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- PDB-3p5d: Structure of the carbohydrate-recognition domain of human Langeri... -

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Basic information

Entry
Database: PDB / ID: 3p5d
TitleStructure of the carbohydrate-recognition domain of human Langerin with man5 (Man alpha1-3(Man alpha1-6)Man alpha1-6)(Man- alpha1-3)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) / D-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) ...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
3alpha-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: 1.8013 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _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_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 / _pdbx_struct_special_symmetry.label_asym_id / _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_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)63,35312
Polymers62,3104
Non-polymers1,0438
Water9,476526
1
A: 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
2
B: 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
3
C: 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
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)79.34, 79.34, 89.67
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11B-446-

HOH

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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-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution: 5 mg/mL langerin CRD, 2.5 mM CaCl2, 10 mM Tris pH 8.0, 25 mM NaCl and 10 mM Man5. reservoir solution: 0.1 M Hepes pH 7.0, 0.25 M MgCl2 and 25% polyethylene glycol 4000, ...Details: protein solution: 5 mg/mL langerin CRD, 2.5 mM CaCl2, 10 mM Tris pH 8.0, 25 mM NaCl and 10 mM Man5. reservoir solution: 0.1 M Hepes pH 7.0, 0.25 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: Mar 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→44.83 Å / Num. obs: 51255 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9

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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: 1.8013→39.03 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2618 5.11 %random
Rwork0.174 ---
obs0.176 51252 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.732 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.5244 Å20 Å2-0 Å2
2--0.5244 Å20 Å2
3----1.0487 Å2
Refinement stepCycle: LAST / Resolution: 1.8013→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 63 526 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074500
X-RAY DIFFRACTIONf_angle_d1.0766080
X-RAY DIFFRACTIONf_dihedral_angle_d13.5541578
X-RAY DIFFRACTIONf_chiral_restr0.083606
X-RAY DIFFRACTIONf_plane_restr0.004769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8013-1.8340.27341450.19812469X-RAY DIFFRACTION97
1.834-1.86930.26271520.20642565X-RAY DIFFRACTION100
1.8693-1.90740.27311350.20772539X-RAY DIFFRACTION100
1.9074-1.94890.27251450.20592531X-RAY DIFFRACTION100
1.9489-1.99430.26521410.19482553X-RAY DIFFRACTION100
1.9943-2.04410.23791520.18742542X-RAY DIFFRACTION100
2.0441-2.09940.26241480.192533X-RAY DIFFRACTION100
2.0994-2.16120.23991320.18422565X-RAY DIFFRACTION100
2.1612-2.23090.24051280.18512545X-RAY DIFFRACTION100
2.2309-2.31060.23991460.18612567X-RAY DIFFRACTION100
2.3106-2.40310.23141490.18212578X-RAY DIFFRACTION100
2.4031-2.51250.21711220.17442550X-RAY DIFFRACTION100
2.5125-2.64490.22651360.17282578X-RAY DIFFRACTION100
2.6449-2.81060.24991280.18352563X-RAY DIFFRACTION100
2.8106-3.02750.25321180.18262579X-RAY DIFFRACTION100
3.0275-3.3320.17591410.17032577X-RAY DIFFRACTION100
3.332-3.81380.1931120.152592X-RAY DIFFRACTION100
3.8138-4.80370.16671450.13152582X-RAY DIFFRACTION100
4.8037-39.04280.19541430.16582626X-RAY DIFFRACTION100

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