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- PDB-6bcs: LilrB2 D1D2 domains complexed with benzamidine -

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Basic information

Entry
Database: PDB / ID: 6bcs
TitleLilrB2 D1D2 domains complexed with benzamidine
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 2
KeywordsIMMUNE SYSTEM / receptor / IG LIKE DOMAINS
Function / homology
Function and homology information


negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway ...negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / positive regulation of long-term synaptic depression / positive regulation of T cell tolerance induction / protein phosphatase 1 binding / positive regulation of regulatory T cell differentiation / regulation of dendritic cell differentiation / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / negative regulation of protein metabolic process / MHC class I protein binding / tertiary granule membrane / negative regulation of calcium ion transport / ficolin-1-rich granule membrane / cellular defense response / positive regulation of T cell proliferation / negative regulation of T cell proliferation / positive regulation of protein dephosphorylation / cell adhesion molecule binding / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / amyloid-beta binding / adaptive immune response / cellular response to lipopolysaccharide / membrane => GO:0016020 / learning or memory / cell surface receptor signaling pathway / immune response / Neutrophil degranulation / protein-containing complex binding / cell surface / signal transduction / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / Leukocyte immunoglobulin-like receptor subfamily B member 2 / Leukocyte immunoglobulin-like receptor subfamily B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCao, Q. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)NIH AG054022 United States
CitationJournal: Nat Chem / Year: 2018
Title: Inhibiting amyloid-beta cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design.
Authors: Cao, Q. / Shin, W.S. / Chan, H. / Vuong, C.K. / Dubois, B. / Li, B. / Murray, K.A. / Sawaya, M.R. / Feigon, J. / Black, D.L. / Eisenberg, D.S. / Jiang, L.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Dec 5, 2018Group: 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_author.identifier_ORCID
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7749
Polymers22,0661
Non-polymers7088
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.050, 57.050, 101.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-207-

DMS

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2


Mass: 22065.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0G2JNQ7, UniProt: Q8N423*PLUS
#2: Chemical
ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.53
Details: 1.03 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.53, 2.76% PEG 3350, 1.4% w/v benzamidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.695 Å / Num. obs: 10310 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.269 % / Biso Wilson estimate: 34.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.093 / Χ2: 0.896 / Net I/σ(I): 17.98 / Num. measured all: 126498 / Scaling rejects: 55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.1512.0340.7373.97450.9090.76999.9
2.15-2.2111.340.5744.627180.9330.602100
2.21-2.2813.1270.4326.417160.9670.449100
2.28-2.3513.2250.3936.976790.9610.408100
2.35-2.4213.0510.3348.166610.9810.348100
2.42-2.5112.9380.2719.556470.9810.282100
2.51-2.612.7820.23310.726330.9910.242100
2.6-2.7112.4190.18612.835990.9920.194100
2.71-2.8311.3460.15214.435750.9930.1699.8
2.83-2.9712.8570.12218.325580.9960.127100
2.97-3.1313.1840.09422.65280.9970.09899.8
3.13-3.3212.9750.0728.295120.9990.073100
3.32-3.5512.7760.06830.764690.9990.0799.8
3.55-3.8311.8240.06133.844500.9990.063100
3.83-4.210.3940.05833.554160.9970.061100
4.2-4.712.0770.05441.23790.9980.05699.7
4.7-5.4211.470.05140.073450.9990.053100
5.42-6.6410.9860.053382910.9970.055100
6.64-9.399.6650.05436.212390.9970.05798.4
9.39-49.69510.0270.04540.221500.9990.047100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.69 Å50.58 Å
Translation1.69 Å50.58 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.6.1phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GW5

2gw5


Resolution: 2.1→49.695 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.35
RfactorNum. reflection% reflection
Rfree0.2328 1031 10 %
Rwork0.1821 --
obs0.1872 10309 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.14 Å2 / Biso mean: 37.5477 Å2 / Biso min: 17.34 Å2
Refinement stepCycle: final / Resolution: 2.1→49.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 46 62 1579
Biso mean--44.93 38.36 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081581
X-RAY DIFFRACTIONf_angle_d1.0232171
X-RAY DIFFRACTIONf_chiral_restr0.06234
X-RAY DIFFRACTIONf_plane_restr0.006280
X-RAY DIFFRACTIONf_dihedral_angle_d18.187934
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0999-2.21060.31921420.223712861428
2.2106-2.34910.27111440.20412961440
2.3491-2.53050.31731440.211112951439
2.5305-2.78510.25821450.195713031448
2.7851-3.18810.26281480.202813261474
3.1881-4.01640.21291480.167813371485
4.0164-49.70870.19181600.163614351595
Refinement TLS params.Method: refined / Origin x: -24.2388 Å / Origin y: 10.7851 Å / Origin z: -2.4184 Å
111213212223313233
T0.2051 Å2-0.001 Å20.0182 Å2-0.2274 Å2-0.0033 Å2--0.233 Å2
L0.3594 °20.2321 °20.226 °2-0.4338 °20.0394 °2--0.4631 °2
S0.051 Å °-0.0169 Å °-0.0383 Å °-0.0355 Å °-0.0164 Å °-0.0731 Å °0.024 Å °0.0319 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 198
2X-RAY DIFFRACTION1allB1 - 4
3X-RAY DIFFRACTION1allC1 - 105
4X-RAY DIFFRACTION1allE2 - 3
5X-RAY DIFFRACTION1allF1 - 2

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