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- PDB-3p7g: Structure of the human Langerin carbohydrate recognition domain i... -

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Basic information

Entry
Database: PDB / ID: 3p7g
TitleStructure of the human Langerin carbohydrate recognition domain in complex with mannose
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) / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / signaling receptor activity / 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-D-mannopyranose / C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 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: 3BC7
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 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)68,29112
Polymers67,4114
Non-polymers8818
Water10,683593
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0733
Polymers16,8531
Non-polymers2202
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)17,0733
Polymers16,8531
Non-polymers2202
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)17,0733
Polymers16,8531
Non-polymers2202
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)17,0733
Polymers16,8531
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.710, 79.710, 89.980
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
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 Mannose; 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, 0.9798, 0.9080
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2005
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.9081
ReflectionResolution: 1.5→30 Å / Num. obs: 89165 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.5
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4 / Num. unique all: 15536 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXDphasing
SHARPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.791 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20742 1789 2 %RANDOM
Rwork0.17221 ---
obs0.17292 87378 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 0 52 593 4924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9256264
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08624.26223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8331513
X-RAY DIFFRACTIONr_chiral_restr0.1320.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213625
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_it1.1741.52671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8982.54319
X-RAY DIFFRACTIONr_scbond_it3.1613.51911
X-RAY DIFFRACTIONr_scangle_it4.56101945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 137 -
Rwork0.248 6390 -
obs--98.79 %
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)
12.7184-0.276-0.66731.5640.18233.3394-0.0542-0.03840.0329-0.0925-0.05050.03010.03-0.02640.10480.06410.042-0.06830.0592-0.0410.08727.097216.1689-33.4657
22.25170.16850.36151.8792-0.21721.7274-0.0684-0.00590.3-0.133-0.05950.126-0.2069-0.08740.12790.09510.0534-0.08610.0725-0.060.12215.183725.7813-33.5852
317.48373.740414.30670.81083.04511.73121.59530.668-2.24280.31710.1432-0.50771.26280.6255-1.73850.4060.1213-0.18640.3870.00130.394328.99664.4132-28.7554
42.2719-0.65510.89823.1963-0.40632.77070.02450.13320.1928-0.1276-0.1071-0.0206-0.12090.02910.08260.02230.01120.010.04230.02560.0331.93926.9726-31.3437
55.01560.7034-1.13738.2555.31947.5502-0.17020.1717-0.3354-0.2555-0.08360.070.177-0.070.25380.06640.0175-0.00530.0590.00240.058824.862915.127-35.1477
61.5721-0.30920.19832.86390.21082.88860.02880.179-0.0371-0.1304-0.0689-0.17620.10120.25350.04010.02450.00840.01840.0790.02660.038736.823519.9247-32.6228
73.84640.7345-1.19342.5389-0.84824.738-0.0546-0.1444-0.23360.04710.0283-0.00820.31-0.13040.02620.063-0.0167-0.01730.01470.01510.024230.237412.9876-7.0324
84.3476-0.73870.68272.65250.21522.4622-0.1262-0.22350.55630.1170.0387-0.0394-0.2951-0.20950.08760.0694-0.001-0.010.061-0.03510.075929.324825.9999-3.9331
93.3764-0.01760.13822.7383-0.3632.9173-0.0973-0.1130.27950.0230.0335-0.0537-0.03680.01270.06370.02860.0121-0.01990.0075-0.01340.029632.900520.747-6.7152
1016.1569-3.8184.30438.8594-1.72989.8254-0.0875-0.34170.44070.02380.00620.2349-0.6242-0.3570.08130.1253-0.05160.03390.0907-0.0530.12217.851834.4148-1.6682
112.6372-0.0524-0.11723.18570.91274.67840.0468-0.0381-0.03360.0302-0.21860.2359-0.0729-0.14310.17180.0135-0.01470.02160.0749-0.0280.06974.257724.1869-7.5285
122.7332-0.8621-0.20412.17910.57392.8302-0.0296-0.1051-0.36810.1629-0.16590.27760.3158-0.16990.19550.0718-0.04640.05150.0965-0.0210.10995.001115.9074-6.697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A198 - 263
2X-RAY DIFFRACTION2A264 - 322
3X-RAY DIFFRACTION3A323 - 332
4X-RAY DIFFRACTION4B196 - 267
5X-RAY DIFFRACTION5B268 - 279
6X-RAY DIFFRACTION6B280 - 325
7X-RAY DIFFRACTION7C198 - 239
8X-RAY DIFFRACTION8C240 - 287
9X-RAY DIFFRACTION9C288 - 331
10X-RAY DIFFRACTION10D196 - 204
11X-RAY DIFFRACTION11D205 - 261
12X-RAY DIFFRACTION12D262 - 325

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