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- PDB-8q5d: PfRH5 bound to monoclonal antibody MAD10-466 -

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Basic information

Entry
Database: PDB / ID: 8q5d
TitlePfRH5 bound to monoclonal antibody MAD10-466
Components
  • Monoclonal antibody MAD10-466 heavy chain
  • Monoclonal antibody MAD10-466 light chain
  • Reticulocyte-binding protein homolog 5
KeywordsCELL ADHESION / Plasmodium falciparum / monoclonal antibody / PfRH5 / 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 / symbiont entry into host cell / 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: 3.2 Å
AuthorsFarrell, B. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust220797/Z/20/Z United Kingdom
CitationJournal: Cell / Year: 2024
Title: Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5.
Authors: Wang, L.T. / Cooper, A.J.R. / Farrell, B. / Miura, K. / Diouf, A. / Muller-Sienerth, N. / Crosnier, C. / Purser, L. / Kirtley, P.J. / Maciuszek, M. / Barrett, J.R. / McHugh, K. / Ogwang, R. ...Authors: Wang, L.T. / Cooper, A.J.R. / Farrell, B. / Miura, K. / Diouf, A. / Muller-Sienerth, N. / Crosnier, C. / Purser, L. / Kirtley, P.J. / Maciuszek, M. / Barrett, J.R. / McHugh, K. / Ogwang, R. / Tucker, C. / Li, S. / Doumbo, S. / Doumtabe, D. / Pyo, C.W. / Skinner, J. / Nielsen, C.M. / Silk, S.E. / Kayentao, K. / Ongoiba, A. / Zhao, M. / Nguyen, D.C. / Lee, F.E. / Minassian, A.M. / Geraghty, D.E. / Traore, B. / Seder, R.A. / Wilder, B.K. / Crompton, P.D. / Wright, G.J. / Long, C.A. / Draper, S.J. / Higgins, M.K. / Tan, J.
History
DepositionAug 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Dec 18, 2024Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description

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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 MAD10-466 heavy chain
C: Monoclonal antibody MAD10-466 light chain
D: Reticulocyte-binding protein homolog 5
E: Monoclonal antibody MAD10-466 heavy chain
F: Monoclonal antibody MAD10-466 light chain


Theoretical massNumber of molelcules
Total (without water)175,7996
Polymers175,7996
Non-polymers00
Water00
1
A: Reticulocyte-binding protein homolog 5
B: Monoclonal antibody MAD10-466 heavy chain
C: Monoclonal antibody MAD10-466 light chain


Theoretical massNumber of molelcules
Total (without water)87,9003
Polymers87,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-27 kcal/mol
Surface area32220 Å2
MethodPISA
2
D: Reticulocyte-binding protein homolog 5
E: Monoclonal antibody MAD10-466 heavy chain
F: Monoclonal antibody MAD10-466 light chain


Theoretical massNumber of molelcules
Total (without water)87,9003
Polymers87,9003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-28 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.464, 140.414, 83.616
Angle α, β, γ (deg.)90.000, 112.740, 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.: 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 Monoclonal antibody MAD10-466 heavy chain


Mass: 23360.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Monoclonal antibody MAD10-466 light chain


Mass: 23576.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Buffer System 3 pH 8.5, 0.1 M Amino Acids, 30% v/v Precipitant Mix 1

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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: Jul 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 3.2→67.59 Å / Num. obs: 28799 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.952 / Net I/σ(I): 2.3
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1404 / CC1/2: 0.345

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→67.59 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.607
RfactorNum. reflection% reflectionSelection details
Rfree0.3167 1464 5.11 %RANDOM
Rwork0.2719 ---
obs0.2742 28644 98.7 %-
Displacement parametersBiso max: 180.55 Å2 / Biso mean: 100.89 Å2 / Biso min: 56.97 Å2
Baniso -1Baniso -2Baniso -3
1--9.1405 Å20 Å2-20.3103 Å2
2--15.1166 Å20 Å2
3----5.9761 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: final / Resolution: 3.2→67.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11181 0 0 0 11181
Num. residues----1407
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3971SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1897HARMONIC5
X-RAY DIFFRACTIONt_it11435HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1537SEMIHARMONIC5
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_contact8490SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11435HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg15471HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion20.88
LS refinement shellResolution: 3.2→3.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4415 35 6.11 %
Rwork0.4538 538 -
all0.453 573 -
obs--87.07 %
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)
11.47110.25451.40081.21360.61944.2009-0.0123-0.1660.1923-0.080.18340.0955-0.14710.0847-0.1711-0.23660.008-0.1571-0.10340.0181-0.138217.04692.040751.7649
20.7905-0.1566-0.97696.59030.68423.0695-0.172-0.15660.138-0.10780.0208-0.15110.21380.10780.1513-0.01880.072-0.1131-0.27640.0935-0.2677-5.371-27.879719.4409
30.90031.34860.33747.5561.51242.18010.06510.12160.0553-0.2193-0.32080.08060.33320.28660.25570.11310.18970.0229-0.25050.1315-0.3644-0.384-27.05521.9057
40.8714-0.13040.48722.3862-0.3191.8813-0.05050.03690.1563-0.147-0.016-0.1296-0.29080.11450.06650.0658-0.0277-0.1306-0.23940.0109-0.1526-22.107425.464224.6511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A157 - 502
2X-RAY DIFFRACTION2{ B|* }B2 - 218
3X-RAY DIFFRACTION3{ C|* }C1 - 210
4X-RAY DIFFRACTION4{ D|* }D157 - 498

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