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- PDB-7kfk: Crystal structure of LILRB1 D3D4 domain in complex with Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 7kfk
TitleCrystal structure of LILRB1 D3D4 domain in complex with Plasmodium RIFIN (PF3D7_1373400) V2 domain
Components
  • Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Rifin
KeywordsIMMUNE SYSTEM / LILRB1 / RIFIN / Malaria
Function / homology
Function and homology information


HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation / MHC class Ib receptor activity ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / negative regulation of serotonin secretion / dendritic cell differentiation / protein phosphatase 1 binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of interferon-beta production / negative regulation of endocytosis / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / T cell proliferation involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-10 production / negative regulation of calcium ion transport / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cell cycle / regulation of immune response / MHC class I protein binding / positive regulation of defense response to virus by host / negative regulation of T cell proliferation / SH2 domain binding / response to virus / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / defense response to virus / cellular response to lipopolysaccharide / adaptive immune response / membrane => GO:0016020 / positive regulation of apoptotic process / external side of plasma membrane / positive regulation of gene expression / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Variant surface antigen Rifin / Rifin / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Variant surface antigen Rifin / Rifin / 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-like fold
Similarity search - Domain/homology
Rifin / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsXu, K. / Kwong, P.D.
CitationJournal: Nature / Year: 2021
Title: Structural basis of malaria RIFIN binding by LILRB1-containing antibodies.
Authors: Yiwei Chen / Kai Xu / Luca Piccoli / Mathilde Foglierini / Joshua Tan / Wenjie Jin / Jason Gorman / Yaroslav Tsybovsky / Baoshan Zhang / Boubacar Traore / Chiara Silacci-Fregni / Claudia ...Authors: Yiwei Chen / Kai Xu / Luca Piccoli / Mathilde Foglierini / Joshua Tan / Wenjie Jin / Jason Gorman / Yaroslav Tsybovsky / Baoshan Zhang / Boubacar Traore / Chiara Silacci-Fregni / Claudia Daubenberger / Peter D Crompton / Roger Geiger / Federica Sallusto / Peter D Kwong / Antonio Lanzavecchia /
Abstract: Some Plasmodium falciparum repetitive interspersed families of polypeptides (RIFINs)-variant surface antigens that are expressed on infected erythrocytes-bind to the inhibitory receptor LAIR1, and ...Some Plasmodium falciparum repetitive interspersed families of polypeptides (RIFINs)-variant surface antigens that are expressed on infected erythrocytes-bind to the inhibitory receptor LAIR1, and insertion of DNA that encodes LAIR1 into immunoglobulin genes generates RIFIN-specific antibodies. Here we address the general relevance of this finding by searching for antibodies that incorporate LILRB1, another inhibitory receptor that binds to β2 microglobulin and RIFINs through their apical domains. By screening plasma from a cohort of donors from Mali, we identified individuals with LILRB1-containing antibodies. B cell clones isolated from three donors showed large DNA insertions in the switch region that encodes non-apical LILRB1 extracellular domain 3 and 4 (D3D4) or D3 alone in the variable-constant (VH-CH1) elbow. Through mass spectrometry and binding assays, we identified a large set of RIFINs that bind to LILRB1 D3. Crystal and cryo-electron microscopy structures of a RIFIN in complex with either LILRB1 D3D4 or a D3D4-containing antibody Fab revealed a mode of RIFIN-LILRB1 D3 interaction that is similar to that of RIFIN-LAIR1. The Fab showed an unconventional triangular architecture with the inserted LILRB1 domains opening up the VH-CH1 elbow without affecting VH-VL or CH1-CL pairing. Collectively, these findings show that RIFINs bind to LILRB1 through D3 and illustrate, with a naturally selected example, the general principle of creating novel antibodies by inserting receptor domains into the VH-CH1 elbow.
History
DepositionOct 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1
B: Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1
E: Rifin
C: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,37117
Polymers81,3714
Non-polymers2,00013
Water99155
1
A: Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1
E: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4456
Polymers40,6862
Non-polymers7604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-20 kcal/mol
Surface area17450 Å2
MethodPISA
2
B: Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1
C: Rifin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,92611
Polymers40,6862
Non-polymers1,2409
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-46 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.044, 111.044, 152.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 222 through 275 or resid 277...
21(chain B and (resid 222 through 275 or resid 277...
12(chain C and (resid 184 or resid 186 through 187...
22(chain E and (resid 184 or resid 186 through 187...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 222 through 275 or resid 277...A222 - 275
121(chain A and (resid 222 through 275 or resid 277...A277 - 363
131(chain A and (resid 222 through 275 or resid 277...A365 - 369
141(chain A and (resid 222 through 275 or resid 277...A371 - 401
151(chain A and (resid 222 through 275 or resid 277...A403
161(chain A and (resid 222 through 275 or resid 277...A405 - 427
171(chain A and (resid 222 through 275 or resid 277...A1200
211(chain B and (resid 222 through 275 or resid 277...B222 - 275
221(chain B and (resid 222 through 275 or resid 277...B277 - 363
231(chain B and (resid 222 through 275 or resid 277...B222 - 1201
241(chain B and (resid 222 through 275 or resid 277...B371 - 401
251(chain B and (resid 222 through 275 or resid 277...B403
261(chain B and (resid 222 through 275 or resid 277...B405 - 427
271(chain B and (resid 222 through 275 or resid 277...B1200
112(chain C and (resid 184 or resid 186 through 187...C184
122(chain C and (resid 184 or resid 186 through 187...C186 - 187
132(chain C and (resid 184 or resid 186 through 187...C189 - 218
142(chain C and (resid 184 or resid 186 through 187...C270 - 303
152(chain C and (resid 184 or resid 186 through 187...C270 - 303
162(chain C and (resid 184 or resid 186 through 187...C306 - 307
212(chain E and (resid 184 or resid 186 through 187...E184
222(chain E and (resid 184 or resid 186 through 187...E186 - 187
232(chain E and (resid 184 or resid 186 through 187...E189 - 218
242(chain E and (resid 184 or resid 186 through 187...E270 - 303
252(chain E and (resid 184 or resid 186 through 187...E270 - 303
262(chain E and (resid 184 or resid 186 through 187...E306 - 307

