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- PDB-5g6u: Crystal structure of langerin carbohydrate recognition domain wit... -

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Basic information

Entry
Database: PDB / ID: 5g6u
TitleCrystal structure of langerin carbohydrate recognition domain with GlcNS6S
ComponentsLANGERIN
KeywordsCARBOHYDRATE BINDING PROTEIN / LANGERIN / CD207 / CLEC4K / C-TYPE LECTINS / CLRS / SULFATED CARBOHYDRATES
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / signaling receptor activity / 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
EUROPIUM ION / Chem-SGN / TRYPTOPHAN / C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsPorkolab, V. / Chabrol, E. / Varga, N. / Ordanini, S. / Sutkeviciute, I. / Thepaut, M. / Bernardi, A. / Fieschi, F.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Rational-Differential Design of Highly Specific Glycomimetic Ligands: Targeting DC-SIGN and Excluding Langerin Recognition.
Authors: Porkolab, V. / Chabrol, E. / Varga, N. / Ordanini, S. / Sutkeviciu Te, I. / Thepaut, M. / Garcia-Jimenez, M.J. / Girard, E. / Nieto, P.M. / Bernardi, A. / Fieschi, F.
History
DepositionJul 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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.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_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LANGERIN
B: LANGERIN
C: LANGERIN
D: LANGERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,32933
Polymers117,8614
Non-polymers3,46729
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-169 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.483, 79.483, 90.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
LANGERIN


Mass: 29465.326 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN
Source method: isolated from a genetically manipulated source
Details: LANGERIN CRD COMPLEXED WITH GLCNS6S / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-30 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q9UJ71
#3: Sugar
ChemComp-SGN / 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose / N,O6-DISULFO-GLUCOSAMINE / 6-O-sulfo-N-sulfo-alpha-D-glucosamine / 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucose / 2-deoxy-6-O-sulfo-2-(sulfoamino)-D-glucose / 2-deoxy-6-O-sulfo-2-(sulfoamino)-glucose


Type: D-saccharide, alpha linking / Mass: 339.298 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO11S2
IdentifierTypeProgram
DGlcpNS[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-sulfo-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpNSO36SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 549 molecules

#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Eu
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.4 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7 / Details: HEPES PH7, 100 MM MGCL2, 150 MM NACL, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: SI(111) DOUBLE CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.84→35.55 Å / Num. obs: 48373 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 1.84→1.96 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C22

