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- PDB-4ak8: Structure of F241L mutant of langerin carbohydrate recognition domain. -

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Basic information

Entry
Database: PDB / ID: 4ak8
TitleStructure of F241L mutant of langerin carbohydrate recognition domain.
ComponentsC-TYPE LECTIN DOMAIN FAMILY 4 MEMBER K
KeywordsSUGAR BINDING PROTEIN / LANGERHANS CELLS / DC-SIGN / HIV / BIRBECK GRANULES
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
C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChabrol, E. / Thepaut, M. / Dezutter-Dambuyant, C. / Vives, C. / Marcoux, J. / Kahn, R. / Valadeau-Guilemond, J. / Vachette, P. / Durand, D. / Fieschi, F.
CitationJournal: Biophys.J. / Year: 2015
Title: Alteration of the Langerin Oligomerization State Affects Birbeck Granule Formation.
Authors: Chabrol, E. / Thepaut, M. / Dezutter-Dambuyant, C. / Vives, C. / Marcoux, J. / Kahn, R. / Valladeau-Guilemond, J. / Vachette, P. / Durand, D. / Fieschi, F.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)71,84513
Polymers71,5524
Non-polymers2939
Water14,538807
1
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

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)143,69026
Polymers143,1048
Non-polymers58618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area12850 Å2
ΔGint-239.9 kcal/mol
Surface area45240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.959, 79.959, 90.419
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 / CD_ANTIGEN=CD207


Mass: 17888.061 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 188-328 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJ71
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 241 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 241 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, PHE 241 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 241 TO LEU ENGINEERED RESIDUE IN CHAIN C, PHE 241 TO LEU ENGINEERED RESIDUE IN CHAIN D, PHE 241 TO LEU
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: 2.02 Å3/Da / Density % sol: 39.2 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: HANGING DROP METHOD 100 MM MES PH 6.0, 200 MM MGCL2 AND 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→19.52 Å / Num. obs: 111133 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.88
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.7 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C22

3c22


Resolution: 1.4→19.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.866 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21859 5529 5 %RANDOM
Rwork0.17536 ---
obs0.17754 105603 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 9 807 5040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.040.0224511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.021.9176172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5565552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05524.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7971513
X-RAY DIFFRACTIONr_chiral_restr0.1950.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213569
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8581.52655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.74424298
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.51831856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0724.51858
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 383 -
Rwork0.255 7632 -
obs--97.03 %

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