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- PDB-9f2d: KIR2DL1 bound to RIFIN RBK21 -

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Basic information

Entry
Database: PDB / ID: 9f2d
TitleKIR2DL1 bound to RIFIN RBK21
Components
  • KIR2DL protein
  • RIFIN RBK21
KeywordsIMMUNE SYSTEM / Plasmodium falciparum / malaria / RIFIN / KIR / immune receptor / infected erythrocyte
Function / homology
Function and homology information


immune response-regulating signaling pathway / plasma membrane
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.886 Å
AuthorsChamberlain, S.G. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust224343/Z/21/Z United Kingdom
CitationJournal: Nature / Year: 2025
Title: KIR2DL1 bound to RIFIN RBK21
Authors: Chamberlain, S.G. / Higgins, M.K.
History
DepositionApr 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIFIN RBK21
B: KIR2DL protein
C: RIFIN RBK21
D: KIR2DL protein
E: RIFIN RBK21
F: KIR2DL protein
G: RIFIN RBK21
H: KIR2DL protein
I: RIFIN RBK21
J: KIR2DL protein
K: RIFIN RBK21
L: KIR2DL protein
M: RIFIN RBK21
N: KIR2DL protein
O: RIFIN RBK21
P: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,33836
Polymers297,18316
Non-polymers5,15520
Water00
1
A: RIFIN RBK21
B: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9585
Polymers37,1482
Non-polymers8103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RIFIN RBK21
D: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7364
Polymers37,1482
Non-polymers5892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RIFIN RBK21
F: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9585
Polymers37,1482
Non-polymers8103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RIFIN RBK21
H: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5904
Polymers37,1482
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: RIFIN RBK21
J: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9585
Polymers37,1482
Non-polymers8103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: RIFIN RBK21
L: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5904
Polymers37,1482
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: RIFIN RBK21
N: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5904
Polymers37,1482
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: RIFIN RBK21
P: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9585
Polymers37,1482
Non-polymers8103
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
G: RIFIN RBK21
H: KIR2DL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5904
Polymers37,1482
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint1 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.399, 99.047, 321.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RIFIN RBK21


Mass: 15639.734 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Homo sapiens (human)
#2: Protein
KIR2DL protein / Killer cell immunoglobulin-like receptor


Mass: 21508.111 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL1, 3DL2 / Production host: Homo sapiens (human) / References: UniProt: A0A191URJ7
#3: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-4-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}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.: 15 / 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
Has ligand of interestN
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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Bicine pH 8.5, 0.1M Amino acid mix, 37.5 % v/v precipitant mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.88→160.57 Å / Num. obs: 53588 / % possible obs: 94.7 % / Redundancy: 6.4 % / CC1/2: 0.994 / Rpim(I) all: 0.013 / Net I/σ(I): 7
Reflection shellResolution: 2.88→3.15 Å / Num. unique obs: 2679 / CC1/2: 0.643 / Rpim(I) all: 0.817

