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- PDB-4qkh: Dimeric form of human LLT1, a ligand for NKR-P1 -

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Basic information

Entry
Database: PDB / ID: 4qkh
TitleDimeric form of human LLT1, a ligand for NKR-P1
ComponentsC-type lectin domain family 2 member D
KeywordsIMMUNE SYSTEM / C-type lectin like fold / ligand for human receptor NKR-P1 / glycosylation / deglycosylated after the first GlcNac unit / 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: 1.8 Å
AuthorsSkalova, T. / Blaha, J. / Harlos, K. / 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 1.2Jun 13, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)32,2706
Polymers31,3852
Non-polymers8854
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1353
Polymers15,6921
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1353
Polymers15,6921
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 57.820, 82.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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.: 4
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.: 214 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30%(w/v) polyethylene glycol 6000, 0.1M HEPES, pH 7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2012 / Details: Kirkpatrick Baez mirror pair
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→47.3 Å / Num. all: 21104 / Num. obs: 21104 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 8.3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3 / Num. unique all: 1087 / % possible all: 81

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Processing

Software
NameVersionClassification
BALBESphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HUP

3hup


Resolution: 1.8→47.3 Å / Cor.coef. Fo:Fc: 0.955 / SU B: 2.024 / SU ML: 0.065 / Cross valid method: throughout (except for the last cycle) / σ(F): 0 / ESU R: 0.148
Stereochemistry target values: CCP4 STEREOCHEMISTRY LIBRARY, VERSION 6.4.0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24992 1104 -random
Rwork0.17499 ---
all0.18041 21045 --
obs0.18041 21045 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0 Å2
2--1.14 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 56 214 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022160
X-RAY DIFFRACTIONr_bond_other_d0.0030.021889
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9342941
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0064333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2595258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5523.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02415342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8131515
X-RAY DIFFRACTIONr_chiral_restr0.1070.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
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_it2.4252.495990
X-RAY DIFFRACTIONr_mcbond_other2.4242.491989
X-RAY DIFFRACTIONr_mcangle_it3.563.7291238
X-RAY DIFFRACTIONr_mcangle_other3.563.7321239
X-RAY DIFFRACTIONr_scbond_it2.752.911170
X-RAY DIFFRACTIONr_scbond_other2.7492.9121171
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.284.2631696
X-RAY DIFFRACTIONr_long_range_B_refined6.54621.9342639
X-RAY DIFFRACTIONr_long_range_B_other6.3421.5792554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 79 -
Rwork0.219 1336 -
obs-1336 80.29 %

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