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- PDB-8qkr: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -

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Basic information

Entry
Database: PDB / ID: 8qkr
TitlePlasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to R5.251
Components
  • R5251VHCH
  • R5251VLCL
  • Reticulocyte-binding protein-like protein 5
KeywordsIMMUNE SYSTEM / malaria RH5 Antibody Clonotype
Function / homologyRh5 coiled-coil domain / Rh5 coiled-coil domain / Reticulocyte-binding protein-like protein 5
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.234 Å
AuthorsWright, N.D. / Barrett, J.R. / Bradshaw, W.J. / Paterson, N.G. / MacLean, E.M. / Ferreira, L. / McHugh, K. / Koekemoer, L. / Draper, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Oxford, Medical Sciences Internal Fund (MSIF) United Kingdom
CitationJournal: Cell / Year: 2024
Title: Analysis of the diverse antigenic landscape of the malaria protein RH5 identifies a potent vaccine-induced human public antibody clonotype.
Authors: Barrett, J.R. / Pipini, D. / Wright, N.D. / Cooper, A.J.R. / Gorini, G. / Quinkert, D. / Lias, A.M. / Davies, H. / Rigby, C.A. / Aleshnick, M. / Williams, B.G. / Bradshaw, W.J. / Paterson, N. ...Authors: Barrett, J.R. / Pipini, D. / Wright, N.D. / Cooper, A.J.R. / Gorini, G. / Quinkert, D. / Lias, A.M. / Davies, H. / Rigby, C.A. / Aleshnick, M. / Williams, B.G. / Bradshaw, W.J. / Paterson, N.G. / Martinson, T. / Kirtley, P. / Picard, L. / Wiggins, C.D. / Donnellan, F.R. / King, L.D.W. / Wang, L.T. / Popplewell, J.F. / Silk, S.E. / de Ruiter Swain, J. / Skinner, K. / Kotraiah, V. / Noe, A.R. / MacGill, R.S. / King, C.R. / Birkett, A.J. / Soisson, L.A. / Minassian, A.M. / Lauffenburger, D.A. / Miura, K. / Long, C.A. / Wilder, B.K. / Koekemoer, L. / Tan, J. / Nielsen, C.M. / McHugh, K. / Draper, S.J.
History
DepositionSep 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte-binding protein-like protein 5
B: R5251VHCH
C: R5251VLCL
D: Reticulocyte-binding protein-like protein 5
E: R5251VHCH
F: R5251VLCL


Theoretical massNumber of molelcules
Total (without water)177,2216
Polymers177,2216
Non-polymers00
Water00
1
A: Reticulocyte-binding protein-like protein 5
B: R5251VHCH
C: R5251VLCL


Theoretical massNumber of molelcules
Total (without water)88,6103
Polymers88,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Reticulocyte-binding protein-like protein 5
E: R5251VHCH
F: R5251VLCL


Theoretical massNumber of molelcules
Total (without water)88,6103
Polymers88,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.927, 92.016, 92.492
Angle α, β, γ (deg.)60.535, 72.132, 79.818
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
32B
42E
53C
63F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHETYRTYRAA10 - 31110 - 311
211PHEPHETYRTYRDD10 - 31110 - 311
322GLUGLULYSLYSBB6 - 2296 - 229
422GLUGLULYSLYSEE6 - 2296 - 229
533ASPASPCYSCYSCC6 - 2206 - 220
633ASPASPCYSCYSFF6 - 2206 - 220

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Reticulocyte-binding protein-like protein 5


Mass: 39258.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: Rh5 / Production host: Homo sapiens (human) / References: UniProt: A0A8F2YHP6
#2: Antibody R5251VHCH


Mass: 25225.182 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 R5251VLCL


Mass: 24126.723 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.3M Calcium chloride 0.1M Magnesium formate HCl 22.5% (v/v) PurePEGs Cocktail

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7911
pseudo-merohedral22-H, K-L, -L20.2089
ReflectionResolution: 3.13→59.104 Å / Num. obs: 30110 / % possible obs: 98.6 % / Redundancy: 3.7 % / CC1/2: 0.955 / Net I/σ(I): 0.405
Reflection shellResolution: 3.23→3.29 Å / Num. unique obs: 5486 / CC1/2: 0.245

