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- PDB-9tuy: PfRIPR EGF6 and 7 bound to monoclonal antibody MAD8-739 -

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Basic information

Entry
Database: PDB / ID: 9tuy
TitlePfRIPR EGF6 and 7 bound to monoclonal antibody MAD8-739
Components
  • Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
  • MAD8-739 scFv
KeywordsCELL ADHESION / Malaria / antibody / vaccine design / erythrocyte invasion / Plasmodium falciparum / PfRIPR / PfPCRCR
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / host cell membrane / immunoglobulin complex / cytoplasmic vesicle / host extracellular region / adaptive immune response / host cell plasma membrane / protein-containing complex ...microneme lumen / microneme / symbiont entry into host / host cell membrane / immunoglobulin complex / cytoplasmic vesicle / host extracellular region / adaptive immune response / host cell plasma membrane / protein-containing complex / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype ...: / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Rh5-interacting protein / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFarrell, B. / Higgins, M.K.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Wellcome Trust220797/Z/20/Z United Kingdom
Bill & Melinda Gates FoundationINV-076909 United States
CitationJournal: To Be Published
Title: Dynamic hinge-motion of PfRIPR revealed by malaria invasion inhibitory antibodies
Authors: Farrell, B. / Higgins, M.K.
History
DepositionJan 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAD8-739 scFv
B: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
C: MAD8-739 scFv
D: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein


Theoretical massNumber of molelcules
Total (without water)139,3824
Polymers139,3824
Non-polymers00
Water1,13563
1
A: MAD8-739 scFv
B: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein


Theoretical massNumber of molelcules
Total (without water)69,6912
Polymers69,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MAD8-739 scFv
D: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein


Theoretical massNumber of molelcules
Total (without water)69,6912
Polymers69,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.637, 89.637, 141.336
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody MAD8-739 scFv


Mass: 29815.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein / Immunoglobulin gamma-1 heavy chain NIE / PfRipr


Mass: 39875.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Plasmodium falciparum 3D7 (eukaryote)
Gene: RIPR, PFC1045C, PF3D7_0323400 / Production host: Homo sapiens (human) / References: UniProt: P0DOX5, UniProt: O97302
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium cacodylate pH 6.0, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.8→42.72 Å / Num. obs: 31298 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.993 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 4549 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34.02 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.883 / SU R Cruickshank DPI: 0.441 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.407 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1520 4.86 %RANDOM
Rwork0.228 ---
obs0.2292 31255 100 %-
Displacement parametersBiso max: 156.53 Å2 / Biso mean: 84.93 Å2 / Biso min: 54.05 Å2
Baniso -1Baniso -2Baniso -3
1--16.4779 Å20 Å20 Å2
2---16.4779 Å20 Å2
3---32.9558 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.8→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 0 63 5143
Biso mean---71.16 -
Num. residues----674
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1786SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes878HARMONIC5
X-RAY DIFFRACTIONt_it5188HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion684SEMIHARMONIC5
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_contact3707SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5188HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg7024HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion17.57
LS refinement shellResolution: 2.8→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3788 26 4.15 %
Rwork0.3596 600 -
all0.3603 626 -
obs--99.68 %
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)
10.26950.2923-1.92021.2724-0.79773.5775-0.1408-0.1109-0.09840.05330.21480.1094-0.12540.1022-0.0739-0.32790.0162-0.0080.0232-0.0351-0.292442.4991-20.092622.0718
27.4534-5.7652-3.71822.79162.59120.7974-0.0073-0.0847-1.13160.3101-0.2460.31750.4216-0.23380.2533-0.2478-0.15260.02440.0517-0.0204-0.190846.5739-46.20598.645
30.3123-0.35621.97991.261-0.8363.7758-0.1380.10510.0776-0.05050.20670.11940.12210.1023-0.0687-0.3306-0.01840.01780.0089-0.0307-0.2908-2.3145-57.52824.6853
47.77735.23333.5033.45052.23720.59260.08520.10910.8656-0.258-0.25690.2588-0.3419-0.16680.1716-0.29520.1075-0.00420.0755-0.0387-0.29991.7611-31.426738.1201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A32 - 287
2X-RAY DIFFRACTION2{ B|* }B719 - 816
3X-RAY DIFFRACTION3{ C|* }C32 - 287
4X-RAY DIFFRACTION4{ D|* }D719 - 816

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