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- PDB-8rz0: Synthetic immunogen RH5-34EM bound to monoclonal antibody R5.016 -

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Basic information

Entry
Database: PDB / ID: 8rz0
TitleSynthetic immunogen RH5-34EM bound to monoclonal antibody R5.016
Components
  • R5.016 scFv
  • RH5-34EM
KeywordsIMMUNE SYSTEM / Malaria / blood stage / synthetic vaccine immunogen / PfRH5
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsFarrell, B. / Harrison, T. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Embo Mol Med / Year: 2024
Title: Rational structure-guided design of a blood stage malaria vaccine immunogen presenting a single epitope from PfRH5.
Authors: Harrison, T.E. / Alam, N. / Farrell, B. / Quinkert, D. / Lias, A.M. / King, L.D.W. / Barfod, L.K. / Draper, S.J. / Campeotto, I. / Higgins, M.K.
History
DepositionFeb 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RH5-34EM
B: R5.016 scFv
C: RH5-34EM
D: R5.016 scFv
E: RH5-34EM
F: R5.016 scFv
G: RH5-34EM
H: R5.016 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,52012
Polymers164,1528
Non-polymers3684
Water22,1941232
1
A: RH5-34EM
B: R5.016 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1303
Polymers41,0382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-9 kcal/mol
Surface area16710 Å2
MethodPISA
2
C: RH5-34EM
D: R5.016 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1303
Polymers41,0382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-9 kcal/mol
Surface area16590 Å2
MethodPISA
3
E: RH5-34EM
F: R5.016 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1303
Polymers41,0382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-7 kcal/mol
Surface area16860 Å2
MethodPISA
4
G: RH5-34EM
H: R5.016 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1303
Polymers41,0382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-6 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.281, 114.012, 217.085
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: Protein
RH5-34EM


Mass: 14216.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody
R5.016 scFv


Mass: 26821.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG8000, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→217.1 Å / Num. obs: 199219 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 12
Reflection shellResolution: 1.63→1.66 Å / Num. unique obs: 9819 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→108.54 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.084
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 9860 4.95 %RANDOM
Rwork0.191 ---
obs0.1917 199083 100 %-
Displacement parametersBiso max: 112.93 Å2 / Biso mean: 36.05 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.8838 Å20 Å20 Å2
2---3.6648 Å20 Å2
3---1.7811 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.63→108.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11002 0 24 1232 12258
Biso mean--39.25 43.62 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1954HARMONIC5
X-RAY DIFFRACTIONt_it11370HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1472SEMIHARMONIC5
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_contact10916SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11370HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg15335HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion15.77
LS refinement shellResolution: 1.63→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2757 174 4.37 %
Rwork0.2639 3808 -
all0.2644 3982 -
obs--99.95 %
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)
11.44140.07010.57340.3153-1.34117.0116-0.1220.12140.29250.09440.03750.0207-0.508-0.09350.0845-0.03280.0151-0.0038-0.13590.0099-0.0548.250460.194632.9041
20.25930.07290.27820.4229-0.03950.6460.01370.01860.03130.0414-0.0143-0.0126-0.00210.03620.0006-0.0913-0.00880.0076-0.0637-0.0067-0.101319.823338.728338.2243
30.9344-0.0162-0.11580.4263-0.03094.3089-0.1058-0.14580.20220.03470.0598-0.0522-0.2306-0.12160.046-0.08940.01450.0037-0.0852-0.0549-0.052-11.108163.050123.4447
40.46410.02560.22970.1550.06750.6366-0.0003-0.0288-0.0099-0.07270.0117-0.06810.04480.0142-0.0115-0.094-0.0040.0314-0.0709-0.022-0.0879-20.193240.567614.5727
50.3291-0.4115-0.08423.90190.36550.70.00340.0549-0.0903-0.1075-0.0380.15530.1387-0.05630.0346-0.0551-0.0089-0.0215-0.0824-0.0281-0.08667.7677-2.921810.8658
60.69840.07750.06540.9543-0.16270.2605-0.0105-0.0624-0.07880.06180.03440.0151-0.065-0.0411-0.024-0.09460.0238-0.0039-0.070.0159-0.103716.23333.022233.8599
71.4126-0.4648-0.245210.3914-1.77041.28250.09170.46390.0227-0.46470.023-0.2884-0.3024-0.229-0.11480.06960.15430.0435-0.07170.0207-0.2457-12.3405-13.589112.2758
80.9329-0.23120.17390.85370.06340.24250.0980.0185-0.1599-0.0839-0.08230.05140.01560.0297-0.0157-0.09170.0412-0.0326-0.10410.0078-0.0649-23.5031-20.717132.8981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 119
2X-RAY DIFFRACTION2{ B|* }B0 - 264
3X-RAY DIFFRACTION3{ C|* }C5 - 119
4X-RAY DIFFRACTION4{ D|* }D1 - 260
5X-RAY DIFFRACTION5{ E|* }E5 - 119
6X-RAY DIFFRACTION6{ F|* }F1 - 262
7X-RAY DIFFRACTION7{ G|* }G6 - 119
8X-RAY DIFFRACTION8{ H|* }H1 - 261

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