystal Structure of the Carbohydrate Recognition Domain of the H... -

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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 / early endosome membrane / adaptive immune response / immune response / lysosomal membrane ...fucose binding / pattern recognition receptor activity / Dectin-2 family / D-mannose binding / endocytosis / carbohydrate binding / early endosome membrane / adaptive immune response / immune response / lysosomal membrane / innate immune response / external side of plasma membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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