3c22


Resolution: 1.844→36.401 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 2440 5 %
Rwork0.1516 --
obs0.153 48406 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 1.844→36.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 147 524 4861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0234617
X-RAY DIFFRACTIONf_angle_d0.7776244
X-RAY DIFFRACTIONf_dihedral_angle_d14.7532664
X-RAY DIFFRACTIONf_chiral_restr0.051612
X-RAY DIFFRACTIONf_plane_restr0.005784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.844-1.88160.23721450.19592560X-RAY DIFFRACTION95
1.8816-1.92250.23471080.19722736X-RAY DIFFRACTION100
1.9225-1.96720.22121320.18652687X-RAY DIFFRACTION100
1.9672-2.01640.21051580.17492724X-RAY DIFFRACTION100
2.0164-2.07090.23041400.17622675X-RAY DIFFRACTION100
2.0709-2.13190.19171390.16552717X-RAY DIFFRACTION100
2.1319-2.20070.19951260.15862730X-RAY DIFFRACTION100
2.2007-2.27930.18781340.16152734X-RAY DIFFRACTION100
2.2793-2.37060.20591540.16382692X-RAY DIFFRACTION100
2.3706-2.47840.17581400.16052698X-RAY DIFFRACTION100
2.4784-2.60910.19741520.15372701X-RAY DIFFRACTION100
2.6091-2.77250.19641570.16052698X-RAY DIFFRACTION100
2.7725-2.98650.18711500.16032702X-RAY DIFFRACTION100
2.9865-3.28680.20241540.15332719X-RAY DIFFRACTION100
3.2868-3.7620.1641500.13382732X-RAY DIFFRACTION100
3.762-4.73810.13551520.11642714X-RAY DIFFRACTION100
4.7381-36.40830.15811490.1532747X-RAY DIFFRACTION99
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)
13.36540.4051-1.12552.9669-1.15362.0058-0.0185-0.1353-0.4326-0.0375-0.1712-0.16110.22260.24950.17250.19670.03980.01160.17890.04030.222572.5137.31252.0466
28.9294-1.9923-5.18383.26743.22124.5533-0.32250.671-0.7338-0.31010.1813-0.03830.6035-0.48410.05220.3242-0.053-0.02280.2345-0.01850.279967.82156.624845.8825
32.2759-0.2130.5062.28070.53382.6920.1708-0.4819-0.14880.6186-0.2528-0.18760.02290.34870.09850.2704-0.0382-0.03840.28220.06530.179973.20315.293659.2132
46.07770.9077-0.27393.0563-1.21615.21030.17770.24610.4532-0.0918-0.14160.1917-0.7126-0.1009-0.03970.23430.0320.0030.15340.01070.14965.883325.820750.9388
53.5046-0.34750.30454.0361.11896.1077-0.102-0.19690.49270.3111-0.0307-0.38-0.34540.4250.13660.2403-0.0659-0.09040.24540.00650.249976.695325.572657.6296
61.47520.1312-2.1182.59-1.67573.6746-0.1366-0.0409-0.0764-0.0757-0.0324-0.18060.05090.2690.15650.14180.0209-0.04690.24220.04770.157672.7513.312653.0239
75.3583-0.46482.10152.6804-2.26332.53670.1563-0.21280.00360.1091-0.13870.2667-0.4985-0.0950.01480.3180.00130.02580.1563-0.09240.282952.9731.017861.4722
85.1694-0.20582.42451.5113-0.52944.3549-0.0448-0.02480.17580.01680.02240.0905-0.1756-0.06740.00450.1864-0.01540.05530.1579-0.03260.198446.152825.659553.2476
94.92890.4530.02793.15950.52164.09980.131-0.16180.22760.2958-0.13950.05930.1103-0.2209-0.02920.2029-0.02450.08760.1328-0.00290.203943.350920.593560.0734
106.72160.18562.22771.0914-2.33936.00830.13940.3743-0.2903-0.092-0.09890.07340.41420.2661-0.08050.2270.03220.0550.1793-0.02370.258152.56211.149651.1414
113.37090.22530.22432.1373-1.19793.7926-0.07230.0056-0.44660.0893-0.00060.13370.313-0.14120.05590.2356-0.02990.10560.1772-0.02610.286941.799411.168657.9953
124.70921.19413.76592.09361.8694.7634-0.32320.26240.1359-0.00530.2250.192-0.18990.08860.03530.1923-0.0060.06470.1342-0.01870.176946.734327.252354.2721
135.1411-1.16731.85951.8663-1.153.7084-0.11110.10670.25910.09180.0211-0.0482-0.36250.18270.07090.1865-0.01830.00610.15680.02890.171772.35128.223330.2064
146.54132.43022.59838.84496.78436.9574-0.01190.3128-0.1326-0.0169-0.16320.2017-0.1082-0.66860.22730.15490.02170.01570.20550.03830.161166.172223.220226.291
154.75860.6530.07233.19220.93791.9133-0.04260.0864-0.49020.0873-0.0946-0.00340.0982-0.22770.11820.15170.01980.03360.1602-0.01070.178169.380416.311627.6797
165.6708-1.8322-4.54198.10273.86284.4461-0.17350.9502-0.3092-0.74220.3953-0.0209-0.0915-0.4092-0.1390.3325-0.05910.01720.5262-0.21380.490162.84788.878821.2993
173.82540.2671-0.52783.27951.2224.3222-0.15450.2174-0.7589-0.05240.0384-0.1770.41270.17120.06760.16980.0170.08120.2038-0.00530.283276.089413.292226.3461
188.1197-4.3329-0.48414.0353-0.95243.9757-0.3562-1.10240.03561.33150.68730.4833-0.7129-0.2846-0.2640.35280.09850.08860.29010.0210.224859.670134.284428.9078
197.7436-0.6687-5.05096.1045-0.54629.5916-0.11390.205-0.0366-0.22250.0977-0.1060.8955-0.17150.02010.2798-0.0124-0.03290.2263-0.00370.250248.17226.922724.0587
203.01640.64660.41773.56891.02315.06280.07370.05840.0058-0.0249-0.25140.26440.2602-0.30420.12870.136-0.0015-0.03210.1849-0.00240.189943.443515.742330.188
218.2903-1.078-2.03429.1493-3.32395.16140.0252-0.16760.41150.0685-0.0417-0.237-0.14770.2891-0.00090.1443-0.0156-0.04610.1786-0.00380.159252.395426.275830.7907
221.44370.821.44574.22740.38145.5093-0.19270.11420.502-0.2297-0.09780.512-0.6367-0.27240.22920.20740.0678-0.08350.26270.01950.349540.472828.038526.8402
235.07341.5394-0.45523.81471.66265.9108-0.13050.0078-0.52030.2741-0.18330.24630.7232-0.07740.21730.22750.0002-0.03050.25090.03870.168243.690412.366931.566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 196:223)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 224:229)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 230:257)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 258:275)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 276:303)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 304:326)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 198:206)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 207:239)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 240:258)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 259:275)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 276:312)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 313:325)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 198:225)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 226:239)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 240:273)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 274:279)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 280:320)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 321:325)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 198:208)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 209:260)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 261:277)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 278:310)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 311:325)

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