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- PDB-8rz1: Synthetic immunogen RH5-34EM bound to monoclonal antibody R5.034 -

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Basic information

Entry
Database: PDB / ID: 8rz1
TitleSynthetic immunogen RH5-34EM bound to monoclonal antibody R5.034
Components
  • R5.034 scFv
  • RH5-34EM
KeywordsIMMUNE SYSTEM / Malaria / blood stage / synthetic vaccine immunogen / PfRH5
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFarrell, B. / 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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: R5.034 scFv
B: RH5-34EM
C: R5.034 scFv
D: RH5-34EM


Theoretical massNumber of molelcules
Total (without water)88,1934
Polymers88,1934
Non-polymers00
Water7,548419
1
A: R5.034 scFv
B: RH5-34EM


Theoretical massNumber of molelcules
Total (without water)44,0972
Polymers44,0972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: R5.034 scFv
D: RH5-34EM


Theoretical massNumber of molelcules
Total (without water)44,0972
Polymers44,0972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.830, 111.830, 91.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Antibody R5.034 scFv


Mass: 29880.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein RH5-34EM


Mass: 14216.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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

CrystalDensity % sol: 34.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Buffer System 1 pH 6.5, 0.06 M Divalents, 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: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.75→55.92 Å / Num. obs: 65543 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.998 / Net I/σ(I): 9.6
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 3252 / CC1/2: 0.598

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→55.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.127 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 3383 5.16 %RANDOM
Rwork0.1975 ---
obs0.1986 65500 100 %-
Displacement parametersBiso max: 118.63 Å2 / Biso mean: 44.94 Å2 / Biso min: 21.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.1764 Å20 Å20 Å2
2---5.1764 Å20 Å2
3---10.3527 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.75→55.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 0 419 5662
Biso mean---45 -
Num. residues----667
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1956SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it5333HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion673SEMIHARMONIC5
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_contact4902SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5333HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg7170HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 1.75→1.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3778 63 4.81 %
Rwork0.3453 1247 -
all0.3468 1310 -
obs--99.78 %
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)
11.2464-0.442-1.03410.708-0.30511.5345-0.10450.07010.0857-0.03430.064-0.05620.1666-0.02070.0405-0.12530.00380.025-0.03760.0091-0.15250.457831.1883-27.4714
24.54311.7816-2.08892.5722-1.10162.70560.0002-0.10250.32870.07540.2710.226-0.2861-0.1285-0.2712-0.11740.01690.0488-0.11050.0086-0.0776-7.920150.8539-16.3943
30.73670.08160.33751.08730.55181.68450.07310.028-0.01650.0998-0.08650.0562-0.06990.05090.0134-0.0660.0106-0.0044-0.1204-0.0375-0.12225.579518.59463.0596
42.1582-2.5338-0.07285.13541.97872.12040.13040.28710.1384-0.25310.0601-0.3701-0.2940.6571-0.1906-0.1875-0.09180.02750.1005-0.0436-0.128446.907919.4319-10.2723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 245
2X-RAY DIFFRACTION2{ B|* }B5 - 118
3X-RAY DIFFRACTION3{ C|* }C1 - 245
4X-RAY DIFFRACTION4{ D|* }D5 - 115

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