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- PDB-4jo8: Crystal structure of the activating Ly49H receptor in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4jo8
TitleCrystal structure of the activating Ly49H receptor in complex with m157 (G1F strain)
Components
  • Killer cell lectin-like receptor 8
  • M157
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / C-type lectin-like domain / natural killer receptor / viral immunoevasin / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


response to virus / carbohydrate binding / cell adhesion / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin-like - #2530 / Murid herpesvirus 1, M157 / MHC class I-like protein M157 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #30 / Ly49-like, N-terminal / : / Ly49-like protein, N-terminal region / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. ...Immunoglobulin-like - #2530 / Murid herpesvirus 1, M157 / MHC class I-like protein M157 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 - #30 / Ly49-like, N-terminal / : / Ly49-like protein, N-terminal region / 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 / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Killer cell lectin-like receptor 8 / M157
Similarity search - Component
Biological speciesMurid herpesvirus 1 (Murine cytomegalovirus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBerry, R. / Ng, N. / Saunders, P.M. / Vivian, J.P. / Lin, J. / Deuss, F.A. / Corbett, A.J. / Forbes, C.A. / Widjaja, J.M. / Sullivan, L.C. ...Berry, R. / Ng, N. / Saunders, P.M. / Vivian, J.P. / Lin, J. / Deuss, F.A. / Corbett, A.J. / Forbes, C.A. / Widjaja, J.M. / Sullivan, L.C. / McAlister, A.D. / Perugini, M.A. / Call, M.J. / Scalzo, A.A. / Degli-Esposti, M.A. / Coudert, J.D. / Beddoe, T. / Brooks, A.G. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2013
Title: Targeting of a natural killer cell receptor family by a viral immunoevasin
Authors: Berry, R. / Ng, N. / Saunders, P.M. / Vivian, J.P. / Lin, J. / Deuss, F.A. / Corbett, A.J. / Forbes, C.A. / Widjaja, J.M. / Sullivan, L.C. / McAlister, A.D. / Perugini, M.A. / Call, M.J. / ...Authors: Berry, R. / Ng, N. / Saunders, P.M. / Vivian, J.P. / Lin, J. / Deuss, F.A. / Corbett, A.J. / Forbes, C.A. / Widjaja, J.M. / Sullivan, L.C. / McAlister, A.D. / Perugini, M.A. / Call, M.J. / Scalzo, A.A. / Degli-Esposti, M.A. / Coudert, J.D. / Beddoe, T. / Brooks, A.G. / Rossjohn, J.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references / Structure summary
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M157
B: Killer cell lectin-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2993
Polymers49,0782
Non-polymers2211
Water00
1
A: M157
B: Killer cell lectin-like receptor 8
hetero molecules

A: M157
B: Killer cell lectin-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5986
Polymers98,1564
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area14950 Å2
Unit cell
Length a, b, c (Å)87.870, 87.870, 133.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein M157


Mass: 30375.441 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: P29A, D30G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 1 (Murine cytomegalovirus)
Gene: m157 / Plasmid: PHLSEC / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / References: UniProt: Q6XK91
#2: Protein Killer cell lectin-like receptor 8 / Lymphocyte antigen 49h / Ly-49h / T-cell surface glycoprotein Ly-49H


Mass: 18702.496 Da / Num. of mol.: 1 / Fragment: UNP residues 107-266 / Mutation: R107M, P108G, Y110M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klra8, Ly-49h, Ly49-h, Ly49H / Plasmid: PET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60682
#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.: 1
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
Has protein modificationY
Sequence detailsTHE SEQUENCE OF ENTITY2 CORRESPONDS TO THE H2 ISOFORM FOUND IN UNP Q60682.

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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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES 0.5% PEG4000, 10% 2-propanol, 50mM magnesium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 3.2→76.1 Å / Num. obs: 9772 / Biso Wilson estimate: 127.74 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NYK

2nyk


Resolution: 3.2→23.19 Å / Cor.coef. Fo:Fc: 0.9089 / Cor.coef. Fo:Fc free: 0.9014 / SU R Cruickshank DPI: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 468 4.81 %RANDOM
Rwork0.2255 ---
obs0.2272 9733 98.12 %-
Displacement parametersBiso mean: 145.48 Å2
Baniso -1Baniso -2Baniso -3
1--3.6766 Å20 Å20 Å2
2---3.6766 Å20 Å2
3---7.3532 Å2
Refine analyzeLuzzati coordinate error obs: 0.865 Å
Refinement stepCycle: LAST / Resolution: 3.2→23.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 14 0 2077
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092118HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072870HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d996SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it2118HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion3.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion291SEMIHARMONIC5
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_contact2264SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.37 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2696 135 4.85 %
Rwork0.2166 2646 -
all0.2193 2781 -
obs--98.12 %
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)
17.5836-1.07920.56062.48371.02927.0492-0.19731.3539-0.1826-0.2889-0.21150.6742-0.478-1.19150.4088-0.40370.2115-0.17530.054-0.1675-0.432321.947-16.97721.04
24.1845-0.94781.9497-2.04125.78891.56370.1046-0.28040.0640.1019-0.0415-0.1053-0.6384-0.0144-0.0631-0.11990.0066-0.0673-0.00050.0718-0.010542.6656-8.753229.5096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|34 - A|291 }A34 - 291
2X-RAY DIFFRACTION2{ B|109 - B|130 }B109 - 130

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