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- PDB-6py1: Crystal Structure of the Carbohydrate Recognition Domain of the H... -

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Basic information

Entry
Database: PDB / ID: 6py1
TitleCrystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to GalNAc
ComponentsC-type lectin domain family 10 member A
KeywordsSIGNALING PROTEIN / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / ACETATE ION / C-type lectin domain family 10 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsBirrane, G. / Murphy, P.V. / Gabba, A. / Luz, J.G.
Funding support Ireland, European Union, 3items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1398 Ireland
Science Foundation Ireland16/IA/4419 Ireland
European Regional Development Fund16/IA/4419European Union
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 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 1.4Oct 30, 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)15,67512
Polymers15,0571
Non-polymers61811
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C-type lectin domain family 10 member A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)31,35024
Polymers30,1152
Non-polymers1,23622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3840 Å2
ΔGint-185 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.825, 51.825, 112.855
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-407-

CL

21A-543-

HOH

31A-589-

HOH

41A-640-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 15057.370 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: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 155 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM Tris pH 6.0 - 7.0, 200mM Magnesium chloride, 2.0 - 2.8M sodium chloride
PH range: 6.0 - 7.0

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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 19, 2018 / Details: BE CRL/SI ELLIPTICAL MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 20014 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.977 / Rpim(I) all: 0.102 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1004 / CC1/2: 0.266 / Rpim(I) all: 0.867

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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: 1.701→41.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.162 / SU B: 1.898 / SU ML: 0.061 / Average fsc free: 0.9368 / Average fsc work: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 933 4.671 %RANDOM SELECTION
Rwork0.1654 19040 --
all0.166 ---
obs-19973 99.905 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 18.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.094 Å20.047 Å20 Å2
2--0.094 Å2-0 Å2
3----0.304 Å2
Refinement stepCycle: LAST / Resolution: 1.701→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 28 145 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131194
X-RAY DIFFRACTIONr_bond_other_d0.0010.018946
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6461643
X-RAY DIFFRACTIONr_angle_other_deg1.5071.6012222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8575.133150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54224.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00415167
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.684154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.684153
X-RAY DIFFRACTIONr_chiral_restr0.0890.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02275
X-RAY DIFFRACTIONr_nbd_refined0.2260.2258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2884
X-RAY DIFFRACTIONr_nbtor_refined0.180.2552
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2106
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.28
X-RAY DIFFRACTIONr_nbd_other0.1890.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2570.212
X-RAY DIFFRACTIONr_mcbond_it1.9181.774549
X-RAY DIFFRACTIONr_mcbond_other1.8041.767547
X-RAY DIFFRACTIONr_mcangle_it2.8772.65692
X-RAY DIFFRACTIONr_mcangle_other2.8752.655693
X-RAY DIFFRACTIONr_scbond_it2.8011.968645
X-RAY DIFFRACTIONr_scbond_other2.8051.971646
X-RAY DIFFRACTIONr_scangle_it4.0962.858944
X-RAY DIFFRACTIONr_scangle_other4.0942.86945
X-RAY DIFFRACTIONr_lrange_it5.53420.6651497
X-RAY DIFFRACTIONr_lrange_other5.37920.231462

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