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- PDB-9tux: PfRIPR bound to monoclonal antibody MAD8-66 -

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Basic information

Entry
Database: PDB / ID: 9tux
TitlePfRIPR bound to monoclonal antibody MAD8-66
Components
  • MAD8-66 heavy chain
  • MAD8-66 light chain
  • Rh5-interacting protein
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 / cytoplasmic vesicle / host extracellular region / 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
Similarity search - Domain/homology
Rh5-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

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Assembly

Deposited unit
A: MAD8-66 light chain
B: MAD8-66 heavy chain
C: Rh5-interacting protein


Theoretical massNumber of molelcules
Total (without water)80,1673
Polymers80,1673
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-34 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.790, 63.240, 250.730
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: Antibody MAD8-66 light chain


Mass: 26167.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody MAD8-66 heavy chain


Mass: 27433.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Rh5-interacting protein / PfRipr


Mass: 26566.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: RIPR, PFC1045C, PF3D7_0323400 / Production host: Homo sapiens (human) / References: UniProt: O97302
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5, 40% w/v MPD, 5% 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: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→63.25 Å / Num. obs: 549427 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.996 / Net I/σ(I): 8.3
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 28167 / CC1/2: 0.415

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.28data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→62.68 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 2034 4.97 %
Rwork0.2303 --
obs0.232 40916 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.5 Å2 / Biso mean: 56.5398 Å2 / Biso min: 30.84 Å2
Refinement stepCycle: final / Resolution: 2.25→62.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4717 0 0 93 4810
Biso mean---54.16 -
Num. residues----605
Refinement TLS params.Method: refined / Origin x: -20.1069 Å / Origin y: 15.047 Å / Origin z: -31.7252 Å
111213212223313233
T0.2822 Å2-0.0084 Å20.0031 Å2-0.52 Å2-0.0361 Å2--0.3963 Å2
L0.1236 °2-0.1578 °2-0.3057 °2-0.5229 °20.6291 °2--1.1484 °2
S-0.0105 Å °-0.0926 Å °0.0273 Å °0.0477 Å °0.0039 Å °-0.0176 Å °-0.0135 Å °0.0535 Å °0.0118 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 217
2X-RAY DIFFRACTION1allB1 - 220
3X-RAY DIFFRACTION1allC907 - 1082
4X-RAY DIFFRACTION1allD1 - 94

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