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- PDB-7uvs: Pfs230 domain 1 bound by LMIV230-02 Fab -

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Basic information

Entry
Database: PDB / ID: 7uvs
TitlePfs230 domain 1 bound by LMIV230-02 Fab
Components
  • Gametocyte surface protein P230
  • LMIV230-02 Fab heavy chain
  • LMIV230-02 Fab light chain
KeywordsCELL INVASION/IMMUNE SYSTEM / Antibody-fragment / malaria transmission / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
Function / homology6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsIvanochko, D. / Julien, J.P.
Funding support Canada, United States, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)428410 Canada
Ontario Early Researcher Awards Canada
Bill & Melinda Gates FoundationOPP1170236 United States
Canada Research Chairs Canada
CitationJournal: Immunity / Year: 2023
Title: Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230.
Authors: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / ...Authors: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / Kraft, L. / Duncan, S. / Lee, S.M. / Kamya, M.R. / Feeney, M.E. / Jagannathan, P. / Greenhouse, B. / Sauerwein, R.W. / Richter King, C. / MacGill, R.S. / Bousema, T. / Jore, M.M. / Julien, J.P.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LMIV230-02 Fab heavy chain
B: LMIV230-02 Fab light chain
C: Gametocyte surface protein P230
D: LMIV230-02 Fab heavy chain
E: LMIV230-02 Fab light chain
F: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2977
Polymers141,2746
Non-polymers231
Water12,845713
1
A: LMIV230-02 Fab heavy chain
B: LMIV230-02 Fab light chain
C: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6604
Polymers70,6373
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-45 kcal/mol
Surface area28000 Å2
MethodPISA
2
D: LMIV230-02 Fab heavy chain
E: LMIV230-02 Fab light chain
F: Gametocyte surface protein P230


Theoretical massNumber of molelcules
Total (without water)70,6373
Polymers70,6373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-34 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.360, 132.470, 125.070
Angle α, β, γ (deg.)90.000, 102.348, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALVALVAL(chain 'A' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))AA22
121LEULEUPHEPHE(chain 'A' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))AA4 - 634 - 64
131GLYGLYTHRTHR(chain 'A' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))AA65 - 20566 - 215
141VALVALPROPRO(chain 'A' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))AA207 - 213217 - 223
211VALVALVALVAL(chain 'D' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))DD22
221LEULEUPHEPHE(chain 'D' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))DD4 - 634 - 64
231GLYGLYTHRTHR(chain 'D' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))DD65 - 20566 - 215
241VALVALPROPRO(chain 'D' and (resid 2 or resid 4 through 63 or resid 65 through 205 or resid 207 through 213))DD207 - 213217 - 223
112ILEILEPROPRO(chain 'B' and (resid 2 through 142 or resid 144...BB2 - 1422 - 148
122GLUGLUTHRTHR(chain 'B' and (resid 2 through 142 or resid 144...BB144 - 165150 - 171
132GLNGLNSERSER(chain 'B' and (resid 2 through 142 or resid 144...BB167 - 169173 - 175
142ASPASPGLUGLU(chain 'B' and (resid 2 through 142 or resid 144...BB171 - 188177 - 194
152HISHISGLUGLU(chain 'B' and (resid 2 through 142 or resid 144...BB190 - 214196 - 220
212ILEILEPROPRO(chain 'E' and (resid 2 through 142 or resid 144...EE2 - 1422 - 148
222GLUGLUTHRTHR(chain 'E' and (resid 2 through 142 or resid 144...EE144 - 165150 - 171
232GLNGLNSERSER(chain 'E' and (resid 2 through 142 or resid 144...EE167 - 169173 - 175
242ASPASPGLUGLU(chain 'E' and (resid 2 through 142 or resid 144...EE171 - 188177 - 194
252HISHISGLUGLU(chain 'E' and (resid 2 through 142 or resid 144...EE190 - 214196 - 220
113ILEILESERSER(chain 'C' and (resid 560 through 578 or resid 580...CC560 - 5789 - 27
123ASPASPTHRTHR(chain 'C' and (resid 560 through 578 or resid 580...CC580 - 60229 - 51
133SERSERVALVAL(chain 'C' and (resid 560 through 578 or resid 580...CC604 - 61353 - 62
143VALVALVALVAL(chain 'C' and (resid 560 through 578 or resid 580...CC615 - 69664 - 145
153ALAALATHRTHR(chain 'C' and (resid 560 through 578 or resid 580...CC699 - 711148 - 160
163ASPASPTYRTYR(chain 'C' and (resid 560 through 578 or resid 580...CC713 - 730162 - 179
213ILEILESERSER(chain 'F' and (resid 560 through 578 or resid 580...FF560 - 5789 - 27
223ASPASPTHRTHR(chain 'F' and (resid 560 through 578 or resid 580...FF580 - 60229 - 51
233SERSERVALVAL(chain 'F' and (resid 560 through 578 or resid 580...FF604 - 61353 - 62
243VALVALVALVAL(chain 'F' and (resid 560 through 578 or resid 580...FF615 - 69664 - 145
253ALAALATHRTHR(chain 'F' and (resid 560 through 578 or resid 580...FF699 - 711148 - 160
263ASPASPTYRTYR(chain 'F' and (resid 560 through 578 or resid 580...FF713 - 730162 - 179

