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- PDB-6zdx: RIFIN variable region bound to LILRB1 ectodomain -

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Basic information

Entry
Database: PDB / ID: 6zdx
TitleRIFIN variable region bound to LILRB1 ectodomain
Components
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Rifin
KeywordsIMMUNE SYSTEM / RIFIN / LILRB1 / inhibitory immune receptor / malaria / infected-erythrocyte / Plasmodium falciparum
Function / homology
Function and homology information


antigenic variation / 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 / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding ...antigenic variation / 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 / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / 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 / negative regulation of natural killer cell mediated cytotoxicity / dendritic cell differentiation / negative regulation of mononuclear cell proliferation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / negative regulation of interleukin-10 production / MHC class I protein binding / 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 / T cell proliferation involved in immune response / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / SH2 domain binding / response to virus / receptor internalization / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / cellular response to lipopolysaccharide / defense response to virus / adaptive immune response / membrane => GO:0016020 / positive regulation of apoptotic process / external side of plasma membrane / positive regulation of gene expression / host cell plasma membrane / 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
Leukocyte immunoglobulin-like receptor subfamily B member 1 / Rifin / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHarrison, T.E. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust101020/Z/13/Z
CitationJournal: Nature / Year: 2020
Title: Structural basis for RIFIN-mediated activation of LILRB1 in malaria.
Authors: Harrison, T.E. / Morch, A.M. / Felce, J.H. / Sakoguchi, A. / Reid, A.J. / Arase, H. / Dustin, M.L. / Higgins, M.K.
History
DepositionJun 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 25, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 24, 2024Group: 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: Rifin
B: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8695
Polymers62,0022
Non-polymers8673
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint4 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.507, 134.507, 277.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Rifin


Mass: 14174.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1254800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I4N9
#2: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1


Mass: 47827.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Production host: Homo sapiens (human) / References: UniProt: A0A0G2JQ46, UniProt: Q8NHL6*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 2
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 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: 5.84 Å3/Da / Density % sol: 78.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium acetate, 100 mM HEPES pH 7.5, 25 % v/v isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3→277.47 Å / Num. obs: 30613 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.99 / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.16 Å / Num. unique obs: 4346 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EWA, 4LL9

6ewa

4ll9


Resolution: 3→89.21 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.358 / SU Rfree Blow DPI: 0.264 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1497 4.91 %RANDOM
Rwork0.234 ---
obs0.235 30517 99.9 %-
Displacement parametersBiso max: 264.52 Å2 / Biso mean: 120.43 Å2 / Biso min: 72.7 Å2
Baniso -1Baniso -2Baniso -3
1--11.308 Å20 Å20 Å2
2---11.308 Å20 Å2
3---22.616 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3→89.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 56 0 3905
Biso mean--176.03 --
Num. residues----496
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1357SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes672HARMONIC5
X-RAY DIFFRACTIONt_it3956HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion524SEMIHARMONIC5
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_contact4415SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d4016HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg5480HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion20.4
LS refinement shellResolution: 3→3.02 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2418 37 6.06 %
Rwork0.2675 574 -
all-611 -
obs--100 %
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)
10.38740.24050.43360.304-0.329100.0633-0.04730.0054-0.0059-0.05390.1419-0.01990.0902-0.00940.0338-0.1984-0.02040.0590.0069-0.0344-10.86-51.5697-8.6181
20.09370.04590.09340.0217-0.10440.0751-0.1370.0370.07340.02960.00350.06960.06640.08050.13350.0938-0.0782-0.1556-0.0380.07620.003127.393-33.2619-8.9475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A163 - 262
2X-RAY DIFFRACTION2{ B|* }B2 - 397

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