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- PDB-7f9m: Crystal structure of the variable region of Plasmodium RIFIN #4 (... -

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Basic information

Entry
Database: PDB / ID: 7f9m
TitleCrystal structure of the variable region of Plasmodium RIFIN #4 (PF3D7_1000500) in complex with LAIR1 (with T67L, N69S and A77T mutations)
Components
  • Leukocyte-associated immunoglobulin-like receptor 1
  • Rifin
KeywordsIMMUNE SYSTEM / malaria / Plasmodium falciparum / RIFIN / LAIR1
Function / homology
Function and homology information


immune response-regulating signaling pathway / tertiary granule membrane / specific granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Neutrophil degranulation / membrane / plasma membrane
Similarity search - Function
Variant surface antigen Rifin / Rifin / : / Immunoglobulin domain / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Rifin / Leukocyte-associated immunoglobulin-like receptor 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXie, Y. / Song, H. / Li, X. / Qi, J. / Gao, G.F.
CitationJournal: Cell Rep / Year: 2021
Title: Structural basis of malarial parasite RIFIN-mediated immune escape against LAIR1.
Authors: Xie, Y. / Li, X. / Chai, Y. / Song, H. / Qi, J. / Gao, G.F.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rifin
B: Rifin
C: Leukocyte-associated immunoglobulin-like receptor 1
D: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)62,7054
Polymers62,7054
Non-polymers00
Water00
1
A: Rifin
C: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)31,3522
Polymers31,3522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-6 kcal/mol
Surface area13830 Å2
MethodPISA
2
B: Rifin
D: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)31,3522
Polymers31,3522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-5 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.782, 73.782, 345.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Rifin


Mass: 18646.406 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_1000500 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A143ZWD5
#2: Protein Leukocyte-associated immunoglobulin-like receptor 1 / LAIR-1 / hLAIR1


Mass: 12705.982 Da / Num. of mol.: 2 / Mutation: T67L, N69S, A77T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAIR1, CD305 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6GTX8
Has protein modificationY

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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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid pH 3.7, 8% w/v polyethylene glycol 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03662 Å
DetectorType: SDMS / Detector: CCD / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03662 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 22348 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 93.28 Å2 / CC1/2: 0.995 / Net I/σ(I): 22.72
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 22348 / CC1/2: 0.606

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGR

3kgr


Resolution: 2.9→47.52 Å / SU ML: 0.5136 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.3623 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3099 1119 5.05 %
Rwork0.254 21022 -
obs0.2568 22141 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.15 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 0 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113960
X-RAY DIFFRACTIONf_angle_d1.33035370
X-RAY DIFFRACTIONf_chiral_restr0.0599628
X-RAY DIFFRACTIONf_plane_restr0.0065692
X-RAY DIFFRACTIONf_dihedral_angle_d11.74792434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.48651380.43712522X-RAY DIFFRACTION99.29
3.03-3.190.41781160.37842588X-RAY DIFFRACTION99.38
3.19-3.390.37061290.33282579X-RAY DIFFRACTION99.49
3.39-3.650.37221270.27582606X-RAY DIFFRACTION99.93
3.65-4.020.35691640.25382592X-RAY DIFFRACTION99.67
4.02-4.60.26661420.21252630X-RAY DIFFRACTION99.82
4.6-5.80.28081380.24072678X-RAY DIFFRACTION99.65
5.8-47.520.27671650.22942827X-RAY DIFFRACTION98.88

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