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- PDB-8pwu: PfRH5 bound to monoclonal antibody MAD10-255 -

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Basic information

Entry
Database: PDB / ID: 8pwu
TitlePfRH5 bound to monoclonal antibody MAD10-255
Components
  • Reticulocyte-binding protein homolog 5
  • monoclonal antibody MAD10-255
KeywordsCELL CYCLE / 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: 3.148 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 MAD10-255
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 MAD10-255
C: Reticulocyte-binding protein homolog 5
D: monoclonal antibody MAD10-255
E: Reticulocyte-binding protein homolog 5
F: monoclonal antibody MAD10-255
G: Reticulocyte-binding protein homolog 5
H: monoclonal antibody MAD10-255
I: Reticulocyte-binding protein homolog 5
J: monoclonal antibody MAD10-255
K: Reticulocyte-binding protein homolog 5


Theoretical massNumber of molelcules
Total (without water)380,51311
Polymers380,51311
Non-polymers00
Water00
1
A: Reticulocyte-binding protein homolog 5
B: monoclonal antibody MAD10-255


Theoretical massNumber of molelcules
Total (without water)67,9102
Polymers67,9102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Reticulocyte-binding protein homolog 5
D: monoclonal antibody MAD10-255


Theoretical massNumber of molelcules
Total (without water)67,9102
Polymers67,9102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Reticulocyte-binding protein homolog 5
F: monoclonal antibody MAD10-255


Theoretical massNumber of molelcules
Total (without water)67,9102
Polymers67,9102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Reticulocyte-binding protein homolog 5
H: monoclonal antibody MAD10-255


Theoretical massNumber of molelcules
Total (without water)67,9102
Polymers67,9102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Reticulocyte-binding protein homolog 5
J: monoclonal antibody MAD10-255


Theoretical massNumber of molelcules
Total (without water)67,9102
Polymers67,9102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Reticulocyte-binding protein homolog 5


Theoretical massNumber of molelcules
Total (without water)40,9621
Polymers40,9621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.309, 134.522, 198.667
Angle α, β, γ (deg.)90.000, 93.560, 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.: 6
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 MAD10-255


Mass: 26947.756 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium sulphate, 0.3 M sodium formate, 0.1 M Tris pH 7.8, 2% w/v g-PGA (Na+ form, LM), 3% w/v PEG 20000

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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: 3.148→87.45 Å / Num. obs: 104997 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Net I/σ(I): 7.3
Reflection shellResolution: 3.15→3.2 Å / Num. unique obs: 5215 / CC1/2: 0.264

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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: 3.148→87.45 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 1.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.873 / SU Rfree Blow DPI: 0.374 / SU Rfree Cruickshank DPI: 0.391
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 5254 5.01 %RANDOM
Rwork0.2419 ---
obs0.2431 104799 99.8 %-
Displacement parametersBiso max: 243.69 Å2 / Biso mean: 136.72 Å2 / Biso min: 68.7 Å2
Baniso -1Baniso -2Baniso -3
1--18.7298 Å20 Å2-9.0908 Å2
2--2.2727 Å20 Å2
3---16.4571 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 3.148→87.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23343 0 0 0 23343
Num. residues----2848
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8506SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3946HARMONIC5
X-RAY DIFFRACTIONt_it23899HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3200SEMIHARMONIC5
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_contact19583SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d23899HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg32253HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion21.08
LS refinement shellResolution: 3.15→3.17 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3973 108 5.15 %
Rwork0.3753 1988 -
all0.3764 2096 -
obs--94.46 %
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)
10.37820.0430.40031.36430.23623.73520.1705-0.20280.2040.3632-0.18850.268-0.0753-0.08410.0181-0.1541-0.2112-0.00580.0002-0.19910.1624-34.76179.456123.2473
22.7643-0.1399-0.40242.63930.28672.20590.26640.08090.4661-0.3055-0.3376-0.1276-0.64980.10330.0712-0.0902-0.0682-0.071-0.4319-0.0330.4569-21.90530.2572-8.998
30.54150.21620.20840.69870.32862.53590.0290.22910.2671-0.4253-0.0892-0.1226-0.1923-0.15420.06010.15820.2872-0.1489-0.00680.07330.0277-35.4527.0028-53.7845
41.4787-0.51850.20064.4735-1.05612.34960.29620.1829-0.1467-0.0686-0.26890.4733-0.193-0.4369-0.0273-0.31470.1826-0.2813-0.1104-0.1660.2937-60.60078.691-21.7712
50.70380.1053-0.23970.636-0.11482.98260.07560.1976-0.1498-0.463-0.16270.08930.35540.10030.08710.29230.3094-0.095-0.1192-0.0777-0.0032-21.9606-14.8745-53.1529
61.6713-1.0052-0.03565.29080.85431.76660.34270.14080.1873-0.1116-0.34-0.55660.23190.27-0.0027-0.33410.18250.05-0.15940.18660.3312.8781-14.2953-21.2328
70.2053-0.1516-0.20381.60410.02632.87850.1386-0.1603-0.09210.4798-0.1361-0.29270.2088-0.0683-0.0024-0.046-0.2512-0.2656-0.00340.13530.1271-23.1808-13.5623.5696
82.8786-0.52960.55392.7974-0.35482.65780.28440.0612-0.5276-0.294-0.28110.18860.7023-0.1863-0.0033-0.0351-0.1241-0.1818-0.4391-0.00770.3992-35.8817-35.7083-7.6092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A158 - 506
2X-RAY DIFFRACTION2{ B|* }B1 - 241
3X-RAY DIFFRACTION3{ C|* }C158 - 506
4X-RAY DIFFRACTION4{ D|* }D1 - 241
5X-RAY DIFFRACTION5{ E|* }E158 - 505
6X-RAY DIFFRACTION6{ F|* }F1 - 241
7X-RAY DIFFRACTION7{ G|* }G158 - 504
8X-RAY DIFFRACTION8{ H|* }H1 - 241

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