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody LMIV230-02 Fab heavy chain


Mass: 23618.240 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: Antibody LMIV230-02 Fab light chain


Mass: 24324.018 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: Protein Gametocyte surface protein P230


Mass: 22694.705 Da / Num. of mol.: 2 / Fragment: domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Homo sapiens (human) / References: UniProt: P68874
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.3 M di-ammonium hydrogen citrate, 15 %(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.03→29.85 Å / Num. obs: 93278 / % possible obs: 98.6 % / Redundancy: 7 % / Biso Wilson estimate: 34.17 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 9.5
Reflection shellResolution: 2.03→2.06 Å / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4062 / CC1/2: 0.562 / Rpim(I) all: 0.542 / Rrim(I) all: 1.343

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ohg

6ohg


Resolution: 2.06→29.85 Å / SU ML: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 2019 2.25 %
Rwork0.1743 87709 -
obs0.1752 89728 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.33 Å2
Refinement stepCycle: LAST / Resolution: 2.06→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9521 0 1 713 10235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00799731
X-RAY DIFFRACTIONf_angle_d1.041513216
X-RAY DIFFRACTIONf_chiral_restr0.0641492
X-RAY DIFFRACTIONf_plane_restr0.00821683
X-RAY DIFFRACTIONf_dihedral_angle_d17.24073545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.29931010.24716001X-RAY DIFFRACTION95.15
2.11-2.170.28122020.22766267X-RAY DIFFRACTION99.86
2.17-2.230.20731010.21356332X-RAY DIFFRACTION99.8
2.23-2.30.26522010.20466252X-RAY DIFFRACTION99.83
2.3-2.390.22031010.20086305X-RAY DIFFRACTION99.77
2.39-2.480.25882020.2016219X-RAY DIFFRACTION99.55
2.48-2.60.23111010.19736307X-RAY DIFFRACTION98.78
2.6-2.730.24271010.19016183X-RAY DIFFRACTION98.02
2.73-2.90.2352020.18526285X-RAY DIFFRACTION99.92
2.9-3.130.22281010.18146345X-RAY DIFFRACTION99.64
3.13-3.440.21262020.17326222X-RAY DIFFRACTION99.67
3.44-3.940.19091010.16226279X-RAY DIFFRACTION98.14
3.94-4.960.16722020.13746300X-RAY DIFFRACTION99.95
4.96-29.850.2381010.16156412X-RAY DIFFRACTION99.07

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