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- PDB-8tui: Crystal structure of Fab-Lirilumab bound to KIR2DL3 -

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Basic information

Entry
Database: PDB / ID: 8tui
TitleCrystal structure of Fab-Lirilumab bound to KIR2DL3
Components
  • Killer cell immunoglobulin-like receptor 2DL3
  • Lirilumab Fab Heavy Chain
  • Lirilumab Fab Light chain
KeywordsIMMUNE SYSTEM / antibody / KIR2DL3 / complex / lirilumab
Function / homology
Function and homology information


immune response-regulating signaling pathway / antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / immune response / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Killer cell immunoglobulin-like receptor 2DL3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLorig-Roach, N. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Sci Rep / Year: 2024
Title: Structural basis for the activity and specificity of the immune checkpoint inhibitor lirilumab.
Authors: Lorig-Roach, N. / Harpell, N.M. / DuBois, R.M.
History
DepositionAug 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Oct 23, 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

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Assembly

Deposited unit
H: Lirilumab Fab Heavy Chain
L: Lirilumab Fab Light chain
A: Killer cell immunoglobulin-like receptor 2DL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7914
Polymers79,5313
Non-polymers1,2601
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-14 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.379, 84.270, 62.268
Angle α, β, γ (deg.)90.000, 115.860, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Lirilumab Fab Heavy Chain


Mass: 27793.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Lirilumab Fab Light chain


Mass: 23548.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Killer cell immunoglobulin-like receptor 2DL3 / CD158 antigen-like family member B2 / KIR-023GB / Killer inhibitory receptor cl 2-3 / NKAT2a / ...CD158 antigen-like family member B2 / KIR-023GB / Killer inhibitory receptor cl 2-3 / NKAT2a / NKAT2b / Natural killer-associated transcript 2 / NKAT-2 / p58 natural killer cell receptor clone CL-6 / p58 NK receptor CL-6 / p58.2 MHC class-I-specific NK receptor


Mass: 28189.141 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL3, CD158B2, KIRCL23, NKAT2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P43628
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY
Sequence detailsPartial proteolysis of the receptor (chain A) may have occurred during crystallization. However, ...Partial proteolysis of the receptor (chain A) may have occurred during crystallization. However, the components of the crystal were not sequenced.

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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: 1.68 Å3/Da / Density % sol: 26.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 200 mM Potassium Sodium Tartrate and 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 13977 / % possible obs: 98.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 60.85 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.058 / Rrim(I) all: 0.146 / Net I/σ(I): 14
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.92 / Num. unique obs: 689 / CC1/2: 0.759 / CC star: 0.929 / Χ2: 0.439 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→46.66 Å / SU ML: 0.4626 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254 570 4.2 %
Rwork0.2109 13004 -
obs0.2126 13574 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.5 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 85 5 4176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834272
X-RAY DIFFRACTIONf_angle_d1.13395811
X-RAY DIFFRACTIONf_chiral_restr0.0742671
X-RAY DIFFRACTIONf_plane_restr0.0052733
X-RAY DIFFRACTIONf_dihedral_angle_d16.29751556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-3.030.38191600.30523011X-RAY DIFFRACTION89.32
3.03-3.460.28961540.25143213X-RAY DIFFRACTION95.3
3.46-4.360.2461330.20763332X-RAY DIFFRACTION97.61
4.36-46.660.20571230.17973448X-RAY DIFFRACTION98.97

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