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- PDB-3p7h: Structure of the human Langerin carbohydrate recognition domain i... -

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Basic information

Entry
Database: PDB / ID: 3p7h
TitleStructure of the human Langerin carbohydrate recognition domain in complex with maltose
ComponentsC-type lectin domain family 4 member K
KeywordsIMMUNE SYSTEM / C-type lectin / membrane protein / glycoprotein / Langerin / DC-SIGN / Carbohydrate binding protein / Calcium binding / sugar binding / Langerhans cells / CD207
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / early endosome membrane / carbohydrate binding / defense response to virus / 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) / C-type lectin-like/link domain superfamily ...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
alpha-maltose / C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSkerra, A. / Schiefner, A.
CitationJournal: Mol.Immunol. / Year: 2008
Title: The carbohydrate recognition domain of Langerin reveals high structural similarity with the one of DC-SIGN but an additional, calcium-independent sugar-binding site.
Authors: Chatwell, L. / Holla, A. / Kaufer, B.B. / Skerra, A.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 3, 2010ID: 3BC6
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)68,94012
Polymers67,4114
Non-polymers1,5308
Water3,675204
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2353
Polymers16,8531
Non-polymers3822
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)17,2353
Polymers16,8531
Non-polymers3822
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)17,2353
Polymers16,8531
Non-polymers3822
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)17,2353
Polymers16,8531
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.970, 79.970, 90.950
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


Mass: 16852.633 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP Residues 193-328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207, CLEC4K, Leucocyte cDNA / Plasmid: pLA1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: Q9UJ71
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: Protein: 10mg/ml Langerin in 10 mM Tris/HCl pH 7.5, 5 mM Maltose; Reservoir: 0.1 M Na-cacodylate, 13 %(w/v) PEG4000, 0.1 M MgCl2, 5mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2005
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 25136 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.039 / Net I/σ(I): 25.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 7.3 / Num. unique all: 2991 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P7G

3p7g


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.666 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22863 1280 5.1 %RANDOM
Rwork0.18077 ---
obs0.18318 23863 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 96 204 4573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9466217
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56424.22218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3511512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213532
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5471.52618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0912.54222
X-RAY DIFFRACTIONr_scbond_it2.4353.51933
X-RAY DIFFRACTIONr_scangle_it4.027101995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 97 -
Rwork0.278 1753 -
obs--97.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6554-0.5417-1.30192.7975-0.42465.1057-0.01830.0282-0.0819-0.2329-0.05380.10080.08610.02790.0720.08730.0151-0.08890.0437-0.01910.10676.952715.7419-34.1143
23.62180.27020.62381.7349-0.24952.5099-0.07470.16560.4572-0.279-0.01130.2377-0.30180.00350.08590.15270.0255-0.09690.0974-0.01520.17215.226325.8021-33.9579
317.055215.1383.653913.4413.24190.78451.2818-0.1164-3.09791.3081-0.3841-2.73330.3572-0.0145-0.89770.82170.2753-0.39020.5786-0.15780.619528.94734.4137-28.8688
43.64580.04220.7074.0019-0.14533.03120.04410.11320.1118-0.1574-0.1734-0.0377-0.01770.07950.12940.06660.00650.00590.08460.01250.008431.397926.0397-31.7639
53.9040.80110.72463.19930.41659.4394-0.06350.3028-0.2364-0.3546-0.0428-0.24040.33420.3470.10630.08410.01710.0710.1183-0.00640.162537.306314.6543-36.0788
61.85292.064-0.53643.0925-2.06893.89130.0020.00940.04050.0236-0.0884-0.1374-0.16290.1050.08640.0395-0.0430.03570.13040.01820.100434.040926.5056-30.1649
74.00520.5571-0.39321.6429-0.57084.3194-0.0656-0.1542-0.0630.15380.0062-0.08070.18120.03920.05950.06970.0057-0.01810.03010.01920.048631.632515.0901-5.4249
812.3601-3.48780.973911.7623.62381.4955-0.0352-0.33591.3109-0.3442-0.2131-0.095-0.1697-0.18260.24830.17390.075-0.03750.1641-0.03170.178623.990728.7099-7.3616
95.1151-0.06530.87332.02230.13623.0044-0.0146-0.15260.67890.1261-0.0194-0.1296-0.1594-0.02430.0340.09010.0125-0.03930.0699-0.0020.12433.441123.2202-5.5366
103.0061-0.5758-0.06254.42661.68524.427-0.0083-0.3160.20280.1408-0.18920.2059-0.2899-0.05690.19750.08010.00060.04130.0918-0.00240.08514.268427.4661-5.9155
118.06470.52122.61917.2897-2.18295.23890.17880.2895-0.5982-0.4509-0.1111-0.120.67050.3653-0.06770.13520.02070.02680.10690.02820.102711.538213.279-11.2686
123.118-0.6943-0.5964.65990.16474.7352-0.0954-0.2232-0.44380.3677-0.080.31830.3972-0.1150.17540.0945-0.00080.07840.13680.02130.15772.43116.7786-6.0426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A198 - 262
2X-RAY DIFFRACTION2A263 - 322
3X-RAY DIFFRACTION3A323 - 332
4X-RAY DIFFRACTION4B196 - 275
5X-RAY DIFFRACTION5B276 - 305
6X-RAY DIFFRACTION6B306 - 325
7X-RAY DIFFRACTION7C198 - 259
8X-RAY DIFFRACTION8C260 - 279
9X-RAY DIFFRACTION9C280 - 331
10X-RAY DIFFRACTION10D196 - 253
11X-RAY DIFFRACTION11D254 - 275
12X-RAY DIFFRACTION12D276 - 325

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