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

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Entry
Database: PDB / ID: 6xiy
TitleCrystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to methyl 2-(acetylamino)-2-deoxy-1-thio-alpha-D-galactopyranose
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 / innate immune response ...fucose binding / pattern recognition receptor activity / Dectin-2 family / D-mannose binding / endocytosis / carbohydrate binding / early endosome membrane / adaptive immune response / immune response / innate immune response / lysosomal membrane / 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
Chem-Q3M / C-type lectin domain family 10 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 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
DepositionJun 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 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 1.2Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)15,46012
Polymers14,8421
Non-polymers61811
Water1,53185
1
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)30,92024
Polymers29,6842
Non-polymers1,23522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2780 Å2
ΔGint-176 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.289, 52.289, 113.274
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-406-

CL

21A-522-

HOH

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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-Q3M / Methyl 2-(acetylamino)-2-deoxy-1-thio-alpha-D-galactopyranose / N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide


Mass: 249.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H19NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 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: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2019 / Details: BE CLR/SI ELLIPTICAL MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 8370 / % possible obs: 99.6 % / Redundancy: 8.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.191 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.5 % / Num. unique obs: 826 / CC1/2: 0.899 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DV8

1dv8


Resolution: 2.307→37.787 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.167 / SU B: 5.192 / SU ML: 0.126 / Average fsc free: 0.9434 / Average fsc work: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.256 / ESU R Free: 0.193
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2019 894 10.709 %
Rwork0.1618 7454 -
all0.166 --
obs-8348 99.654 %
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: 34.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.016 Å20.008 Å20 Å2
2--0.016 Å2-0 Å2
3----0.051 Å2
Refinement stepCycle: LAST / Resolution: 2.307→37.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 26 85 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131162
X-RAY DIFFRACTIONr_bond_other_d0.0010.018907
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6461566
X-RAY DIFFRACTIONr_angle_other_deg1.3321.612124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9915.072138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17924.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62715157
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg9.947152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.862153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
X-RAY DIFFRACTIONr_nbd_refined0.1950.2208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.2805
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2521
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0540.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.28
X-RAY DIFFRACTIONr_nbd_other0.190.215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0860.26
X-RAY DIFFRACTIONr_mcbond_it4.5083.423531
X-RAY DIFFRACTIONr_mcbond_other4.4523.417527
X-RAY DIFFRACTIONr_mcangle_it5.1865.124657
X-RAY DIFFRACTIONr_mcangle_other5.1825.13658
X-RAY DIFFRACTIONr_scbond_it7.0983.88631
X-RAY DIFFRACTIONr_scbond_other7.0923.881632
X-RAY DIFFRACTIONr_scangle_it9.3895.554904
X-RAY DIFFRACTIONr_scangle_other9.3835.555905
X-RAY DIFFRACTIONr_lrange_it9.97438.3031344
X-RAY DIFFRACTIONr_lrange_other9.9938.1971336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.307-2.3660.273820.21518X-RAY DIFFRACTION99.1736
2.366-2.4310.246700.191503X-RAY DIFFRACTION99.6522
2.431-2.5010.246650.181522X-RAY DIFFRACTION99.4915
2.501-2.5780.219380.159501X-RAY DIFFRACTION99.2634
2.578-2.6620.195670.15471X-RAY DIFFRACTION100
2.662-2.7550.203580.15476X-RAY DIFFRACTION99.8131
2.755-2.8590.225540.171446X-RAY DIFFRACTION100
2.859-2.9750.269350.183457X-RAY DIFFRACTION99.7972
2.975-3.1070.214460.164415X-RAY DIFFRACTION100
3.107-3.2580.198520.15402X-RAY DIFFRACTION99.7802
3.258-3.4330.219450.173390X-RAY DIFFRACTION99.7706
3.433-3.640.202250.158387X-RAY DIFFRACTION99.7579
3.64-3.890.16410.157339X-RAY DIFFRACTION100
3.89-4.1990.226490.147314X-RAY DIFFRACTION100
4.199-4.5950.18400.132296X-RAY DIFFRACTION100
4.595-5.1310.112330.107281X-RAY DIFFRACTION100
5.131-5.9120.154170.149263X-RAY DIFFRACTION100
5.912-7.2110.189380.174193X-RAY DIFFRACTION97.8814
7.211-10.070.157180.172177X-RAY DIFFRACTION100
10.07-37.7870.192210.277103X-RAY DIFFRACTION

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