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- PDB-3p7f: Structure of the human Langerin carbohydrate recognition domain -

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Basic information

Entry
Database: PDB / ID: 3p7f
TitleStructure of the human Langerin carbohydrate recognition domain
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) / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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: 3BBS
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,3838
Polymers67,2234
Non-polymers1604
Water1,964109
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8462
Polymers16,8061
Non-polymers401
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)16,8462
Polymers16,8061
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-type lectin domain family 4 member K
hetero molecules


  • defined by author
  • 16.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)16,8462
Polymers16,8061
Non-polymers401
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)16,8462
Polymers16,8061
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.760, 79.760, 90.560
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: 16805.736 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
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; 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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2006
RadiationMonochromator: Osmic confocal Max-Flux Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 19624 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2159 / % possible all: 99.9

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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: 2.5→28.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 21.295 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.979 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24288 991 5.1 %RANDOM
Rwork0.18655 ---
obs0.18938 18632 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 4 109 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.9096077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29324.22218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5715663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0611512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2589
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_it0.4031.52618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8222.54222
X-RAY DIFFRACTIONr_scbond_it1.7493.51837
X-RAY DIFFRACTIONr_scangle_it2.908101855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 99 -
Rwork0.237 1341 -
obs--99.86 %
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)
12.9885-0.9243-0.73813.1068-0.01084.04360.00030.0529-0.0796-0.0586-0.04360.08410.0707-0.07870.04320.04650.0112-0.06080.0914-0.02760.08957.017415.9775-33.8065
23.21920.5020.17942.8154-0.56992.7482-0.07160.09150.3303-0.2872-0.03760.2253-0.268-0.14220.10920.11440.0653-0.07790.087-0.0360.13854.787325.8897-33.9789
314.380816.04597.884517.94589.24769.43661.23860.2311-2.57881.60730.2464-2.8651.28861.7783-1.4850.60430.2886-0.23490.9472-0.10020.492627.36254.6427-29.621
43.4211-0.57011.67123.3811-1.40183.08710.110.20590.3746-0.1778-0.1178-0.1789-0.30520.19110.00780.107-0.00390.05260.09710.03090.099832.721429.4943-32.4
55.34570.61280.26483.49351.49030.70.21130.2224-0.55260.0125-0.2340.05870.1439-0.08650.02270.30730.0402-0.01950.07520.00590.095228.473413.9707-32.8286
62.19960.64060.19522.9626-0.44193.22040.05410.1603-0.1141-0.2034-0.053-0.29660.19460.3237-0.0010.0541-0.02040.02320.14040.01130.062136.645121.0547-31.8773
74.71861.484-0.79962.6921-1.43393.0878-0.056-0.136-0.27080.07320.0147-0.16950.42280.03090.04130.10260.0043-0.03030.02230.02890.082630.542313.0401-6.3511
85.6903-0.87660.71982.83261.65191.5758-0.1329-0.11150.71010.1206-0.0089-0.0761-0.2844-0.08010.14180.3440.0258-0.04420.0787-0.01070.140132.232526.8129-4.5719
94.7363-1.3266-0.40190.64-0.42494.1137-0.01270.1945-0.3321-0.25880.07140.29350.5228-0.3388-0.05870.313-0.0574-0.1920.13340.07260.205127.200210.9797-8.7827
1020.3796-0.5773-0.609613.7660.935411.3907-0.00460.0730.8824-0.2363-0.09270.1698-0.8969-0.60330.09730.2176-0.04710.07540.1401-0.06970.12478.350533.9532-2.4336
113.5209-0.99570.2693.91080.36514.37840.1141-0.0158-0.03310.0391-0.21940.20860.0018-0.18040.10530.0583-0.05070.04250.0831-0.0170.08915.847121.4806-8.1842
122.96940.0392-0.06013.50730.58044.8860.0945-0.109-0.27640.3559-0.23350.22650.4215-0.40510.13890.109-0.03640.07150.1719-0.03340.15012.147716.8305-6.1852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A198 - 263
2X-RAY DIFFRACTION2A264 - 321
3X-RAY DIFFRACTION3A322 - 331
4X-RAY DIFFRACTION4B196 - 256
5X-RAY DIFFRACTION5B257 - 284
6X-RAY DIFFRACTION6B285 - 325
7X-RAY DIFFRACTION7C198 - 241
8X-RAY DIFFRACTION8C242 - 312
9X-RAY DIFFRACTION9C313 - 331
10X-RAY DIFFRACTION10D196 - 207
11X-RAY DIFFRACTION11D208 - 276
12X-RAY DIFFRACTION12D277 - 325

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