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- PDB-7uvi: Pfs230 domain 1 bound by RUPA-55 Fab -

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Basic information

Entry
Database: PDB / ID: 7uvi
TitlePfs230 domain 1 bound by RUPA-55 Fab
Components
  • Gametocyte surface protein P230
  • RUPA-55 Fab heavy chain
  • RUPA-55 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: 2.92 Å
AuthorsIvanochko, D. / Newton, J. / 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: RUPA-55 Fab heavy chain
B: RUPA-55 Fab light chain
C: Gametocyte surface protein P230
D: RUPA-55 Fab heavy chain
E: RUPA-55 Fab light chain
F: Gametocyte surface protein P230


Theoretical massNumber of molelcules
Total (without water)140,3816
Polymers140,3816
Non-polymers00
Water00
1
A: RUPA-55 Fab heavy chain
B: RUPA-55 Fab light chain
C: Gametocyte surface protein P230


Theoretical massNumber of molelcules
Total (without water)70,1913
Polymers70,1913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RUPA-55 Fab heavy chain
E: RUPA-55 Fab light chain
F: Gametocyte surface protein P230


Theoretical massNumber of molelcules
Total (without water)70,1913
Polymers70,1913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.020, 100.780, 425.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
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
111VALVALPHEPHE(chain 'A' and (resid 2 through 29 or resid 31...AA2 - 292 - 29
121SERSERTYRTYR(chain 'A' and (resid 2 through 29 or resid 31...AA31 - 5931 - 60
131SERSERMETMET(chain 'A' and (resid 2 through 29 or resid 31...AA62 - 8263 - 83
141ALAALATHRTHR(chain 'A' and (resid 2 through 29 or resid 31...AA84 - 11688 - 127
151GLYGLYSERSER(chain 'A' and (resid 2 through 29 or resid 31...AA118 - 127129 - 138
161SERSERPROPRO(chain 'A' and (resid 2 through 29 or resid 31...AA130 - 147141 - 158
171PROPROVALVAL(chain 'A' and (resid 2 through 29 or resid 31...AA149 - 150160 - 161
181VALVALVALVAL(chain 'A' and (resid 2 through 29 or resid 31...AA152 - 169163 - 180
191SERSERLEULEU(chain 'A' and (resid 2 through 29 or resid 31...AA172 - 189183 - 200
1101GLNGLNHISHIS(chain 'A' and (resid 2 through 29 or resid 31...AA192 - 200203 - 211
1111PROPROTHRTHR(chain 'A' and (resid 2 through 29 or resid 31...AA202 - 205213 - 216
1121VALVALASPASP(chain 'A' and (resid 2 through 29 or resid 31...AA207 - 208218 - 219
1131LYSLYSVALVAL(chain 'A' and (resid 2 through 29 or resid 31...AA210 - 211221 - 222
1141PROPROPROPRO(chain 'A' and (resid 2 through 29 or resid 31...AA213224
211VALVALPHEPHE(chain 'D' and (resid 2 through 29 or resid 31...DD2 - 292 - 29
221SERSERTYRTYR(chain 'D' and (resid 2 through 29 or resid 31...DD31 - 5931 - 60
231SERSERMETMET(chain 'D' and (resid 2 through 29 or resid 31...DD62 - 8263 - 83
241ALAALATHRTHR(chain 'D' and (resid 2 through 29 or resid 31...DD84 - 11688 - 127
251GLYGLYSERSER(chain 'D' and (resid 2 through 29 or resid 31...DD118 - 127129 - 138
261SERSERPROPRO(chain 'D' and (resid 2 through 29 or resid 31...DD130 - 147141 - 158
271PROPROVALVAL(chain 'D' and (resid 2 through 29 or resid 31...DD149 - 150160 - 161
281VALVALVALVAL(chain 'D' and (resid 2 through 29 or resid 31...DD152 - 169163 - 180
291SERSERLEULEU(chain 'D' and (resid 2 through 29 or resid 31...DD172 - 189183 - 200
2101GLNGLNHISHIS(chain 'D' and (resid 2 through 29 or resid 31...DD192 - 200203 - 211
2111PROPROTHRTHR(chain 'D' and (resid 2 through 29 or resid 31...DD202 - 205213 - 216
2121VALVALASPASP(chain 'D' and (resid 2 through 29 or resid 31...DD207 - 208218 - 219
2131LYSLYSVALVAL(chain 'D' and (resid 2 through 29 or resid 31...DD210 - 211221 - 222
2141PROPROPROPRO(chain 'D' and (resid 2 through 29 or resid 31...DD213224
112GLUGLUPROPRO(chain 'B' and (resid 1 through 9 or resid 11...BB1 - 81 - 8
122LEULEUSERSER(chain 'B' and (resid 1 through 9 or resid 11...BB11 - 2611 - 26
132SERSERVALVAL(chain 'B' and (resid 1 through 9 or resid 11...BB28 - 2928 - 29
142SERSERPROPRO(chain 'B' and (resid 1 through 9 or resid 11...BB31 - 4431 - 44
