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- PDB-9hye: Structure of the Mus musclus Langerin carbohydrate recognition do... -

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Basic information

Entry
Database: PDB / ID: 9hye
TitleStructure of the Mus musclus Langerin carbohydrate recognition domain with depleted Calcium
ComponentsC-type lectin domain family 4 member K
KeywordsIMMUNE SYSTEM / C-TYPE LECTIN / GLYCOPROTEIN / CARBOHYDRATE BINDING PROTEIN / CALCIUM BINDING / CRD DOMAIN / LECTIN
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / carbohydrate binding / defense response to virus / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / 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
Similarity search - Domain/homology
C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsRuwolt, M. / Neu, U. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: to be published
Title: Structure of the Mus musclus Langerin carbohydrate recognition domain with depleted Calcium
Authors: Ruwolt, M. / Neu, U. / Loll, B.
History
DepositionJan 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9965
Polymers35,8902
Non-polymers1063
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-39 kcal/mol
Surface area14170 Å2
Unit cell
Length a, b, c (Å)34.917, 80.706, 52.179
Angle α, β, γ (deg.)90.000, 105.250, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 17944.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd207, Clec4k / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8VBX4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 21% (w/v) polyethylene glycol 3350 and 200 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 34064 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.62 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.161 / Net I/σ(I): 8.1
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5380 / CC1/2: 0.37 / Rrim(I) all: 2.109 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→40.35 Å / SU ML: 0.2374 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 1704 5 %
Rwork0.1536 32358 -
obs0.1566 34062 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 1.64→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 3 224 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01072526
X-RAY DIFFRACTIONf_angle_d1.00293437
X-RAY DIFFRACTIONf_chiral_restr0.0666326
X-RAY DIFFRACTIONf_plane_restr0.0115450
X-RAY DIFFRACTIONf_dihedral_angle_d14.1459925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.36231360.30382567X-RAY DIFFRACTION93.72
1.69-1.740.33731420.25052711X-RAY DIFFRACTION99.93
1.74-1.80.32651420.21122695X-RAY DIFFRACTION99.86
1.8-1.870.25861430.18192718X-RAY DIFFRACTION99.79
1.87-1.960.22721410.17892678X-RAY DIFFRACTION99.54
1.96-2.060.22971410.14192678X-RAY DIFFRACTION98.39
2.06-2.190.20581430.13092720X-RAY DIFFRACTION99.79
2.19-2.360.23051420.14242692X-RAY DIFFRACTION99.79
2.36-2.60.21961430.14322727X-RAY DIFFRACTION99.31
2.6-2.970.20931420.15342701X-RAY DIFFRACTION99.75
2.97-3.750.19611440.14182726X-RAY DIFFRACTION99.48
3.75-40.350.17351450.1392745X-RAY DIFFRACTION99.04

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