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- PDB-4qkj: Glycosylated form of human LLT1, a ligand for NKR-P1, in this str... -

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Basic information

Entry
Database: PDB / ID: 4qkj
TitleGlycosylated form of human LLT1, a ligand for NKR-P1, in this structure forming hexamers
ComponentsC-type lectin domain family 2 member D
KeywordsIMMUNE SYSTEM / C-type lectin like fold / ligand for human receptor NKR-P1 / GlcNAc2Man5 glycosylation / anchored in membrane on cell surface
Function / homology
Function and homology information


Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
: / Natural killer cell receptor-like, C-type lectin-like domain / 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 ...: / Natural killer cell receptor-like, C-type lectin-like domain / 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 2 member D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSkalova, T. / Blaha, J. / Duskova, J. / Koval, T. / Stransky, J. / Hasek, J. / Vanek, O. / Dohnalek, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states
Authors: Skalova, T. / Blaha, J. / Harlos, K. / Duskova, J. / Koval, T. / Stransky, J. / Hasek, J. / Vanek, O. / Dohnalek, J.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jul 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 / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.6Nov 8, 2023Group: 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9142
Polymers15,6921
Non-polymers2211
Water27015
1
A: C-type lectin domain family 2 member D
hetero molecules

A: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8274
Polymers31,3852
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.060, 70.060, 101.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein C-type lectin domain family 2 member D / Lectin-like NK cell receptor / Lectin-like transcript 1 / LLT-1 / Osteoclast inhibitory lectin


Mass: 15692.363 Da / Num. of mol.: 1 / Fragment: extracellular part, UNP residues 72-191 / Mutation: H176C
Source method: isolated from a genetically manipulated source
Details: protein secreted into medium / Source: (gene. exp.) Homo sapiens (human) / Gene: CLAX, CLEC2B, CLEC2D, LLT1, OCIL / Plasmid: pTT28 / Cell line (production host): HEK293S GnTI- / Production host: HOMO SAPIENS (human) / References: UniProt: Q9UHP7
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 40%(v/v) PEG300 and 0.1M citrate phosphate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2011
Details: Si Mirror, double crystal Si monochromator, Rh mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→39 Å / Num. all: 4431 / Num. obs: 4431 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 66.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.2
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2 / Num. unique all: 273 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
Sawayaet al.data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HUP

3hup


Resolution: 2.75→39 Å / Cor.coef. Fo:Fc: 0.894 / SU B: 11.069 / SU ML: 0.22 / Cross valid method: throughout (except for the last cycle) / σ(F): 0 / ESU R: 1.171
Stereochemistry target values: CCP4 STEREOCHEMISTRY LIBRARY, VERSION 6.4.0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 223 -RANDOM
Rwork0.22133 ---
all0.23022 4186 --
obs0.23022 4186 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.052 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.75→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 14 15 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02993
X-RAY DIFFRACTIONr_bond_other_d0.0060.02860
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9191344
X-RAY DIFFRACTIONr_angle_other_deg0.97131977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8285114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.45123.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56215158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.554157
X-RAY DIFFRACTIONr_chiral_restr0.1080.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
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_it3.9593.878459
X-RAY DIFFRACTIONr_mcbond_other3.9573.868458
X-RAY DIFFRACTIONr_mcangle_it6.5155.788572
X-RAY DIFFRACTIONr_mcangle_other6.515.799573
X-RAY DIFFRACTIONr_scbond_it3.784.165534
X-RAY DIFFRACTIONr_scbond_other3.7774.165534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.076.131773
X-RAY DIFFRACTIONr_long_range_B_refined10.19531.21222
X-RAY DIFFRACTIONr_long_range_B_other10.19231.2411223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 12 -
Rwork0.293 293 -
obs-281 99.66 %

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