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- PDB-7f9n: Crystal structure of the variable region of Plasmodium RIFIN #4 (... -

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Basic information

Entry
Database: PDB / ID: 7f9n
TitleCrystal structure of the variable region of Plasmodium RIFIN #4 (PF3D7_1000500) in complex with LAIR1
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: 3 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

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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)62,6754
Polymers62,6754
Non-polymers00
Water00
1
A: Rifin
C: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)31,3372
Polymers31,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-3 kcal/mol
Surface area13650 Å2
MethodPISA
2
B: Rifin
D: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)31,3372
Polymers31,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-4 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.435, 73.435, 341.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#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: 12690.928 Da / Num. of mol.: 2
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: 3.67 Å3/Da / Density % sol: 66.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen citrate, 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97894 Å
DetectorType: SDMS / Detector: CCD / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19913 / % possible obs: 100 % / Redundancy: 21 % / Biso Wilson estimate: 108.28 Å2 / CC1/2: 0.997 / Net I/σ(I): 21.7
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 19913 / CC1/2: 0.637

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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: 3→49.67 Å / SU ML: 0.5031 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.436 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3302 996 5.04 %
Rwork0.2642 18772 -
obs0.2674 19768 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.33 Å2
Refinement stepCycle: LAST / Resolution: 3→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 0 0 3875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01593939
X-RAY DIFFRACTIONf_angle_d1.39445342
X-RAY DIFFRACTIONf_chiral_restr0.0632623
X-RAY DIFFRACTIONf_plane_restr0.0071690
X-RAY DIFFRACTIONf_dihedral_angle_d15.27692420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.150.44791190.3952600X-RAY DIFFRACTION98.66
3.15-3.350.40371400.37372624X-RAY DIFFRACTION99.39
3.35-3.610.40861450.32942593X-RAY DIFFRACTION99.82
3.61-3.970.35261410.29052647X-RAY DIFFRACTION99.82
3.97-4.550.33391470.25742682X-RAY DIFFRACTION99.89
4.55-5.730.3091560.24822707X-RAY DIFFRACTION99.9
5.73-49.670.29911480.23092919X-RAY DIFFRACTION99.8

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