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- PDB-3c22: Crystal structure of the carbohydrate recognition domain of human... -

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Basic information

Entry
Database: PDB / ID: 3c22
TitleCrystal structure of the carbohydrate recognition domain of human Langerin
ComponentsC-type lectin domain family 4 member K
KeywordsIMMUNE SYSTEM / SUGAR BINDING PROTEIN / C-type lectin domain / Coiled coil / Glycoprotein / Membrane / Signal-anchor / Transmembrane
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / pattern recognition receptor activity / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / carbohydrate binding / early endosome membrane / defense response to virus / immune response / external side of plasma membrane / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsThepaut, M.
Citation
Journal: Biochemistry / Year: 2009
Title: Structural studies of langerin and Birbeck granule: a macromolecular organization model
Authors: Thepaut, M. / Valladeau, J. / Nurisso, A. / Kahn, R. / Arnou, B. / Vives, C. / Saeland, S. / Ebel, C. / Monnier, C. / Dezutter-Dambuyant, C. / Imberty, A. / Fieschi, F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Overproduction, purification and preliminary crystallographic analysis of the carbohydrate-recognition domain of human langerin
Authors: Thepaut, M. / Vives, C. / Pompidor, G. / Kahn, R. / Fieschi, F.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 4 member K
B: C-type lectin domain family 4 member K
C: C-type lectin domain family 4 member K
D: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,10214
Polymers71,7964
Non-polymers30610
Water15,727873
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0133
Polymers17,9491
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0384
Polymers17,9491
Non-polymers893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0384
Polymers17,9491
Non-polymers893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0133
Polymers17,9491
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.555, 79.555, 90.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
C-type lectin domain family 4 member K / Langerin / CD207 antigen


Mass: 17949.035 Da / Num. of mol.: 4
Fragment: carbohydrate recognition domain, UNP residues 188-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UJ71
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 873 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 400mM MgCl2, 25% PEG 3350, 100mM HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97966 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2007 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97966 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 90252 / Num. obs: 89721 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 25.4
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.1 / Num. unique all: 14378 / Rsym value: 0.331 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Xnemodata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→47.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928
Isotropic thermal model: Isotropic except for Ca and Mg atoms
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4474 5 %RANDOM
Rwork0.189 ---
all0.192 90252 --
obs0.192 89582 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.873 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 10 873 5340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224659
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9156398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5565591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89224.359234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5441516
X-RAY DIFFRACTIONr_chiral_restr0.1110.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023716
X-RAY DIFFRACTIONr_nbd_refined0.2150.22449
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2673
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.249
X-RAY DIFFRACTIONr_mcbond_it1.0191.52716
X-RAY DIFFRACTIONr_mcangle_it1.7124424
X-RAY DIFFRACTIONr_scbond_it2.05431943
X-RAY DIFFRACTIONr_scangle_it2.9844.51937
X-RAY DIFFRACTIONr_sphericity_free12.201310
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 334 -
Rwork0.27 6224 -
obs-6558 99.91 %

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