152LEULEUSERSER(chain 'B' and (resid 1 through 9 or resid 11...BB46 - 8046 - 80
162ASPASPLYSLYS(chain 'B' and (resid 1 through 9 or resid 11...BB82 - 12682 - 127
172GLYGLYGLUGLU(chain 'B' and (resid 1 through 9 or resid 11...BB128 - 143129 - 144
182VALVALTRPTRP(chain 'B' and (resid 1 through 9 or resid 11...BB146 - 148147 - 149
192VALVALLEULEU(chain 'B' and (resid 1 through 9 or resid 11...BB150 - 154151 - 155
1102GLYGLYSERSER(chain 'B' and (resid 1 through 9 or resid 11...BB157 - 168158 - 169
1112ASPASPSERSER(chain 'B' and (resid 1 through 9 or resid 11...BB170 - 171171 - 172
1122TYRTYRGLUGLU(chain 'B' and (resid 1 through 9 or resid 11...BB173 - 187174 - 188
1132HISHISPHEPHE(chain 'B' and (resid 1 through 9 or resid 11...BB189 - 209190 - 210
212GLUGLUPROPRO(chain 'E' and (resid 1 through 9 or resid 11...EE1 - 81 - 8
222LEULEUSERSER(chain 'E' and (resid 1 through 9 or resid 11...EE11 - 2611 - 26
232SERSERVALVAL(chain 'E' and (resid 1 through 9 or resid 11...EE28 - 2928 - 29
242SERSERPROPRO(chain 'E' and (resid 1 through 9 or resid 11...EE31 - 4431 - 44
252LEULEUSERSER(chain 'E' and (resid 1 through 9 or resid 11...EE46 - 8046 - 80
262ASPASPLYSLYS(chain 'E' and (resid 1 through 9 or resid 11...EE82 - 12682 - 127
272GLYGLYGLUGLU(chain 'E' and (resid 1 through 9 or resid 11...EE128 - 143129 - 144
282VALVALTRPTRP(chain 'E' and (resid 1 through 9 or resid 11...EE146 - 148147 - 149
292VALVALLEULEU(chain 'E' and (resid 1 through 9 or resid 11...EE150 - 154151 - 155
2102GLYGLYSERSER(chain 'E' and (resid 1 through 9 or resid 11...EE157 - 168158 - 169
2112ASPASPSERSER(chain 'E' and (resid 1 through 9 or resid 11...EE170 - 171171 - 172
2122TYRTYRGLUGLU(chain 'E' and (resid 1 through 9 or resid 11...EE173 - 187174 - 188
2132HISHISPHEPHE(chain 'E' and (resid 1 through 9 or resid 11...EE189 - 209190 - 210
113ASPASPASNASN(chain 'C' and (resid 580 through 586 or resid 590...CC580 - 58629 - 35
123GLUGLUVALVAL(chain 'C' and (resid 580 through 586 or resid 590...CC590 - 61339 - 62
133VALVALGLUGLU(chain 'C' and (resid 580 through 586 or resid 590...CC615 - 63364 - 82
143LEULEUPROPRO(chain 'C' and (resid 580 through 586 or resid 590...CC635 - 64384 - 92
153LYSLYSTHRTHR(chain 'C' and (resid 580 through 586 or resid 590...CC645 - 65294 - 101
163LEULEUGLUGLU(chain 'C' and (resid 580 through 586 or resid 590...CC658 - 660107 - 109
173LEULEUASNASN(chain 'C' and (resid 580 through 586 or resid 590...CC662 - 677111 - 126
183GLUGLUHISHIS(chain 'C' and (resid 580 through 586 or resid 590...CC680 - 697129 - 146
193ALAALAASNASN(chain 'C' and (resid 580 through 586 or resid 590...CC699 - 715148 - 164
1103LYSLYSASNASN(chain 'C' and (resid 580 through 586 or resid 590...CC717 - 719166 - 168
1113GLYGLYTYRTYR(chain 'C' and (resid 580 through 586 or resid 590...CC721 - 730170 - 179
1123PHEPHEPHEPHE(chain 'C' and (resid 580 through 586 or resid 590...CC740189
213ASPASPASNASN(chain 'F' and (resid 580 through 586 or resid 590...FF580 - 58629 - 35
223GLUGLUVALVAL(chain 'F' and (resid 580 through 586 or resid 590...FF590 - 61339 - 62
233VALVALGLUGLU(chain 'F' and (resid 580 through 586 or resid 590...FF615 - 63364 - 82
243LEULEUPROPRO(chain 'F' and (resid 580 through 586 or resid 590...FF635 - 64384 - 92
253LYSLYSTHRTHR(chain 'F' and (resid 580 through 586 or resid 590...FF645 - 65294 - 101
263LEULEUGLUGLU(chain 'F' and (resid 580 through 586 or resid 590...FF658 - 660107 - 109
273LEULEUASNASN(chain 'F' and (resid 580 through 586 or resid 590...FF662 - 677111 - 126
283GLUGLUHISHIS(chain 'F' and (resid 580 through 586 or resid 590...FF680 - 697129 - 146
293ALAALAASNASN(chain 'F' and (resid 580 through 586 or resid 590...FF699 - 715148 - 164
2103LYSLYSASNASN(chain 'F' and (resid 580 through 586 or resid 590...FF717 - 719166 - 168
2113GLYGLYTYRTYR(chain 'F' and (resid 580 through 586 or resid 590...FF721 - 730170 - 179
2123PHEPHEPHEPHE(chain 'F' and (resid 580 through 586 or resid 590...FF740189

