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- PDB-5mgr: Human receptor NKR-P1 in glycosylated form, extracellular domain -

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Basic information

Entry
Database: PDB / ID: 5mgr
TitleHuman receptor NKR-P1 in glycosylated form, extracellular domain
ComponentsKiller cell lectin-like receptor subfamily B member 1
KeywordsIMMUNE SYSTEM / receptor / CTL fold / natural killer cell
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 / cell surface / 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
Killer cell lectin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSkalova, T. / Blaha, J. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 8, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 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: Killer cell lectin-like receptor subfamily B member 1
B: Killer cell lectin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8056
Polymers34,2172
Non-polymers2,5884
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint50 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.241, 68.241, 127.195
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: lymphocytes, natural killer cell / Gene: KLRB1, CLEC5B, NKRP1A / Plasmid: pOPINGGTneo / Cell line (production host): HEK293S GnTI- / Organ (production host): Human embryonic kidney / Production host: Homo sapiens (human) / References: UniProt: Q12918
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.32 Å3/Da / Density % sol: 47 %
Description: A hexagonal crystal with dimensions 150, 150, 20 um
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20% (w/v) PEG 3350, 200 mM di-sodium tartrate pH 7.2 PROTEIN CONCENTRATION 20 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: 1.8→43.3 Å / Num. obs: 32555 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 39.5 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 41
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 40.5 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1900 / CC1/2: 0.975 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ff7

3ff7


Resolution: 1.8→43.3 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 1.787 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1580 5 %random
Rwork0.167 ---
obs0.168 32508 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.8→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 172 225 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022327
X-RAY DIFFRACTIONr_bond_other_d0.0020.022125
X-RAY DIFFRACTIONr_angle_refined_deg1.7362.0233186
X-RAY DIFFRACTIONr_angle_other_deg0.97634943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35425.234107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02520
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_it2.832.8961010
X-RAY DIFFRACTIONr_mcbond_other2.7832.8951009
X-RAY DIFFRACTIONr_mcangle_it3.9324.3191262
X-RAY DIFFRACTIONr_mcangle_other3.934.3191263
X-RAY DIFFRACTIONr_scbond_it4.0183.5931317
X-RAY DIFFRACTIONr_scbond_other4.0183.5931317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2755.211919
X-RAY DIFFRACTIONr_long_range_B_refined8.2225.7912791
X-RAY DIFFRACTIONr_long_range_B_other8.19225.3862701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å
RfactorNum. reflection% reflection
Rfree0.257 131 5 %
Rwork0.208 2403 -
obs--100 %

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