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- PDB-3p5f: Structure of the carbohydrate-recognition domain of human Langeri... -

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Basic information

Entry
Database: PDB / ID: 3p5f
TitleStructure of the carbohydrate-recognition domain of human Langerin with man2 (Man alpha1-2 Man)
ComponentsC-type lectin domain family 4 member K
KeywordsSUGAR BINDING PROTEIN / C-type lectin / carbohydrate-binding
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
2alpha-alpha-mannobiose / alpha-D-mannopyranose / C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7501 Å
AuthorsFeinberg, H. / Taylor, M.E. / Razi, N. / McBride, R. / Knirel, Y.A. / Graham, S.A. / Drickamer, K. / Weis, W.I.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for Langerin Recognition of Diverse Pathogen and Mammalian Glycans through a Single Binding Site.
Authors: Feinberg, H. / Taylor, M.E. / Razi, N. / McBride, R. / Knirel, Y.A. / Graham, S.A. / Drickamer, K. / Weis, W.I.
History
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_alt_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_alt_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.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_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)63,69513
Polymers62,3104
Non-polymers1,3859
Water10,791599
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7983
Polymers15,5771
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)15,9603
Polymers15,5771
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)16,1404
Polymers15,5771
Non-polymers5633
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)15,7983
Polymers15,5771
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.78, 79.78, 90.47
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: 15577.376 Da / Num. of mol.: 4 / Fragment: Langerin CRD (UNP residues 193-328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207, CLEC4K / Plasmid: pINIIIompA2 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 / References: UniProt: Q9UJ71
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
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: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution: 5 mg mL-1 langerin CRD, 2.5 mM CaCl2, 10 mM Tris pH 8.0, 25 mM NaCl and 30 mM Man5. reservoir solution: 0.1 M Hepes pH 7.0, 0.10 M MgCl2 and 25% polyethylene glycol 4000, ...Details: protein solution: 5 mg mL-1 langerin CRD, 2.5 mM CaCl2, 10 mM Tris pH 8.0, 25 mM NaCl and 30 mM Man5. reservoir solution: 0.1 M Hepes pH 7.0, 0.10 M MgCl2 and 25% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.75→39.89 Å / Num. obs: 57096 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 7.3 / Num. unique all: 8309 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7501→39.35 Å / SU ML: 0.22 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2896 5.09 %random
Rwork0.173 ---
obs0.175 56934 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.803 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.7947 Å2-0 Å20 Å2
2---0.7947 Å2-0 Å2
3---1.5894 Å2
Refinement stepCycle: LAST / Resolution: 1.7501→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 86 599 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074538
X-RAY DIFFRACTIONf_angle_d1.0736127
X-RAY DIFFRACTIONf_dihedral_angle_d14.5051605
X-RAY DIFFRACTIONf_chiral_restr0.08628
X-RAY DIFFRACTIONf_plane_restr0.005763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.77880.25571420.19232469X-RAY DIFFRACTION96
1.7788-1.80950.27271180.19152562X-RAY DIFFRACTION100
1.8095-1.84240.23121450.19022546X-RAY DIFFRACTION100
1.8424-1.87780.26331460.18782583X-RAY DIFFRACTION100
1.8778-1.91620.25421440.192544X-RAY DIFFRACTION100
1.9162-1.95780.24091500.18792593X-RAY DIFFRACTION100
1.9578-2.00340.22371400.18042537X-RAY DIFFRACTION100
2.0034-2.05350.24711540.17752568X-RAY DIFFRACTION100
2.0535-2.1090.22471420.1892574X-RAY DIFFRACTION100
2.109-2.1710.23661370.17832563X-RAY DIFFRACTION100
2.171-2.24110.23921270.17952570X-RAY DIFFRACTION100
2.2411-2.32120.23831500.18192580X-RAY DIFFRACTION100
2.3212-2.41410.24241490.19092566X-RAY DIFFRACTION100
2.4141-2.5240.23761230.18322566X-RAY DIFFRACTION100
2.524-2.6570.23771370.17682599X-RAY DIFFRACTION100
2.657-2.82350.24581310.18462603X-RAY DIFFRACTION100
2.8235-3.04140.24811180.17472590X-RAY DIFFRACTION100
3.0414-3.34730.17231420.17442595X-RAY DIFFRACTION100
3.3473-3.83130.1811110.1462594X-RAY DIFFRACTION100
3.8313-4.82570.15231470.12282602X-RAY DIFFRACTION100
4.8257-39.35980.18691430.16162634X-RAY DIFFRACTION100

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