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- PDB-5mgt: Complex of human NKR-P1 and LLT1 in deglycosylated forms -

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Basic information

Entry
Database: PDB / ID: 5mgt
TitleComplex of human NKR-P1 and LLT1 in deglycosylated forms
Components
  • C-type lectin domain family 2 member D
  • Killer cell lectin-like receptor subfamily B member 1
KeywordsIMMUNE SYSTEM / receptor / CTL fold / natural killer cell / receptor-ligand complex
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / 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 ...: / : / 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
Killer cell lectin-like receptor subfamily B member 1 / C-type lectin domain family 2 member D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBlaha, J. / Skalova, T. / Stransky, J. / Koval, T. / Hasek, J. / Yuguang, Z. / Harlos, K. / Vanek, O. / Dohnalek, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation15-15181S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLG14009 Czech Republic
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
Authors: Blaha, J. / Skalova, T. / Kalouskova, B. / Skorepa, O. / Cmunt, D. / Grobarova, V. / Pazicky, S. / Polachova, E. / Abreu, C. / Stransky, J. / Koval, T. / Duskova, J. / Zhao, Y. / Harlos, K. ...Authors: Blaha, J. / Skalova, T. / Kalouskova, B. / Skorepa, O. / Cmunt, D. / Grobarova, V. / Pazicky, S. / Polachova, E. / Abreu, C. / Stransky, J. / Koval, T. / Duskova, J. / Zhao, Y. / Harlos, K. / Hasek, J. / Dohnalek, J. / Vanek, O.
History
DepositionNov 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 8, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 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
B: C-type lectin domain family 2 member D
C: Killer cell lectin-like receptor subfamily B member 1
D: Killer cell lectin-like receptor subfamily B member 1
E: Killer cell lectin-like receptor subfamily B member 1
F: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,18026
Polymers99,8186
Non-polymers3,36220
Water12,448691
1
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)32,65410
Polymers31,3852
Non-polymers1,2698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Killer cell lectin-like receptor subfamily B member 1
D: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3299
Polymers34,2172
Non-polymers1,1127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Killer cell lectin-like receptor subfamily B member 1
F: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1987
Polymers34,2172
Non-polymers9815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.580, 80.150, 272.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ABCDEF

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


Mass: 15692.363 Da / Num. of mol.: 2 / Mutation: H176C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER CELLS, ACTIVATED MONOCYTES, B-CELLS / Gene: CLEC2D, CLAX, LLT1, OCIL / Plasmid: pTT28 / Details (production host): pTT28 / Cell line (production host): HEK293S GnTI- / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Human embryonic kidney / References: UniProt: Q9UHP7
#2: Protein
Killer cell lectin-like receptor subfamily B member 1 / C-type lectin domain family 5 member B / HNKR-P1a / NKR-P1A / Natural killer cell surface protein P1A


Mass: 17108.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER CELLS, NKT CELLS, TH17 CELLS / Gene: KLRB1, CLEC5B, NKRP1A / Plasmid: pOPINGGTneo / Cell line (production host): HEK293S GnTI- / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Human embryonic kidney / References: UniProt: Q12918

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Sugars , 1 types, 12 molecules

#3: 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.: 12
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

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Non-polymers , 3 types, 699 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 49.64 %
Description: A tetragonal crystal with dimensions 30, 30, 80 um
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.200 M Ammonium Sulphate, 20 %w/v Polyethylene Glycol MME 5000, 0.1 M Tris pH 7.5, total protein concentration 8 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→76.91 Å / Num. obs: 78617 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 18.5 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 18 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3 / Num. unique all: 4472 / CC1/2: 0.89 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BPD

2bpd


Resolution: 1.9→76.91 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 2.033 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3915 5 %random
Rwork0.162 ---
obs0.162 78515 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2---0.55 Å20 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.9→76.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 204 691 6922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026527
X-RAY DIFFRACTIONr_bond_other_d0.0040.025887
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9588896
X-RAY DIFFRACTIONr_angle_other_deg1.053313607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7935.091769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86224.892325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.223151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2941534
X-RAY DIFFRACTIONr_chiral_restr0.1130.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021587
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_it2.5262.2262983
X-RAY DIFFRACTIONr_mcbond_other2.5262.2252982
X-RAY DIFFRACTIONr_mcangle_it3.6353.3113731
X-RAY DIFFRACTIONr_mcangle_other3.6353.3133732
X-RAY DIFFRACTIONr_scbond_it3.6272.7313544
X-RAY DIFFRACTIONr_scbond_other3.5982.7023517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6793.8885107
X-RAY DIFFRACTIONr_long_range_B_refined7.98219.6427847
X-RAY DIFFRACTIONr_long_range_B_other7.77319.0187527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.257 268 5 %
Rwork0.23 5763 -
obs--99.86 %

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