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- PDB-3p5i: Structure of the carbohydrate-recognition domain of human Langeri... -

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Basic information

Entry
Database: PDB / ID: 3p5i
TitleStructure of the carbohydrate-recognition domain of human Langerin with 6-SO4-Gal-GlcNAc
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
C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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_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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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 / _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)64,32312
Polymers62,3104
Non-polymers2,0148
Water8,629479
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0813
Polymers15,5771
Non-polymers5032
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)16,0813
Polymers15,5771
Non-polymers5032
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)16,0813
Polymers15,5771
Non-polymers5032
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)16,0813
Polymers15,5771
Non-polymers5032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.81, 79.81, 90.74
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
6-O-sulfo-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 463.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalp[6S]b1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5_6*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp6SO3]{}}LINUCSPDB-CARE
#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.: 479 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution: 2.5 mg/mL langerin CRD, 1.25 mM CaCl2, 5 mM Tris pH 8.0, 12.5 mM NaCl and 7.5 mM 6SO4-Gal-GlcNAc. reservoir solution: 0.1 M Hepes pH 7.0, 0.1 M MgCl2 and 25% PEG 4000, ...Details: protein solution: 2.5 mg/mL langerin CRD, 1.25 mM CaCl2, 5 mM Tris pH 8.0, 12.5 mM NaCl and 7.5 mM 6SO4-Gal-GlcNAc. reservoir solution: 0.1 M Hepes pH 7.0, 0.1 M MgCl2 and 25% PEG 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: May 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→47.92 Å / Num. obs: 52682 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 6.5 / % 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: 1.8→39.905 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2669 5.1 %random
Rwork0.178 ---
obs0.181 52365 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.839 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.3904 Å20 Å20 Å2
2---0.3904 Å2-0 Å2
3---0.7807 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 124 479 4789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074548
X-RAY DIFFRACTIONf_angle_d1.0846161
X-RAY DIFFRACTIONf_dihedral_angle_d18.9621611
X-RAY DIFFRACTIONf_chiral_restr0.081620
X-RAY DIFFRACTIONf_plane_restr0.005771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83270.28331220.21852364X-RAY DIFFRACTION90
1.8327-1.8680.2951500.21152582X-RAY DIFFRACTION100
1.868-1.90610.26791490.20972644X-RAY DIFFRACTION100
1.9061-1.94760.2531460.20432618X-RAY DIFFRACTION100
1.9476-1.99290.23691550.19772563X-RAY DIFFRACTION100
1.9929-2.04270.281480.19242660X-RAY DIFFRACTION100
2.0427-2.09790.24521530.20192615X-RAY DIFFRACTION100
2.0979-2.15970.2451360.1942618X-RAY DIFFRACTION100
2.1597-2.22940.27221300.18952616X-RAY DIFFRACTION100
2.2294-2.3090.24181550.19132585X-RAY DIFFRACTION100
2.309-2.40150.26031520.20082630X-RAY DIFFRACTION100
2.4015-2.51080.27371270.19722666X-RAY DIFFRACTION100
2.5108-2.64310.23961390.18232605X-RAY DIFFRACTION100
2.6431-2.80870.27151310.19872653X-RAY DIFFRACTION100
2.8087-3.02550.27761210.19122646X-RAY DIFFRACTION100
3.0255-3.32980.1981440.18262643X-RAY DIFFRACTION100
3.3298-3.81130.21180.15522666X-RAY DIFFRACTION100
3.8113-4.80050.15061460.12462643X-RAY DIFFRACTION100
4.8005-39.91480.15061470.14212679X-RAY DIFFRACTION99

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