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- PDB-6k7o: Complex structure of LILRB4 and h128-3 antibody -

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Basic information

Entry
Database: PDB / ID: 6k7o
TitleComplex structure of LILRB4 and h128-3 antibody
Components
  • Leukocyte immunoglobulin-like receptor subfamily B member 4
  • h128-3 Fab heavy chain
  • h128-3 Fab light chain
KeywordsIMMUNE SYSTEM / LILRB4 / antibody / Immune therapy.
Function / homology
Function and homology information


transmembrane receptor protein tyrosine kinase inhibitor activity / negative regulation of cytotoxic T cell differentiation / negative regulation of IP-10 production / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / tolerance induction / negative regulation of protein tyrosine kinase activity / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of T cell cytokine production ...transmembrane receptor protein tyrosine kinase inhibitor activity / negative regulation of cytotoxic T cell differentiation / negative regulation of IP-10 production / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / tolerance induction / negative regulation of protein tyrosine kinase activity / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of T cell cytokine production / negative regulation of interleukin-5 production / positive regulation of CD8-positive, alpha-beta T cell differentiation / positive regulation of T cell anergy / negative regulation of monocyte activation / negative regulation of chemokine production / signaling receptor inhibitor activity / positive regulation of regulatory T cell differentiation / negative regulation of protein localization to nucleus / negative regulation of interleukin-2 production / negative regulation of interleukin-1 beta production / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-10 production / negative regulation of MAPK cascade / negative regulation of osteoclast differentiation / negative regulation of activated T cell proliferation / apolipoprotein binding / negative regulation of interleukin-6 production / negative regulation of type II interferon production / fibronectin binding / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / negative regulation of canonical NF-kappaB signal transduction / negative regulation of signaling receptor activity / negative regulation of T cell proliferation / negative regulation of miRNA transcription / cytoplasmic side of plasma membrane / receptor internalization / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein phosphatase binding / adaptive immune response / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte immunoglobulin-like receptor subfamily B member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsSong, H. / Chai, Y. / Xu, X. / Gao, F.G.
CitationJournal: Cancer Immunol Res / Year: 2019
Title: Disrupting LILRB4/APOE Interaction by an Efficacious Humanized Antibody Reverses T-cell Suppression and Blocks AML Development.
Authors: Gui, X. / Deng, M. / Song, H. / Chen, Y. / Xie, J. / Li, Z. / He, L. / Huang, F. / Xu, Y. / Anami, Y. / Yu, H. / Yu, C. / Li, L. / Yuan, Z. / Xu, X. / Wang, Q. / Chai, Y. / Huang, T. / Shi, ...Authors: Gui, X. / Deng, M. / Song, H. / Chen, Y. / Xie, J. / Li, Z. / He, L. / Huang, F. / Xu, Y. / Anami, Y. / Yu, H. / Yu, C. / Li, L. / Yuan, Z. / Xu, X. / Wang, Q. / Chai, Y. / Huang, T. / Shi, Y. / Tsuchikama, K. / Liao, X.C. / Xia, N. / Gao, G.F. / Zhang, N. / Zhang, C.C. / An, Z.
History
DepositionJun 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Leukocyte immunoglobulin-like receptor subfamily B member 4
B: h128-3 Fab heavy chain
C: h128-3 Fab light chain
D: h128-3 Fab heavy chain
E: h128-3 Fab light chain
F: h128-3 Fab heavy chain
G: h128-3 Fab light chain
H: h128-3 Fab heavy chain
L: h128-3 Fab light chain
P: Leukocyte immunoglobulin-like receptor subfamily B member 4
R: Leukocyte immunoglobulin-like receptor subfamily B member 4
Q: Leukocyte immunoglobulin-like receptor subfamily B member 4


Theoretical massNumber of molelcules
Total (without water)235,46212
Polymers235,46212
Non-polymers00
Water0
1
A: Leukocyte immunoglobulin-like receptor subfamily B member 4
H: h128-3 Fab heavy chain
L: h128-3 Fab light chain


Theoretical massNumber of molelcules
Total (without water)58,8653
Polymers58,8653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: h128-3 Fab heavy chain
C: h128-3 Fab light chain
P: Leukocyte immunoglobulin-like receptor subfamily B member 4