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody RUPA-55 Fab heavy chain


Mass: 24075.102 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 RUPA-55 Fab light chain


Mass: 23420.938 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

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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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CAPS pH 10.5, 0.8 M di-potassium hydrogen phosphate, 0.2 M lithium sulfate, 1.2 M sodium di-hydrogen phosphate

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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: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.92→29.67 Å / Num. obs: 43033 / % possible obs: 99.7 % / Redundancy: 26.9 % / Biso Wilson estimate: 82.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.274 / Rpim(I) all: 0.054 / Rrim(I) all: 0.28 / Net I/σ(I): 11.5
Reflection shellResolution: 2.92→3.03 Å / Rmerge(I) obs: 2.995 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4474 / CC1/2: 0.776 / Rpim(I) all: 0.571 / Rrim(I) all: 3.049

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Processing

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

6ohg


Resolution: 2.92→29.67 Å / SU ML: 0.4357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 2033 4.73 %
Rwork0.2181 40952 -
obs0.219 42985 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.5 Å2
Refinement stepCycle: LAST / Resolution: 2.92→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9476 0 0 0 9476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429697
X-RAY DIFFRACTIONf_angle_d0.929213174
X-RAY DIFFRACTIONf_chiral_restr0.05581483
X-RAY DIFFRACTIONf_plane_restr0.0071680
X-RAY DIFFRACTIONf_dihedral_angle_d18.13743534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.990.43951210.39532688X-RAY DIFFRACTION99.68
2.99-3.060.40571010.34492753X-RAY DIFFRACTION99.79
3.06-3.150.35812000.32212639X-RAY DIFFRACTION99.72
3.15-3.240.3231010.29812724X-RAY DIFFRACTION99.86
3.24-3.340.35581010.27652720X-RAY DIFFRACTION99.82
3.34-3.460.30691990.25742626X-RAY DIFFRACTION99.33
3.46-3.60.25211010.23642739X-RAY DIFFRACTION99.61
3.6-3.760.24811010.23742741X-RAY DIFFRACTION99.79
3.76-3.960.26762020.21882671X-RAY DIFFRACTION99.97
3.96-4.210.23321010.1962765X-RAY DIFFRACTION99.9
4.21-4.530.22241010.1692767X-RAY DIFFRACTION99.9
4.53-4.990.19482020.16752657X-RAY DIFFRACTION99.86
4.99-5.70.23121010.18042789X-RAY DIFFRACTION99.04
5.7-7.170.25632020.2162745X-RAY DIFFRACTION99.9
7.17-29.670.1349990.20952928X-RAY DIFFRACTION98.95

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