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- PDB-6e7d: Structure of the inhibitory NKR-P1B receptor bound to the host-en... -

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Basic information

Entry
Database: PDB / ID: 6e7d
TitleStructure of the inhibitory NKR-P1B receptor bound to the host-encoded ligand, Clr-b
Components
  • C-type lectin domain family 2 member D
  • Killer cell lectin-like receptor subfamily B member 1B allele B
KeywordsIMMUNE SYSTEM / Natural Killer cell receptor / C-type lectin related ligand / immune complex / innate immunity
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of osteoclast differentiation / plasma membrane => GO:0005886 / cellular defense response / protection from natural killer cell mediated cytotoxicity / transmembrane signaling receptor activity / signaling receptor activity / carbohydrate binding ...regulation of natural killer cell mediated cytotoxicity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of osteoclast differentiation / plasma membrane => GO:0005886 / cellular defense response / protection from natural killer cell mediated cytotoxicity / transmembrane signaling receptor activity / signaling receptor activity / carbohydrate binding / external side of plasma membrane / cell surface / identical protein binding / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
C-type lectin domain family 2 member D / Killer cell lectin-like receptor subfamily B member 1B allele B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBalaji, G.R. / Rossjohn, J. / Berry, R.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1109901 Australia
Australian Research Council (ARC)FL160100049 Australia
CitationJournal: Nat Commun / Year: 2018
Title: Recognition of host Clr-b by the inhibitory NKR-P1B receptor provides a basis for missing-self recognition.
Authors: Balaji, G.R. / Aguilar, O.A. / Tanaka, M. / Shingu-Vazquez, M.A. / Fu, Z. / Gully, B.S. / Lanier, L.L. / Carlyle, J.R. / Rossjohn, J. / Berry, R.
History
DepositionJul 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 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 1.4Oct 11, 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

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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
C: C-type lectin domain family 2 member D
D: C-type lectin domain family 2 member D
E: C-type lectin domain family 2 member D
F: C-type lectin domain family 2 member D
G: C-type lectin domain family 2 member D
H: C-type lectin domain family 2 member D
I: C-type lectin domain family 2 member D
J: C-type lectin domain family 2 member D
K: C-type lectin domain family 2 member D
L: C-type lectin domain family 2 member D
M: C-type lectin domain family 2 member D
N: C-type lectin domain family 2 member D
O: C-type lectin domain family 2 member D
P: C-type lectin domain family 2 member D
Q: Killer cell lectin-like receptor subfamily B member 1B allele B
R: Killer cell lectin-like receptor subfamily B member 1B allele B
S: Killer cell lectin-like receptor subfamily B member 1B allele B
T: Killer cell lectin-like receptor subfamily B member 1B allele B
U: Killer cell lectin-like receptor subfamily B member 1B allele B
V: Killer cell lectin-like receptor subfamily B member 1B allele B
W: Killer cell lectin-like receptor subfamily B member 1B allele B
X: Killer cell lectin-like receptor subfamily B member 1B allele B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,90141
Polymers361,26724
Non-polymers2,63417
Water1448
1
A: C-type lectin domain family 2 member D
D: C-type lectin domain family 2 member D
E: C-type lectin domain family 2 member D
F: C-type lectin domain family 2 member D
I: C-type lectin domain family 2 member D
J: C-type lectin domain family 2 member D
O: C-type lectin domain family 2 member D
P: C-type lectin domain family 2 member D
Q: Killer cell lectin-like receptor subfamily B member 1B allele B
S: Killer cell lectin-like receptor subfamily B member 1B allele B
U: Killer cell lectin-like receptor subfamily B member 1B allele B
X: Killer cell lectin-like receptor subfamily B member 1B allele B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,99821
Polymers180,63312
Non-polymers1,3659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25540 Å2
ΔGint-133 kcal/mol
Surface area60920 Å2
MethodPISA
2
B: C-type lectin domain family 2 member D
C: C-type lectin domain family 2 member D
G: C-type lectin domain family 2 member D
H: C-type lectin domain family 2 member D
K: C-type lectin domain family 2 member D
L: C-type lectin domain family 2 member D
M: C-type lectin domain family 2 member D
N: C-type lectin domain family 2 member D
R: Killer cell lectin-like receptor subfamily B member 1B allele B
T: Killer cell lectin-like receptor subfamily B member 1B allele B
V: Killer cell lectin-like receptor subfamily B member 1B allele B
W: Killer cell lectin-like receptor subfamily B member 1B allele B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,90220
Polymers180,63312
Non-polymers1,2698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24810 Å2
ΔGint-120 kcal/mol
Surface area61460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.930, 122.069, 131.561
Angle α, β, γ (deg.)73.12, 82.08, 84.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
C-type lectin domain family 2 member D / C-type lectin-related protein B / Clr-b / Lectin-like transmembrane protein / Osteoclast inhibitory lectin


