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- PDB-6w12: Crystal Structure of the Carbohydrate Recognition Domain of the H... -

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Basic information

Entry
Database: PDB / ID: 6w12
TitleCrystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to the Tumor-Associated Tn Antigen
ComponentsC-type lectin domain family 10 member A
KeywordsSIGNALING PROTEIN / CRD
Function / homology
Function and homology information


fucose binding / Dectin-2 family / D-mannose binding / endocytosis / carbohydrate binding / adaptive 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / SERINE / C-type lectin domain family 10 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: 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 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

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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)15,65215
Polymers14,8421
Non-polymers80914
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
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)31,30330
Polymers29,6842
Non-polymers1,61928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3910 Å2
ΔGint-280 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.155, 52.155, 112.667
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-532-

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: 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
#6: 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
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 , 5 types, 117 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200mM Magnesium chloride, 100mM Tris, 2-3M NaCl / 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: 0.9863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2019 / Details: BE CRL/Si ELLIPTICAL MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9863 Å / Relative weight: 1
ReflectionResolution: 2→42.2 Å / Num. obs: 12784 / % possible obs: 99.6 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1241 / CC1/2: 0.89 / Rpim(I) all: 0.28 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DV8

1dv8


Resolution: 2→37.584 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.358 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1961 633 4.964 %
Rwork0.1677 --
all0.169 --
obs-12751 98.891 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 16.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.072 Å20.036 Å20 Å2
2--0.072 Å2-0 Å2
3----0.233 Å2
Refinement stepCycle: LAST / Resolution: 2→37.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 33 104 1184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131146
X-RAY DIFFRACTIONr_bond_other_d0.0010.018905
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6351573
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5872123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.935.072138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92523.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52215157
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg9.207152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.237153
X-RAY DIFFRACTIONr_chiral_restr0.0770.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined0.250.2252
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.2836
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2526
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.272
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.27
X-RAY DIFFRACTIONr_nbd_other0.1960.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3980.21
X-RAY DIFFRACTIONr_mcbond_it3.281.247528
X-RAY DIFFRACTIONr_mcbond_other3.2831.253529
X-RAY DIFFRACTIONr_mcangle_it4.2871.817659
X-RAY DIFFRACTIONr_mcangle_other4.3081.827660
X-RAY DIFFRACTIONr_scbond_it6.1021.612618
X-RAY DIFFRACTIONr_scbond_other6.0981.613619
X-RAY DIFFRACTIONr_scangle_it8.4092.221909
X-RAY DIFFRACTIONr_scangle_other8.4052.222910
X-RAY DIFFRACTIONr_lrange_it8.51114.2771423
X-RAY DIFFRACTIONr_lrange_other8.54214.0691400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0350.356460.22795X-RAY DIFFRACTION88.9947
2.035-2.090.243490.193875X-RAY DIFFRACTION99.1416
2.151-2.2170.189430.186802X-RAY DIFFRACTION99.7639
2.217-2.2890.193330.186804X-RAY DIFFRACTION99.5244
2.289-2.370.214510.148765X-RAY DIFFRACTION99.6337
2.37-2.4590.19420.151703X-RAY DIFFRACTION99.7323
2.459-2.5590.21420.156718X-RAY DIFFRACTION99.8686
2.559-2.6720.25270.165713X-RAY DIFFRACTION100
2.672-2.8020.195500.172643X-RAY DIFFRACTION100
2.802-2.9530.228300.175625X-RAY DIFFRACTION99.8476
2.953-3.1310.22210.178627X-RAY DIFFRACTION99.6923
3.131-3.3470.248270.175553X-RAY DIFFRACTION100
3.347-3.6130.168280.154529X-RAY DIFFRACTION100
3.613-3.9550.05590.147510X-RAY DIFFRACTION99.6161
3.955-4.4180.239130.119451X-RAY DIFFRACTION99.7849
4.418-5.0930.097240.122411X-RAY DIFFRACTION99.5423
Refinement TLS params.Method: refined / Origin x: 15.335 Å / Origin y: -3.6214 Å / Origin z: -4.4363 Å
111213212223313233
T0.0312 Å20.0078 Å2-0.0013 Å2-0.0225 Å20.0031 Å2--0.0009 Å2
L0.7184 °2-0.3091 °2-0.2013 °2-0.1668 °20.211 °2--0.5659 °2
S-0.0109 Å °-0.0506 Å °0.0032 Å °0.0035 Å °0.0121 Å °-0.0017 Å °0.0346 Å °0.0041 Å °-0.0012 Å °
Refinement TLS groupSelection: ALL

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