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- PDB-4n34: Structure of langerin CRD I313 with alpha-MeGlcNAc -

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Basic information

Entry
Database: PDB / ID: 4n34
TitleStructure of langerin CRD I313 with alpha-MeGlcNAc
ComponentsC-type lectin domain family 4 member K
KeywordsSUGAR BINDING PROTEIN / CRD carbohydrate complex / carbohydrate-recognition domain / C-type lectin on Langerhans cells / Carbohydrate/Sugar Binding / receptor on Langerhans cells
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
Chem-2F8 / C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsFeinberg, H. / Rowntree, T.J.W. / Tan, S.L.W. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Common polymorphisms in human langerin change specificity for glycan ligands.
Authors: Feinberg, H. / Rowntree, T.J. / Tan, S.L. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _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.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_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 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 1.5Nov 27, 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)63,34712
Polymers62,2454
Non-polymers1,1018
Water13,187732
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8373
Polymers15,5611
Non-polymers2752
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)15,8373
Polymers15,5611
Non-polymers2752
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)15,8373
Polymers15,5611
Non-polymers2752
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)15,8373
Polymers15,5611
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: C-type lectin domain family 4 member K
C: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6736
Polymers31,1232
Non-polymers5514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-25 kcal/mol
Surface area12650 Å2
MethodPISA
6
B: 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)31,6736
Polymers31,1232
Non-polymers5514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-25 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 80.060, 90.170
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
11D-637-

HOH

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Components

#1: Protein
C-type lectin domain family 4 member K / Langerin


Mass: 15561.354 Da / Num. of mol.: 4 / Mutation: K313I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207, CLEC4K / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJ71
#2: Sugar
ChemComp-2F8 / methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside / methyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside / methyl 2-acetamido-2-deoxy-alpha-D-glucoside / methyl 2-acetamido-2-deoxy-D-glucoside / methyl 2-acetamido-2-deoxy-glucoside


Type: D-saccharide / Mass: 235.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO6
IdentifierTypeProgram
DGlcpNAc[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-N-acetyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
#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


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 2.3-4.0 mg/mL langerin, 2.5 mM CaCl2, 10-100 mM Tris (pH 8.0), 25 mM NaCl and 50mM alpha-Me-GlcNAc. The reservoir solution contained 0.1 M HEPES (pH 7.0), 0.1-0.2 M MgCl2, ...Details: Protein solution: 2.3-4.0 mg/mL langerin, 2.5 mM CaCl2, 10-100 mM Tris (pH 8.0), 25 mM NaCl and 50mM alpha-Me-GlcNAc. The reservoir solution contained 0.1 M HEPES (pH 7.0), 0.1-0.2 M MgCl2, and 20-35% polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2011
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.75→47.94 Å / Num. obs: 56552 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.27 Å2 / Rsym value: 0.035 / Net I/σ(I): 37.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.847.20.0888.25877481670.08897.9
1.84-1.967.50.06510.85861977650.06598.1
1.96-2.097.50.0513.65482672800.0598.4
2.09-2.267.50.04215.45113968210.04298.7
2.26-2.477.50.03716.84710363210.03799.2
2.47-2.777.40.03219.84248357270.03299.2
2.77-3.27.30.03317.63697850550.03399.5
3.2-3.917.10.03616.43074043010.03699.6
3.91-5.536.80.02821.32241233110.02899.4
5.53-39.2847.40.02624.31343118040.02696.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3P5G

3p5g


Resolution: 1.75→35.8 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8429 / SU ML: 0.23 / σ(F): 0 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 2858 5.08 %
Rwork0.1758 --
obs0.1784 56239 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.97 Å2 / Biso mean: 22.247 Å2 / Biso min: 5.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 68 732 4981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074475
X-RAY DIFFRACTIONf_angle_d1.126050
X-RAY DIFFRACTIONf_chiral_restr0.087603
X-RAY DIFFRACTIONf_plane_restr0.005768
X-RAY DIFFRACTIONf_dihedral_angle_d13.9781560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7505-1.78060.32991380.24842399253789
1.7806-1.8130.31081300.2362644277498
1.813-1.84790.30471470.21152647279498
1.8479-1.88560.24231570.20062657281498
1.8856-1.92660.25811440.20422662280698
1.9266-1.97140.26621510.1972638278998
1.9714-2.02070.25981490.2072665281498
2.0207-2.07530.26491580.20332644280298
2.0753-2.13640.261420.20272683282599
2.1364-2.20540.25321420.19142667280999
2.2054-2.28420.27031490.19642672282199
2.2842-2.37560.24221530.19652672282599
2.3756-2.48370.24661270.18942718284599
2.4837-2.61460.23971470.17772691283899
2.6146-2.77840.26751370.18032723286099
2.7784-2.99280.21911230.183627252848100
2.9928-3.29380.19891480.17112700284899
3.2938-3.76990.19661230.14682751287499
3.7699-4.7480.16421480.12412715286399
4.748-35.81140.18841450.15332708285397

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