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- PDB-8pwv: PfRH5 bound to monoclonal antibody MAD8-502 -

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Basic information

Entry
Database: PDB / ID: 8pwv
TitlePfRH5 bound to monoclonal antibody MAD8-502
Components
  • Reticulocyte-binding protein homolog 5
  • monoclonal antibody MAD8-502
KeywordsCELL ADHESION / Plasmodium falciparum / malaria / monoclonal antibody / growth-inhibition / blood stage / erythrocyte invasion
Function / homology
Function and homology information


rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding ...rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding / host cell plasma membrane / protein-containing complex / extracellular region / membrane
Similarity search - Function
Rh5 coiled-coil domain / Rh5 coiled-coil domain
Similarity search - Domain/homology
Reticulocyte-binding protein homolog 5
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsFarrell, B. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust220797/Z/20/Z United Kingdom
CitationJournal: To Be Published
Title: PfRH5 bound to monoclonal antibody MAD8-502
Authors: Farrell, B. / Higgins, M.K.
History
DepositionJul 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte-binding protein homolog 5
B: monoclonal antibody MAD8-502
C: Reticulocyte-binding protein homolog 5
D: monoclonal antibody MAD8-502
E: Reticulocyte-binding protein homolog 5
F: monoclonal antibody MAD8-502
G: Reticulocyte-binding protein homolog 5
H: monoclonal antibody MAD8-502


Theoretical massNumber of molelcules
Total (without water)270,9378
Polymers270,9378
Non-polymers00
Water7,530418
1
A: Reticulocyte-binding protein homolog 5
B: monoclonal antibody MAD8-502


Theoretical massNumber of molelcules
Total (without water)67,7342
Polymers67,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Reticulocyte-binding protein homolog 5
D: monoclonal antibody MAD8-502


Theoretical massNumber of molelcules
Total (without water)67,7342
Polymers67,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Reticulocyte-binding protein homolog 5
F: monoclonal antibody MAD8-502


Theoretical massNumber of molelcules
Total (without water)67,7342
Polymers67,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Reticulocyte-binding protein homolog 5
H: monoclonal antibody MAD8-502


Theoretical massNumber of molelcules
Total (without water)67,7342
Polymers67,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.970, 158.011, 113.017
Angle α, β, γ (deg.)90.000, 94.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Reticulocyte-binding protein homolog 5 / PfRH5


Mass: 40962.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: RH5, PFD1145c, PF3D7_0424100 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IFM5
#2: Antibody
monoclonal antibody MAD8-502


Mass: 26771.846 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.04 M potassium phosphate monobasic, 16% w/v PEG 8000, 20% w/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.07→79.01 Å / Num. obs: 181986 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 7.5
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 8654 / CC1/2: 0.37

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.28data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→79 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 8804 5.02 %RANDOM
Rwork0.2687 ---
obs0.2692 175452 96.2 %-
Displacement parametersBiso max: 156.44 Å2 / Biso mean: 72.13 Å2 / Biso min: 28.31 Å2
Baniso -1Baniso -2Baniso -3
1--21.4215 Å20 Å2-5.6819 Å2
2--7.0257 Å20 Å2
3---14.3959 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.07→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16499 0 0 418 16917
Biso mean---63.56 -
Num. residues----2038
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5988SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2798HARMONIC5
X-RAY DIFFRACTIONt_it16879HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2224SEMIHARMONIC5
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_contact12573SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16879HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg22760HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion19.25
LS refinement shellResolution: 2.07→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5123 197 5.61 %
Rwork0.5123 3313 -
all0.5123 3510 -
obs--51.17 %
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)
10.13690.0373-0.45521.02210.39441.5085-0.0938-0.00220.01040.31940.13-0.00260.45960.2067-0.03620.34380.11230.0624-0.25280.033-0.27224.44675.17238.6366
21.04340.6140.02231.34550.14221.1042-0.04480.03030.0592-0.09740.0244-0.0037-0.00190.00790.02040.0577-0.00690.0249-0.1422-0.0337-0.143210.106319.5633-2.5428
30.05210.0178-0.04871.0344-0.12941.47980.1224-0.0015-0.020.06870.1029-0.0084-0.2815-0.1703-0.22530.1620.03480.081-0.1972-0.0025-0.1916-5.895-19.0781-18.9111
41.06260.8008-0.34741.72850.00891.88960.05630.0518-0.0528-0.3050.0855-0.10640.1086-0.1831-0.14180.20190.00440.0363-0.1970.0343-0.2438-5.0285-33.3189-60.4406
50.18680.3004-0.41530.256-2.9208-0.0679-0.04610.23610.14830.6264-0.0378-0.15090.9240.0370.0839-0.14210.0082-0.00230.0421-0.0721-0.0558-33.16267.7627-17.5567
61.09931.4192-1.12742.19030.01424.6836-0.00970.29010.1069-0.14070.02-0.1133-0.2548-0.8657-0.0102-0.03280.06140.02930.0277-0.0301-0.2671-27.92821.8565-58.6974
70.00410.1568-0.13040.6869-0.42562.61890.3257-0.00590.06610.31790.04270.2198-0.55470.238-0.36840.325-0.24510.1498-0.1618-0.0823-0.3012-52.8371-16.504837.6335
81.21541.1661-0.24743.0079-0.44291.670.07030.0174-0.0845-0.242-0.0139-0.11590.15210.1983-0.05640.0138-0.02670.0068-0.1010.0233-0.173-52.7536-30.5811-3.9592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A156 - 502
2X-RAY DIFFRACTION2{ B|* }B2 - 243
3X-RAY DIFFRACTION3{ C|* }C156 - 502
4X-RAY DIFFRACTION4{ D|* }D2 - 243
5X-RAY DIFFRACTION5{ E|* }E156 - 501
6X-RAY DIFFRACTION6{ F|* }F2 - 242
7X-RAY DIFFRACTION7{ G|* }G158 - 502
8X-RAY DIFFRACTION8{ H|* }H3 - 243

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