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- PDB-7odu: Natural killer cell receptor NKR-P1B from Rattus norvegicus in co... -

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Basic information

Entry
Database: PDB / ID: 7odu
TitleNatural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate ligand Clr-11
Components
  • C-type lectin domain family 2 member D11
  • Killer cell lectin-like receptor subfamily B member 1B allele A
KeywordsIMMUNE SYSTEM / RECEPTOR / CTLD FOLD / NATURAL KILLER CELL / PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / natural killer cell lectin-like receptor binding / signaling receptor activity / carbohydrate binding / membrane => GO:0016020 / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / 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
Similarity search - Domain/homology
Killer cell lectin-like receptor subfamily B member 1B allele A / C-type lectin domain family 2 member D11
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSkalova, T. / Blaha, J. / Kalouskova, B. / Skorepa, O. / Vanek, O. / Dohnalek, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation18-10687S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
Citation
Journal: To Be Published
Title: Natural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate ligand Clr-11
Authors: Skalova, T. / Vanek, O. / Kalouskova, B. / Skorepa, O. / Blaha, J. / Harlos, K. / Dohnalek, J.
#1: Journal: Sci.Rep. / Year: 2019
Title: Production of recombinant soluble dimeric C-type lectin-like receptors of rat natural killer cells
Authors: Vanek, O. / Celadova, P. / Skorepa, O. / Blaha, J. / Kalouskova, B. / Dvorska, A. / Polachova, E. / Pucholtova, H. / Kavan, D. / Pompach, P. / Hofbauerova, K. / Kopecky Jr, V. / Mesci, A. / ...Authors: Vanek, O. / Celadova, P. / Skorepa, O. / Blaha, J. / Kalouskova, B. / Dvorska, A. / Polachova, E. / Pucholtova, H. / Kavan, D. / Pompach, P. / Hofbauerova, K. / Kopecky Jr, V. / Mesci, A. / Voigt, S. / Carlyle, J.R.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 D11
B: C-type lectin domain family 2 member D11
C: Killer cell lectin-like receptor subfamily B member 1B allele A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8819
Polymers48,3033
Non-polymers1,5786
Water0
1
A: C-type lectin domain family 2 member D11
C: Killer cell lectin-like receptor subfamily B member 1B allele A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9317
Polymers32,5742
Non-polymers1,3575
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Killer cell lectin-like receptor subfamily B member 1B allele A
hetero molecules

C: Killer cell lectin-like receptor subfamily B member 1B allele A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9816
Polymers33,6892
Non-polymers1,2914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
3
A: C-type lectin domain family 2 member D11
B: C-type lectin domain family 2 member D11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3916
Polymers31,4582
Non-polymers9324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-11 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.593, 111.593, 110.107
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 74 - 194 / Label seq-ID: 1 - 121

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein C-type lectin domain family 2 member D11 / C-type lectin-related protein B / Clr-b / Lectin-like transmembrane protein / Osteoclast inhibitory lectin


Mass: 15729.235 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: strain of rat: WAG / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: strain of rat: WAG / Gene: Clec2d11, Clrb, Ocil / Plasmid: pTW5sec / Details (production host): pTW5sec_C2 / Cell line (production host): HEK293S GnTI- / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): HUMAN EMBRYONIC KIDNEY / References: UniProt: Q0H8B9
#2: Protein Killer cell lectin-like receptor subfamily B member 1B allele A / CD161 antigen-like family member B / Natural killer cell surface protein NKR-P1B allele RNK/SD/BN/F344


Mass: 16844.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: NATURAL KILLER CELLS / Gene: Klrb1b, Nkrp1b / Plasmid: pYD5 / Details (production host): pYD5_S1 / Cell line (production host): HEK293S GnTI- / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): HUMAN EMBRYONIC KIDNEY / References: UniProt: A4KWA1
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
14.5873merged data from two crystals from the same crystallization condition
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 200 mM NaCl, 100 mM sodium acetate, 20 mM ZnCl2, 20% PEG 6000, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→49.77 Å / Num. obs: 16302 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.131 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.188.71.6771.326030.7370.6021.783100
9-49.777.50.04834.26770.9990.0190.05299.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FF8

3ff8


Resolution: 3→49.77 Å / Cor.coef. Fo:Fc: 0.945 / SU B: 16.169 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES WERE REFINED INDIVIDUALLY; ALL REFLECTIONS WERE USED IN THE LAST REFINEMENT CYCLE
RfactorNum. reflection% reflectionSelection details
Rfree0.25943 861 5.3 %random
Rwork0.2081 ---
obs0.2081 16275 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 234.05 Å2 / Biso mean: 107.312 Å2 / Biso min: 70.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å21.41 Å20 Å2
2--2.83 Å2-0 Å2
3----9.17 Å2
Refinement stepCycle: final / Resolution: 3→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 99 0 3154
Biso mean--150.73 --
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133255
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182800
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6814423
X-RAY DIFFRACTIONr_angle_other_deg1.2351.6276463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0985369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48721.915188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.43115509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6271521
X-RAY DIFFRACTIONr_chiral_restr0.0650.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02840
Refine LS restraints NCS

Ens-ID: 1 / Number: 3880 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.39 1191 -
obs--99.92 %

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