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.886→57.37 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.507
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 2692 5.02 %RANDOM
Rwork0.2562 ---
obs0.2577 53578 78.8 %-
Displacement parametersBiso max: 234.88 Å2 / Biso mean: 96.98 Å2 / Biso min: 34.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.3478 Å20 Å20 Å2
2---1.2897 Å20 Å2
3---0.9419 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.886→57.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17892 0 330 0 18222
Biso mean--104.31 --
Num. residues----2339
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6325SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3152HARMONIC5
X-RAY DIFFRACTIONt_it18693HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2557SEMIHARMONIC5
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_contact12769SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d18693HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg25408HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion18.35
LS refinement shellResolution: 2.89→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3763 48 4.48 %
Rwork0.3189 1024 -
all0.3212 1072 -
obs--9.39 %
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)
17.7669-3.1785-0.76696.06411.3143.1475-0.02660.6094-0.6103-0.4065-0.12620.00230.12720.26210.15290.00530.00320.065-0.0607-0.10250.043-12.895640.876362.6489
23.71821.8289-1.13513.1525-0.90721.10320.06380.140.328-0.1471-0.02270.53170.0370.0142-0.0412-0.05670.0196-0.0437-0.1594-0.02450.1992-43.359747.368275.9167
38.529-5.7199-2.904213.83065.82083.38020.21330.56940.73030.0588-0.25220.234-0.7446-0.20520.03890.55630.304-0.0331-0.41020.0468-0.5591-26.24981.51345.2549
41.7528-0.59340.93631.3121-2.29884.7486-0.0539-0.03310.0355-0.1024-0.0075-0.0985-0.3797-0.0960.06140.0725-0.01890.0006-0.06050.0285-0.0373-9.548-24.904255.4647
58.0557-4.1078-1.4579.27132.92055.032-0.0650.5963-0.3577-0.2291-0.04860.20040.4281-0.10530.1136-0.0169-0.14880.0648-0.0815-0.067-0.070232.4634-10.743362.7927
64.88080.9338-0.84051.88040.09792.1006-0.18310.15850.5342-0.3026-0.06710.27480.0678-0.23140.2502-0.1228-0.0112-0.1202-0.1488-0.01640.15693.68161.143375.6132
74.8564-5.8208-1.742610.4080.94173.12020.1472-0.01790.6851-0.14980.67530.0639-1.0885-0.8921-0.8225-0.01160.25230.15970.10550.0476-0.1746-71.147947.181248.7271
81.3004-0.97480.09132.3186-2.51344.3828-0.05360.1293-0.0747-0.20880.0411-0.1190.1004-0.2970.01250.0153-0.07510.0692-0.0536-0.01020.0114-53.022220.699955.3173
915.8073-4.0825-2.81844.5921.69954.4791-0.2788-1.08850.45140.123-0.34380.2949-0.8093-0.53870.6226-0.11970.0221-0.231-0.5304-0.09260.1009-28.93372.86319.0943
101.72590.11930.59835.92482.11012.9688-0.04730.41890.1882-0.34930.1727-0.5571-0.46460.2647-0.1255-0.0186-0.1584-0.03310.0910.0062-0.0988-11.973-22.05378.6557
1115.0092-5.2083-5.82083.86281.16440-0.1848-0.5122-0.61040.04980.4109-0.72080.59280.734-0.22610.26510.304-0.18750.1020.1963-0.341928.0037-10.783933.1078
122.5748-1.28873.09693.8765-2.5336.5339-0.0644-0.5233-0.2190.19920.1580.47210.0025-0.7654-0.0937-0.1943-0.08810.01620.1017-0.0029-0.02596.555512.872722.9381
1313.9715.82080.63494.88591.23810.88110.00570.13080.3085-0.0820.577-0.5139-0.58410.4499-0.58260.3431-0.02250.17830.06050.2489-0.569628.97310.5623-32.1302
143.05681.0326-3.68923.0693-1.73335.06280.11280.79360.5334-0.15050.2280.4858-0.0879-1.0451-0.3408-0.11690.11870.00160.29290.123-0.1336.6879-12.6898-23.6442
1516.46135.82082.89894.7142-0.31691.4629-0.2191.0254-0.9299-0.2998-0.14860.7520.7651-0.69560.3677-0.13080.02220.2455-0.3836-0.3040.102-28.4081-2.2119-19.9334
161.6115-1.1056-1.04047.52422.80533.3474-0.1032-0.2272-0.06390.45790.1764-0.31360.5720.3079-0.0732-0.04070.22340.03140.12250.0031-0.1856-11.546822.7311-8.8598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A165 - 275
2X-RAY DIFFRACTION2{ B|* }B27 - 220
3X-RAY DIFFRACTION3{ C|* }C167 - 273
4X-RAY DIFFRACTION4{ D|* }D28 - 221
5X-RAY DIFFRACTION5{ E|* }E166 - 274
6X-RAY DIFFRACTION6{ F|* }F27 - 221
7X-RAY DIFFRACTION7{ G|* }G166 - 274
8X-RAY DIFFRACTION8{ H|* }H27 - 221
9X-RAY DIFFRACTION9{ I|* }I166 - 273
10X-RAY DIFFRACTION10{ J|* }J27 - 221
11X-RAY DIFFRACTION11{ K|* }K166 - 273
12X-RAY DIFFRACTION12{ L|* }L27 - 221
13X-RAY DIFFRACTION13{ M|* }M166 - 272
14X-RAY DIFFRACTION14{ N|* }N29 - 221
15X-RAY DIFFRACTION15{ O|* }O167 - 273
16X-RAY DIFFRACTION16{ P|* }P28 - 221

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