Theoretical massNumber of molelcules
Total (without water)58,8653
Polymers58,8653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: h128-3 Fab heavy chain
E: h128-3 Fab light chain
Q: Leukocyte immunoglobulin-like receptor subfamily B member 4


Theoretical massNumber of molelcules
Total (without water)58,8653
Polymers58,8653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: h128-3 Fab heavy chain
G: h128-3 Fab light chain
R: Leukocyte immunoglobulin-like receptor subfamily B member 4


Theoretical massNumber of molelcules
Total (without water)58,8653
Polymers58,8653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.276, 187.276, 183.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
Leukocyte immunoglobulin-like receptor subfamily B member 4 / LILRB4 / CD85 antigen-like family member K / Immunoglobulin-like transcript 3 / ILT-3 / Leukocyte ...LILRB4 / CD85 antigen-like family member K / Immunoglobulin-like transcript 3 / ILT-3 / Leukocyte immunoglobulin-like receptor 5 / LIR-5 / Monocyte inhibitory receptor HM18


Mass: 10898.212 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB4, ILT3, LIR5 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8NHJ6
#2: Antibody
h128-3 Fab heavy chain


Mass: 24208.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody
h128-3 Fab light chain


Mass: 23758.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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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: 3.95 Å3/Da / Density % sol: 68.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium dihydrogen phosphate, 0.1M Tris pH8.5, 50 % v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0401 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0401 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 72345 / % possible obs: 99.7 % / Redundancy: 5.1 % / Net I/σ(I): 15.971
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2.595 / Num. unique obs: 7232

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P2T

3p2t


Resolution: 3.004→44.214 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2699 3459 4.93 %
Rwork0.228 --
obs0.2302 70146 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.004→44.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16436 0 0 0 16436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416875
X-RAY DIFFRACTIONf_angle_d0.6622986
X-RAY DIFFRACTIONf_dihedral_angle_d18.8996142
X-RAY DIFFRACTIONf_chiral_restr0.0452520
X-RAY DIFFRACTIONf_plane_restr0.0052949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0042-3.04540.3724810.2921797X-RAY DIFFRACTION65
3.0454-3.08880.32371260.28332228X-RAY DIFFRACTION81
3.0888-3.13490.3503890.27482459X-RAY DIFFRACTION89
3.1349-3.18390.35931670.27122570X-RAY DIFFRACTION94
3.1839-3.23610.32121550.2792637X-RAY DIFFRACTION96
3.2361-3.29190.32691690.27932638X-RAY DIFFRACTION97
3.2919-3.35170.30441240.27492753X-RAY DIFFRACTION99
3.3517-3.41620.29841370.25772730X-RAY DIFFRACTION99
3.4162-3.48590.33881360.24962653X-RAY DIFFRACTION97
3.4859-3.56160.28581460.24862732X-RAY DIFFRACTION99
3.5616-3.64440.29281530.23592771X-RAY DIFFRACTION100
3.6444-3.73550.28451480.23072726X-RAY DIFFRACTION100
3.7355-3.83650.27671450.23652771X-RAY DIFFRACTION100
3.8365-3.94930.29711380.23582752X-RAY DIFFRACTION100
3.9493-4.07670.28421190.22882802X-RAY DIFFRACTION100
4.0767-4.22230.25081500.21182758X-RAY DIFFRACTION100
4.2223-4.39120.28071570.20052750X-RAY DIFFRACTION100
4.3912-4.59090.23451210.19752787X-RAY DIFFRACTION100
4.5909-4.83260.21931660.19112692X-RAY DIFFRACTION98
4.8326-5.1350.24111110.19812790X-RAY DIFFRACTION100
5.135-5.53080.24351290.20172777X-RAY DIFFRACTION100
5.5308-6.08610.25641420.22392794X-RAY DIFFRACTION100
6.0861-6.96380.27761700.24082744X-RAY DIFFRACTION100
6.9638-8.76240.23911450.22252791X-RAY DIFFRACTION100
8.7624-44.21890.20151350.21932785X-RAY DIFFRACTION98

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