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- PDB-4u1g: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -

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Basic information

Entry
Database: PDB / ID: 4u1g
TitlePlasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to monoclonal antibody QA1
Components
  • QA1 monoclonal antibody heavy chain
  • QA1 monoclonal antibody light chain
  • Reticulocyte binding protein 5
KeywordsIMMUNE SYSTEM / malaria erythrocyte invasion antibody-mediated inhibition
Function / homologyRh5 coiled-coil domain / Rh5 coiled-coil domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Reticulocyte binding protein 5
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K.
CitationJournal: Nature / Year: 2014
Title: Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies.
Authors: Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Illingworth, J.J. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Jul 22, 2015Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: 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: Reticulocyte binding protein 5
B: QA1 monoclonal antibody heavy chain
C: QA1 monoclonal antibody light chain
D: Reticulocyte binding protein 5
E: QA1 monoclonal antibody heavy chain
F: QA1 monoclonal antibody light chain


Theoretical massNumber of molelcules
Total (without water)234,4136
Polymers234,4136
Non-polymers00
Water0
1
A: Reticulocyte binding protein 5
B: QA1 monoclonal antibody heavy chain
C: QA1 monoclonal antibody light chain


Theoretical massNumber of molelcules
Total (without water)117,2063
Polymers117,2063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Reticulocyte binding protein 5
E: QA1 monoclonal antibody heavy chain
F: QA1 monoclonal antibody light chain


Theoretical massNumber of molelcules
Total (without water)117,2063
Polymers117,2063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.120, 137.300, 228.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Reticulocyte binding protein 5


Mass: 63128.816 Da / Num. of mol.: 2 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B2L3N7
#2: Antibody QA1 monoclonal antibody heavy chain


Mass: 27635.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Oryctolagus cuniculus (rabbit)
#3: Antibody QA1 monoclonal antibody light chain


Mass: 26442.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Oryctolagus cuniculus (rabbit)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M mix of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol. 0.1 M MES-imidazole (pH 6.5) 20% (w/v) PEG 550 MM 10% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.1→47.24 Å / Num. obs: 36313 / % possible obs: 95.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 100.72 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0R, 1I7Z, 2ZN9

4u0r

1i7z

2zn9


Resolution: 3.1→46.57 Å / Cor.coef. Fo:Fc: 0.8973 / Cor.coef. Fo:Fc free: 0.8572 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.485
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 1793 4.94 %RANDOM
Rwork0.2358 ---
obs0.238 36259 95.14 %-
Displacement parametersBiso mean: 102.61 Å2
Baniso -1Baniso -2Baniso -3
1--29.8685 Å20 Å20 Å2
2--32.3883 Å20 Å2
3----2.5198 Å2
Refine analyzeLuzzati coordinate error obs: 0.796 Å
Refinement stepCycle: 1 / Resolution: 3.1→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11478 0 0 0 11478
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111759HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3215912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4071SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes276HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1668HARMONIC5
X-RAY DIFFRACTIONt_it11759HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion24.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1570SEMIHARMONIC5
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_contact12847SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.19 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.343 140 4.77 %
Rwork0.2661 2796 -
all0.2701 2936 -
obs--95.14 %
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)
10.19160.8062-0.10053.462-1.27410.2862-0.0954-0.0264-0.0103-0.252-0.0087-0.08920.1067-0.0540.1041-0.2109-0.15010.0087-0.3040.152-0.211785.2029131.245-54.3669
21.21430.5067-0.4513.5027-1.67351.4331-0.2108-0.3516-0.20540.0467-0.1208-0.062-0.08290.46770.3316-0.24850.01230.0047-0.10310.1322-0.236570.914875.5889-19.3285
31.24541.4212-0.46541.8004-0.76821.7226-0.30180.0878-0.3686-0.31780.0623-0.10210.24630.13420.2395-0.22290.0660.152-0.30020.038-0.23466.391562.3222-31.3985
40.0647-0.61170.98254.2457-2.17951.1749-0.1002-0.3813-0.0926-0.08280.0974-0.1349-0.1582-0.10210.0028-0.05740.0712-0.152-0.3040.152-0.276282.5973146.66-28.1282
52.0206-1.74851.17485.177-2.31112.04-0.23130.1473-0.03310.1788-0.03510.1774-0.0904-0.01210.2665-0.2671-0.0374-0.1516-0.23960.0734-0.30496.917688.84043.5845
61.1974-1.68061.12353.2113-1.47910.351-0.2935-0.09720.06070.08660.04270.0448-0.19510.05650.25080.05830.0529-0.1476-0.27340.0895-0.3031101.4492.775521.0726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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