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- PDB-7f9l: Crystal structure of the variable region of Plasmodium RIFIN #6 (... -

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Basic information

Entry
Database: PDB / ID: 7f9l
TitleCrystal structure of the variable region of Plasmodium RIFIN #6 (PF3D7_1400600) in complex with LAIR1 (with T67L, N69S and A77T mutations)
Components
  • Leukocyte-associated immunoglobulin-like receptor 1
  • Rifin
KeywordsIMMUNE SYSTEM / malaria / Plasmodium falciparum / RIFIN
Function / homology
Function and homology information


antigenic variation / 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 / host cell plasma membrane / 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
Leukocyte-associated immunoglobulin-like receptor 1 / Rifin
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.4Nov 13, 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: Rifin
D: Rifin
E: Rifin
F: Rifin
G: Leukocyte-associated immunoglobulin-like receptor 1
H: Leukocyte-associated immunoglobulin-like receptor 1
I: Leukocyte-associated immunoglobulin-like receptor 1
J: Leukocyte-associated immunoglobulin-like receptor 1
K: Leukocyte-associated immunoglobulin-like receptor 1
L: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)176,63512
Polymers176,63512
Non-polymers00
Water2,774154
1
A: Rifin

J: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)29,4392
Polymers29,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area14070 Å2
MethodPISA
2
B: Rifin
G: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)29,4392
Polymers29,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-9 kcal/mol
Surface area14000 Å2
MethodPISA
3
C: Rifin

H: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)29,4392
Polymers29,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area1830 Å2
ΔGint-9 kcal/mol
Surface area13880 Å2
MethodPISA
4
D: Rifin

K: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)29,4392
Polymers29,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area1810 Å2
ΔGint-7 kcal/mol
Surface area13780 Å2
MethodPISA
5
E: Rifin

I: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)29,4392
Polymers29,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area1830 Å2
ΔGint-8 kcal/mol
Surface area14070 Å2
MethodPISA
6
F: Rifin
L: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)29,4392
Polymers29,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-6 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.133, 94.119, 126.033
Angle α, β, γ (deg.)90.000, 117.941, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Rifin


Mass: 17002.520 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1400600 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8IM82
#2: Protein
Leukocyte-associated immunoglobulin-like receptor 1 / LAIR-1 / hLAIR1


Mass: 12436.640 Da / Num. of mol.: 6 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 3.6, 40% v/v polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: SDMS / Detector: CCD / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 68571 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 45.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.17
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 68571 / CC1/2: 0.519

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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: 2.7→41.88 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.646 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2701 2585 4.43 %
Rwork0.2134 55705 -
obs0.2159 58290 84.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11655 0 0 154 11809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009811843
X-RAY DIFFRACTIONf_angle_d1.112116072
X-RAY DIFFRACTIONf_chiral_restr0.05511920
X-RAY DIFFRACTIONf_plane_restr0.00642043
X-RAY DIFFRACTIONf_dihedral_angle_d11.2317234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.3586260.278941X-RAY DIFFRACTION25.58
2.75-2.80.2934440.28781262X-RAY DIFFRACTION34.29
2.8-2.870.3287820.29091640X-RAY DIFFRACTION45.3
2.87-2.930.36951140.29052157X-RAY DIFFRACTION59.79
2.93-3.010.37551460.29792768X-RAY DIFFRACTION77.29
3.01-3.090.3681910.27213224X-RAY DIFFRACTION90.27
3.09-3.180.35381980.26773470X-RAY DIFFRACTION96.6
3.18-3.280.29771610.26293610X-RAY DIFFRACTION99.6
3.28-3.40.31281310.24333683X-RAY DIFFRACTION99.95
3.4-3.530.28041540.2283641X-RAY DIFFRACTION99.84
3.53-3.690.28781720.21873614X-RAY DIFFRACTION100
3.69-3.890.27051540.20983657X-RAY DIFFRACTION100
3.89-4.130.25111550.19373681X-RAY DIFFRACTION99.95
4.13-4.450.2241780.17693632X-RAY DIFFRACTION100
4.45-4.90.24541500.16933669X-RAY DIFFRACTION100
4.9-5.610.26091880.19583637X-RAY DIFFRACTION99.84
5.61-7.060.27921440.22023711X-RAY DIFFRACTION99.77
7.06-41.880.19231970.17773708X-RAY DIFFRACTION99.26

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