NCS ensembles :
ID
1
2

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Components

#1: Protein Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1 / Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / Immunoglobulin-like ...Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / Immunoglobulin-like transcript 2 / ILT-2 / Monocyte/macrophage immunoglobulin-like receptor 7 / MIR-7


Mass: 25264.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1, ILT2, LIR1, MIR7 / Production host: Homo sapiens (human) / References: UniProt: Q8NHL6-2
#2: Protein Rifin


Mass: 15420.644 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1373400 / Production host: Homo sapiens (human) / References: UniProt: C0H5N9
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / 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
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris 8.3, 11% PEG3350, 1.1mM AmSO4, 0.2mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 28673 / % possible obs: 99.8 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.045 / Rrim(I) all: 0.207 / Χ2: 1.492 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.716.91.30614100.8960.3221.3460.44999.9
2.7-2.7418.81.29314080.9560.3031.3290.45100
2.74-2.8201.20214000.9210.2741.2340.458100
2.8-2.8520.60.99814130.9550.2241.0230.506100
2.85-2.9219.80.83814070.9580.1920.860.557100
2.92-2.9819.40.74514170.9620.1710.7650.577100
2.98-3.0623.80.66813970.9780.140.6830.618100
3.06-3.14250.59514140.9840.1220.6080.661100
3.14-3.2325.40.4714220.9880.0950.480.784100
3.23-3.34250.38314140.9840.0790.3910.939100
3.34-3.4624.80.34314260.9920.070.351.102100
3.46-3.624.40.28114340.9930.0580.2871.325100
3.6-3.7623.70.23814360.9960.050.2431.644100
3.76-3.9622.40.20114250.9950.0440.2061.97799.9
3.96-4.2120.10.16614310.9970.0390.172.491100
4.21-4.5318.10.13614480.9960.0340.1412.95899.9
4.53-4.9921.10.11414590.9980.0270.1183.12299.9
4.99-5.7121.20.11114600.9980.0260.1143.10699.9
5.71-7.1920.50.10115010.9980.0240.1043.02199.9
7.19-5014.50.0715510.9980.0190.0733.79396.2

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LLA

4lla


Resolution: 2.63→37.44 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 1415 4.94 %
Rwork0.2269 27200 -
obs0.2291 28615 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.02 Å2 / Biso mean: 64.2505 Å2 / Biso min: 27.79 Å2
Refinement stepCycle: final / Resolution: 2.63→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 119 55 5151
Biso mean--103.85 55.15 -
Num. residues----671
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1196X-RAY DIFFRACTION9.555TORSIONAL
12B1196X-RAY DIFFRACTION9.555TORSIONAL
21C660X-RAY DIFFRACTION9.555TORSIONAL
22E660X-RAY DIFFRACTION9.555TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.63-2.730.44251250.3838253894
2.73-2.840.39241400.32552677100
2.84-2.970.37061440.28882686100
2.97-3.120.36961410.28952698100
3.12-3.320.33551480.28012712100
3.32-3.570.35871280.26642728100
3.57-3.930.27141470.21822732100
3.93-4.50.22981360.18852763100
4.5-5.670.22241620.17982758100
5.67-100.20891440.2015290898

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