Mass: 14763.428 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clec2d, Clrb, Ocil / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91V08
#2: Protein
Killer cell lectin-like receptor subfamily B member 1B allele B / CD161 antigen-like family member B / Inhibitory receptor NKR-P1B / Lymphocyte antigen 55d / Ly-55d ...CD161 antigen-like family member B / Inhibitory receptor NKR-P1B / Lymphocyte antigen 55d / Ly-55d / NKR-P1D / Natural killer cell surface protein NKR-P1B allele B6


Mass: 15631.460 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klrb1b, Klrb1d, Ly55d, Nkrp1b, Nkrp1d / Production host: Homo sapiens (human) / References: UniProt: Q99JB4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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 / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21 % (w/v) PEG 3350 0.1 M Bis/Tris pH 5.9 5 % glycerol (v/v) 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.9→66.1 Å / Num. obs: 80841 / % possible obs: 92.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 57.84 Å2 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.114 / Net I/σ(I): 6.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12101 / Rpim(I) all: 0.363 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RS1, 5TZN

3rs1

5tzn


Resolution: 2.9→42.46 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.845 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4053 5.02 %RANDOM
Rwork0.186 ---
obs0.188 80766 92.6 %-
Displacement parametersBiso mean: 53.01 Å2
Baniso -1Baniso -2Baniso -3
1--12.8822 Å2-0.6042 Å20.9312 Å2
2--6.9982 Å2-1.0471 Å2
3---5.8839 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.9→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22828 0 157 8 22993
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123696HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1332291HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10414SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes605HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3463HARMONIC5
X-RAY DIFFRACTIONt_it23696HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion3.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3082SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25604SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 269 4.58 %
Rwork0.214 5605 -
all0.217 5874 -
obs--91.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.94140.0573-0.42353.2914-0.34852.3813-0.04880.0756-0.0245-0.2259-0.02260.64120.7045-0.49590.07150.1211-0.175-0.0272-0.1116-0.0551-0.1768-12.3183-5.642-1.9367
21.59221.41540.85424.13730.02724.8656-0.24460.2733-0.0917-0.23730.1827-0.7086-0.25040.98880.0619-0.0861-0.2050.0318-0.0078-0.0833-0.136824.366126.336568.9707
3-0.0565-0.17610.0983.173-1.6113.8082-0.13110.14570.0168-0.5850.32120.43010.7911-0.5525-0.19010.3017-0.3367-0.1703-0.1558-0.0031-0.27650.90315.061657.5279
41.4192-1.8885-0.36153.8154-0.18112.36230.0893-0.04030.1593-0.5804-0.1783-0.2839-0.23590.23550.0890.1348-0.09080.1356-0.1331-0.0703-0.1890.7311-38.21943.7426
54.20311.5781.5964.82381.37723.27210.08730.4324-0.006-0.2751-0.2524-0.7902-0.0760.69320.1652-0.1584-0.02250.10510.03790.0781-0.163613.71533.80834.9933
63.85890.5242-2.04393.2309-2.00859.81580.11320.0337-0.16810.14330.05040.52070.2095-1.1821-0.1636-0.3455-0.08480.07550.0664-0.1086-0.0381-17.128-42.452425.9323
