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- PDB-5tzn: Structure of the viral immunoevasin m12 (Smith) bound to the natu... -

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Basic information

Entry
Database: PDB / ID: 5tzn
TitleStructure of the viral immunoevasin m12 (Smith) bound to the natural killer cell receptor NKR-P1B (B6)
Components
  • Glycoprotein family protein m12
  • Killer cell lectin-like receptor subfamily B member 1B allele B
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / C-type lectin-like domain / immonoglobulin like domain / CELL INVASION / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / signaling receptor activity / carbohydrate binding / membrane => GO:0016020 / external side of plasma membrane / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Immune evasion protein / Immune evasion protein / 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 ...Immune evasion protein / Immune evasion protein / 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
IODIDE ION / Glycoprotein family protein m12 / Killer cell lectin-like receptor subfamily B member 1B allele B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Murid herpesvirus 1 (Murine cytomegalovirus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBerry, R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Cell / Year: 2017
Title: A Viral Immunoevasin Controls Innate Immunity by Targeting the Prototypical Natural Killer Cell Receptor Family.
Authors: Aguilar, O.A. / Berry, R. / Rahim, M.M. / Reichel, J.J. / Popovic, B. / Tanaka, M. / Fu, Z. / Balaji, G.R. / Lau, T.N. / Tu, M.M. / Kirkham, C.L. / Mahmoud, A.B. / Mesci, A. / Krmpotic, A. / ...Authors: Aguilar, O.A. / Berry, R. / Rahim, M.M. / Reichel, J.J. / Popovic, B. / Tanaka, M. / Fu, Z. / Balaji, G.R. / Lau, T.N. / Tu, M.M. / Kirkham, C.L. / Mahmoud, A.B. / Mesci, A. / Krmpotic, A. / Allan, D.S. / Makrigiannis, A.P. / Jonjic, S. / Rossjohn, J. / Carlyle, J.R.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Killer cell lectin-like receptor subfamily B member 1B allele B
F: Glycoprotein family protein m12
G: Glycoprotein family protein m12
W: Killer cell lectin-like receptor subfamily B member 1B allele B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,91112
Polymers73,6974
Non-polymers3,2148
Water61334
1
A: Killer cell lectin-like receptor subfamily B member 1B allele B
F: Glycoprotein family protein m12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1926
Polymers36,8492
Non-polymers1,3434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Glycoprotein family protein m12
W: Killer cell lectin-like receptor subfamily B member 1B allele B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7196
Polymers36,8492
Non-polymers1,8714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.276, 61.912, 66.159
Angle α, β, γ (deg.)90.00, 101.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules AWFG

#1: 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.: 2 / Fragment: UNP residues 89-2215 / Mutation: C118G
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
#2: Protein Glycoprotein family protein m12


Mass: 21217.166 Da / Num. of mol.: 2 / Fragment: UNP residues 61-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 1 (Murine cytomegalovirus)
Gene: m12 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: D3XDJ6

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Sugars , 4 types, 6 molecules

#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b3-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 36 molecules

#7: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 41 % PEG400 0.1M Bis/Tris ph 6.3 0.4M sodium iodide

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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: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.6→44.8 Å / Num. obs: 19331 / Biso Wilson estimate: 54.46 Å2 / Rmerge(I) obs: 0.165
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2863 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M9Z, 4PN6

3m9z

4pn6


Resolution: 2.6→44.8 Å / Cor.coef. Fo:Fc: 0.9059 / Cor.coef. Fo:Fc free: 0.8618 / SU R Cruickshank DPI: 0.702 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.633 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.252 982 5.08 %RANDOM
Rwork0.2045 ---
obs0.207 19331 94.98 %-
Displacement parametersBiso mean: 40.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.656 Å20 Å20.2636 Å2
2---0.1424 Å20 Å2
3---2.7984 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: 1 / Resolution: 2.6→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 197 34 4211
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135871HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1948SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes614HARMONIC5
X-RAY DIFFRACTIONt_it4293HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion2.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion646SEMIHARMONIC5
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_contact4576SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.74 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 150 5.37 %
Rwork0.2173 2641 -
all0.2193 2791 -
obs--94.98 %
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)
10.5846-0.4304-0.61621.26260.2692.263-0.0708-0.4442-0.10780.35680.02090.0008-0.2515-0.04840.0499-0.05710.0342-0.06930.0226-0.0205-0.0905-27.52543.319478.6743
21.8083-0.45610.09292.97430.13241.1090.00970.02520.1420.03010.0235-0.0358-0.2335-0.107-0.0333-0.13540.0149-0.007-0.07250.0293-0.0643-36.402442.927656.0472
30.890.922-0.25772.50040.53660.71210.1633-0.049-0.25280.1647-0.0639-0.2720.22810.0854-0.0994-0.10990.0187-0.0655-0.09250.04090.0044-35.124110.652456.3403
42.68121.28420.4422.74850.21383.91430.02540.3795-0.0602-0.32240.01690.2143-0.03910.025-0.0423-0.11840.02480.0328-0.0956-0.0597-0.0292-34.647511.848732.2939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ F|* }
3X-RAY DIFFRACTION3{ G|* }
4X-RAY DIFFRACTION4{ W|* }

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