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- PDB-9tuw: PfRIPR EGF6 and 7 bound to monoclonal antibody RP.012 -

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Basic information

Entry
Database: PDB / ID: 9tuw
TitlePfRIPR EGF6 and 7 bound to monoclonal antibody RP.012
Components
  • Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
  • RP.012 heavy chain
  • RP.012 light chain
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 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: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
B: RP.012 heavy chain
C: RP.012 light chain
D: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
E: RP.012 heavy chain
F: RP.012 light chain


Theoretical massNumber of molelcules
Total (without water)180,7416
Polymers180,7416
Non-polymers00
Water2,828157
1
A: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
B: RP.012 heavy chain
C: RP.012 light chain


Theoretical massNumber of molelcules
Total (without water)90,3703
Polymers90,3703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-34 kcal/mol
Surface area21740 Å2
MethodPISA
2
D: Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein
E: RP.012 heavy chain
F: RP.012 light chain


Theoretical massNumber of molelcules
Total (without water)90,3703
Polymers90,3703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-34 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.160, 50.983, 109.782
Angle α, β, γ (deg.)76.820, 83.260, 76.500
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Immunoglobulin gamma-1 heavy chain,Rh5-interacting protein / Immunoglobulin gamma-1 heavy chain NIE / PfRipr


Mass: 38406.172 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
#2: Antibody RP.012 heavy chain


Mass: 25965.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody RP.012 light chain


Mass: 25998.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Buffer Sytem 3 pH 8.5, 0.1 M Carboxylic acids, 37.5% v/v Precipitant Mix 4

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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: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.196→48.67 Å / Num. obs: 51504 / % possible obs: 98.3 % / Redundancy: 3.6 % / CC1/2: 0.995 / Net I/σ(I): 11.1
Reflection shellResolution: 2.196→2.23 Å / Num. unique obs: 2453 / CC1/2: 0.317

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
PDB_EXTRACT3.28data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.196→48.66 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.297 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 2699 5.24 %RANDOM
Rwork0.2413 ---
obs0.2421 51479 98.2 %-
Displacement parametersBiso max: 140.96 Å2 / Biso mean: 65.45 Å2 / Biso min: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.9011 Å2-4.2147 Å2-6.1308 Å2
2---17.5505 Å2-7.226 Å2
3---16.6494 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.196→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7385 0 0 157 7542
Biso mean---55.29 -
Num. residues----959
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2555SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1254HARMONIC5
X-RAY DIFFRACTIONt_it7576HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1025SEMIHARMONIC5
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_contact5690SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7576HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg10290HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion18.81
LS refinement shellResolution: 2.2→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3808 41 3.98 %
Rwork0.4208 989 -
all0.4191 1030 -
obs--86.86 %
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)
13.1999-1.27290.10852.0532-2.30524.54330.15940.4242-0.0362-0.4868-0.09480.21760.33130.0203-0.0646-0.1107-0.0106-0.1374-0.02480.04440.1266-20.202117.0037-26.19
22.17170.07381.06810.7108-1.89773.39140.21010.0263-0.08910.1434-0.26610.0362-0.10850.32530.056-0.0226-0.0989-0.0841-0.19150.01550.10951.708715.13914.4747
32.13940.52670.88960.3335-1.34613.22920.3175-0.3707-0.24490.1013-0.20460.17540.0633-0.281-0.1129-0.0146-0.1778-0.1079-0.20790.06690.1089-10.47074.511112.5172
42.75290.5241.54431.2029-0.62884.9899-0.0444-0.29330.08650.2570.00150.1656-0.195-0.20750.0429-0.1414-0.0287-0.0747-0.01970.10.1281-6.682-14.7732-23.3643
51.30110.6203-0.55411.2088-1.8732.4164-0.1847-0.02330.0435-0.27260.15990.03730.2199-0.00820.0248-0.0448-0.0988-0.1294-0.06530.05190.032114.9218-12.7674-54.567
60.91220.3625-0.77510.3873-1.09492.4033-0.09040.34110.1409-0.13140.27060.2733-0.0569-0.5055-0.1802-0.1001-0.0827-0.16210.1210.2096-0.01612.3908-2.7544-62.7911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A781 - 853
2X-RAY DIFFRACTION2{ B|* }B21 - 233
3X-RAY DIFFRACTION3{ C|* }C21 - 230
4X-RAY DIFFRACTION4{ D|* }D781 - 853
5X-RAY DIFFRACTION5{ E|* }E21 - 232
6X-RAY DIFFRACTION6{ F|* }F21 - 231

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