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.234→59.104 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.78 / WRfactor Rfree: 0.308 / WRfactor Rwork: 0.225 / SU B: 69.978 / SU ML: 1.043 / Average fsc free: 0.9207 / Average fsc work: 0.9461 / Cross valid method: FREE R-VALUE / ESU R Free: 0.691
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3268 1403 4.66 %
Rwork0.2536 28705 -
all0.257 --
obs-30108 98.54 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 71.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.118 Å20.872 Å23.203 Å2
2--3.125 Å20.102 Å2
3----0.734 Å2
Refinement stepCycle: LAST / Resolution: 3.234→59.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11728 0 0 0 11728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212042
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611229
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.82116306
X-RAY DIFFRACTIONr_angle_other_deg0.5011.76825958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.17151475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.99543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.774102142
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.27110538
X-RAY DIFFRACTIONr_chiral_restr0.0660.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022767
X-RAY DIFFRACTIONr_nbd_refined0.2510.23397
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.211946
X-RAY DIFFRACTIONr_nbtor_refined0.1890.25854
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.26571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2499
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.235
X-RAY DIFFRACTIONr_nbd_other0.2190.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.24
X-RAY DIFFRACTIONr_mcbond_it5.8167.2475886
X-RAY DIFFRACTIONr_mcbond_other5.8117.2485886
X-RAY DIFFRACTIONr_mcangle_it9.63813.0057350
X-RAY DIFFRACTIONr_mcangle_other9.64113.0067351
X-RAY DIFFRACTIONr_scbond_it5.0087.3326156
X-RAY DIFFRACTIONr_scbond_other5.0087.3336157
X-RAY DIFFRACTIONr_scangle_it8.63613.4758950
X-RAY DIFFRACTIONr_scangle_other8.63513.4768951
X-RAY DIFFRACTIONr_lrange_it14.72571.8914526
X-RAY DIFFRACTIONr_lrange_other14.72971.89214527
X-RAY DIFFRACTIONr_ncsr_local_group_10.1390.0510179
X-RAY DIFFRACTIONr_ncsr_local_group_20.1280.056683
X-RAY DIFFRACTIONr_ncsr_local_group_30.1760.056117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.139490.05009
12AX-RAY DIFFRACTIONLocal ncs0.139490.05009
23AX-RAY DIFFRACTIONLocal ncs0.128370.05009
24AX-RAY DIFFRACTIONLocal ncs0.128370.05009
35AX-RAY DIFFRACTIONLocal ncs0.175670.05008
36AX-RAY DIFFRACTIONLocal ncs0.175670.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.234-3.3170.3471050.37420250.37322900.8920.8893.01310.38
3.317-3.4080.3581070.3620550.3621850.8640.90198.94740.366
3.408-3.5060.319930.33920110.33821280.9280.91798.87220.342
3.506-3.6140.355850.33119660.33220720.9080.92198.98650.338
3.614-3.7320.385830.31919190.32120220.8760.92599.01090.315
3.732-3.8620.281890.29518490.29419530.9430.93899.23190.282
3.862-4.0080.352830.26717720.27118710.90.95299.14480.254
4.008-4.170.361860.25816970.26317980.9290.95699.16570.239
4.17-4.3550.322910.2216430.22517460.9280.96999.31270.195
4.355-4.5660.268820.18115640.18516560.9490.97999.39610.153
4.566-4.8120.276760.18414650.18915550.9480.97999.09970.157
4.812-5.1010.276710.20314160.20715040.9560.97598.86970.178
5.101-5.4510.364760.21113220.21914190.9350.97698.52010.184
5.451-5.8830.363600.24511630.25112820.9380.96695.39780.216
5.883-6.4380.347530.22811540.23312120.9220.96999.58750.193
6.438-7.1880.323490.21510290.2210820.9310.97199.63030.184
7.188-8.2790.309450.2079150.2129630.9370.97699.68850.168
8.279-10.0910.336390.1967710.2038110.9330.98199.87670.172
10.091-14.0670.314160.2176160.2196340.9520.97999.68450.194
14.067-59.1040.335140.3593520.3583660.9430.931000.356

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