71.1099-1.33760.12862.8763-0.04742.0867-0.01480.19890.1795-0.632-0.0282-0.2545-0.41710.42130.0430.0564-0.18540.1723-0.0491-0.0467-0.144214.713-16.84666.0929
85.3266-1.7803-2.00324.9995-0.50585.1565-0.21930.3357-0.77670.0012-0.06331.01350.2167-0.69220.2826-0.3498-0.1080.069-0.0666-0.1755-0.016-7.1638-21.417684.1813
90.17651.086-0.66153.0597-0.20935.1270.15090.20410.1350.57290.0010.3364-0.6979-0.1545-0.15190.086-0.01630.1443-0.099-0.0447-0.1475-4.9692-26.116245.7273
102.67270.687-0.79055.88811.97065.60820.0125-0.2639-0.2547-0.24970.0819-0.47340.4771.1055-0.0944-0.4349-0.01210.07290.258-0.0651-0.038212.8555-41.720129.2863
112.01350.8511-0.25932.3364-0.06054.0765-0.14310.10270.33230.34110.11080.47-0.5539-0.29450.03230.116200.098-0.1447-0.0151-0.1189-0.7425-5.0265106.3625
123.76110.9019-1.53473.96850.54854.0689-0.2534-0.5103-0.6504-0.02940.1159-0.58490.06891.04630.1375-0.3725-0.07320.110.0844-0.007-0.136721.2083-19.686393.4217
131.67631.86991.02434.43490.10064.713-0.0198-0.0481-0.10910.6404-0.0672-0.49450.33710.13640.0870.2223-0.0986-0.1063-0.2096-0.0599-0.244818.27124.788296.6958
142.3664-0.59041.17033.7689-0.48966.0808-0.1379-0.10120.2996-0.07640.18490.9197-0.6564-0.8702-0.047-0.1019-0.0116-0.0226-0.1091-0.0089-0.084-3.243233.219479.0198
151.51811.58050.19061.66990.52453.64680.052-0.151-0.3920.5348-0.2484-0.58520.22160.56630.19640.2127-0.2543-0.1265-0.15710.054-0.254612.95782.316333.3709
162.67860.36950.4672.1423-2.05135.10220.1523-0.24610.33870.42010.0070.3399-0.388-0.327-0.15930.0095-0.11250.1334-0.1131-0.1025-0.1119-11.10811.944120.1643
170.06681.2142-0.59767.2648-1.21512.89950.19360.31430.1155-0.6902-0.1090.091-0.1775-0.5276-0.0846-0.01220.0877-0.062-0.1029-0.0064-0.0406-20.220318.7874-12.9625
185.0075-0.78522.21977.3352-1.18934.10180.08620.26330.428-0.4711-0.03170.3836-0.3651-0.1999-0.05440.1488-0.2481-0.2965-0.19280.1357-0.2426-5.092937.489844.0357
192.2270.06160.09267.1986-3.00355.15530.28260.2192-0.5637-0.50340.21560.20270.8928-0.0434-0.49820.0560.01620.081-0.2079-0.0901-0.14159.3786-64.73222.0313
203.2752.407-2.41997.2667-4.1897.31590.06620.3546-0.3981-0.64090.29370.16030.3926-0.259-0.3599-0.23360.01560.1812-0.0741-0.0885-0.012323.1818-43.001466.5503
214.07070.4308-1.49099.40611.52248.09880.2643-0.5798-0.51590.958-0.0885-0.02690.7881-0.1078-0.1758-0.036-0.15080.1578-0.12060.0431-0.2876-12.7712-46.360160.9308
223.2178-1.32890.19646.87480.79851.8154-0.1084-0.5088-0.46580.61760.0375-0.29880.3348-0.00970.0709-0.09680.01620.2093-0.0590.0484-0.0571-9.1567-27.2184119.3105
231.98121.0318-0.30027.2291-3.80174.71980.1332-0.00230.44020.47610.3735-0.4739-0.88530.3413-0.5066-0.0837-0.1804-0.0935-0.1925-0.14910.005131.218849.20595.303
241.2851.1355-0.72347.8462-2.48477.4829-0.0508-0.24110.48810.5626-0.1268-0.572-1.26110.53680.1776-0.1095-0.3736-0.2076-0.08610.1306-0.131725.561425.504530.1419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ M|* }
14X-RAY DIFFRACTION14{ N|* }
15X-RAY DIFFRACTION15{ O|* }
16X-RAY DIFFRACTION16{ P|* }
17X-RAY DIFFRACTION17{ Q|* }
18X-RAY DIFFRACTION18{ R|* }
19X-RAY DIFFRACTION19{ S|* }
20X-RAY DIFFRACTION20{ T|* }
21X-RAY DIFFRACTION21{ U|* }
22X-RAY DIFFRACTION22{ V|* }
23X-RAY DIFFRACTION23{ W|* }
24X-RAY DIFFRACTION24{ X|* }

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