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- PDB-8pww: PfRH5 bound to monoclonal antibody MAD8-151 -

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Basic information

Entry
Database: PDB / ID: 8pww
TitlePfRH5 bound to monoclonal antibody MAD8-151
Components
  • Reticulocyte-binding protein homolog 5
  • scFv fragment for antibody MAD8-151
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
DI(HYDROXYETHYL)ETHER / Reticulocyte-binding protein homolog 5
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 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 MAD8-151
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: scFv fragment for antibody MAD8-151
C: Reticulocyte-binding protein homolog 5
D: scFv fragment for antibody MAD8-151
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,90311
Polymers135,2904
Non-polymers6137
Water9,602533
1
A: Reticulocyte-binding protein homolog 5
B: scFv fragment for antibody MAD8-151
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9976
Polymers67,6452
Non-polymers3524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Reticulocyte-binding protein homolog 5
D: scFv fragment for antibody MAD8-151
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9055
Polymers67,6452
Non-polymers2603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.303, 121.380, 78.998
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

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


Mass: 40962.371 Da / Num. of mol.: 2
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 scFv fragment for antibody MAD8-151


Mass: 26682.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 540 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M sodium HEPES pH 7 .5, 12% w/v PEG 8000

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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: 1.945→79 Å / Num. obs: 106577 / % possible obs: 98.5 % / Redundancy: 6.9 % / CC1/2: 0.993 / Net I/σ(I): 6
Reflection shellResolution: 1.945→1.98 Å / Num. unique obs: 5404 / CC1/2: 0.337

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.28data extraction
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.945→79 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.161 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 5117 4.85 %RANDOM
Rwork0.2301 ---
obs0.2312 105428 97.5 %-
Displacement parametersBiso max: 87.74 Å2 / Biso mean: 32.98 Å2 / Biso min: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.0859 Å20 Å2-1.8606 Å2
2---8.2099 Å20 Å2
3---8.2958 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.945→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8395 0 40 533 8968
Biso mean--51.16 37.3 -
Num. residues----1034
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3074SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1431HARMONIC5
X-RAY DIFFRACTIONt_it8631HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1148SEMIHARMONIC5
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_contact7931SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8631HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg11642HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion16.97
LS refinement shellResolution: 1.95→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3648 85 4.03 %
Rwork0.3526 2024 -
all0.3531 2109 -
obs--85.89 %
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)
10.7544-0.3616-0.54140.29170.41290.51970.02740.0806-0.0425-0.0245-0.0703-0.0215-0.0359-0.0450.0429-0.07280.02110.0302-0.04310.0099-0.0095-4.096622.7194-37.6632
21.02640.5857-0.12010.70930.03850.25460.0577-0.0557-0.01790.078-0.06740.00740.04160.05940.0097-0.0749-0.00480.0052-0.07570.00670.0132-9.015724.84612.4945
30.7951-0.44630.6310.4037-0.48890.6723-0.00650.08170.0167-0.0274-0.0370.03010.00220.06120.0435-0.0841-0.0045-0.0048-0.00110.0026-0.0512-34.0474-15.1086-29.6254
41.1770.6821-0.19530.8261-0.00950.38820.0547-0.0197-0.04690.1207-0.0449-0.014-0.0494-0.0206-0.0098-0.07370.00120.0023-0.08220.0028-0.0012-30.1175-16.31939.6294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A156 - 454
2X-RAY DIFFRACTION2{ B|* }B1 - 241
3X-RAY DIFFRACTION3{ C|* }C156 - 453
4X-RAY DIFFRACTION4{ D|* }D1 - 241

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