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- PDB-7uvh: Pfs230 domain 1 bound by RUPA-32 Fab -

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Basic information

Entry
Database: PDB / ID: 7uvh
TitlePfs230 domain 1 bound by RUPA-32 Fab
Components
  • Gametocyte surface protein P230
  • RUPA-32 Fab Heavy Chain
  • RUPA-32 Fab Light Chain
KeywordsCELL INVASION/IMMUNE SYSTEM / Antibody-fragment / malaria transmission / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


cell surface / plasma membrane
Similarity search - Function
: / 6-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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
AMMONIUM ION / Gametocyte surface protein P230
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUPA-32 Fab Heavy Chain
B: RUPA-32 Fab Light Chain
C: Gametocyte surface protein P230
D: RUPA-32 Fab Heavy Chain
E: RUPA-32 Fab Light Chain
F: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,81623
Polymers139,9956
Non-polymers82117
Water1,58588
1
A: RUPA-32 Fab Heavy Chain
B: RUPA-32 Fab Light Chain
C: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,51014
Polymers69,9983
Non-polymers51211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RUPA-32 Fab Heavy Chain
E: RUPA-32 Fab Light Chain
F: Gametocyte surface protein P230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3069
Polymers69,9983
Non-polymers3096
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.870, 80.470, 124.960
Angle α, β, γ (deg.)90.000, 111.811, 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
Components on special symmetry positions
IDModelComponents
11D-302-

CL

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
111VALVALGLYGLY(chain 'A' and (resid 2 through 10 or resid 12...AA2 - 92 - 9
121VALVALLEULEU(chain 'A' and (resid 2 through 10 or resid 12...AA12 - 2012 - 20
131CYSCYSVALVAL(chain 'A' and (resid 2 through 10 or resid 12...AA22 - 6322 - 64
141GLYGLYASNASN(chain 'A' and (resid 2 through 10 or resid 12...AA65 - 7366 - 74
151LYSLYSTHRTHR(chain 'A' and (resid 2 through 10 or resid 12...AA76 - 11677 - 125
161GLYGLYSERSER(chain 'A' and (resid 2 through 10 or resid 12...AA118 - 128127 - 137
171GLYGLYPROPRO(chain 'A' and (resid 2 through 10 or resid 12...AA133 - 147142 - 156
181PROPROASNASN(chain 'A' and (resid 2 through 10 or resid 12...AA149 - 155158 - 164
191LEULEUTHRTHR(chain 'A' and (resid 2 through 10 or resid 12...AA159 - 160168 - 169
1101GLYGLYTHRTHR(chain 'A' and (resid 2 through 10 or resid 12...AA162 - 191171 - 200
1111TYRTYRSERSER(chain 'A' and (resid 2 through 10 or resid 12...AA194 - 203203 - 212
1121VALVALPROPRO(chain 'A' and (resid 2 through 10 or resid 12...AA207 - 213216 - 222
211VALVALGLYGLY(chain 'D' and (resid 2 through 10 or resid 12...DD2 - 92 - 9
221VALVALLEULEU(chain 'D' and (resid 2 through 10 or resid 12...DD12 - 2012 - 20
231CYSCYSVALVAL(chain 'D' and (resid 2 through 10 or resid 12...DD22 - 6322 - 64
241GLYGLYASNASN(chain 'D' and (resid 2 through 10 or resid 12...DD65 - 7366 - 74
251LYSLYSTHRTHR(chain 'D' and (resid 2 through 10 or resid 12...DD76 - 11677 - 125
261GLYGLYSERSER(chain 'D' and (resid 2 through 10 or resid 12...DD118 - 128127 - 137
271GLYGLYPROPRO(chain 'D' and (resid 2 through 10 or resid 12...DD133 - 147142 - 156
281PROPROASNASN(chain 'D' and (resid 2 through 10 or resid 12...DD149 - 155158 - 164
291LEULEUTHRTHR(chain 'D' and (resid 2 through 10 or resid 12...DD159 - 160168 - 169
2101GLYGLYTHRTHR(chain 'D' and (resid 2 through 10 or resid 12...DD162 - 191171 - 200
2111TYRTYRSERSER(chain 'D' and (resid 2 through 10 or resid 12...DD194 - 203203 - 212
2121VALVALPROPRO(chain 'D' and (resid 2 through 10 or resid 12...DD207 - 213216 - 222
112GLUGLUGLUGLU(chain 'B' and (resid 1 through 17 or resid 19...BB1 - 171 - 17
122ALAALACYSCYS(chain 'B' and (resid 1 through 17 or resid 19...BB19 - 2319 - 23
132THRTHRSERSER(chain 'B' and (resid 1 through 17 or resid 19...BB25 - 4925 - 49
142ARGARGTRPTRP(chain 'B' and (resid 1 through 17 or resid 19...BB54 - 14854 - 149
152VALVALASNASN(chain 'B' and (resid 1 through 17 or resid 19...BB150 - 152151 - 153
162GLNGLNTHRTHR(chain 'B' and (resid 1 through 17 or resid 19...BB155 - 164156 - 165
172GLNGLNSERSER(chain 'B' and (resid 1 through 17 or resid 19...BB166 - 168167 - 169
182ASPASPTHRTHR(chain 'B' and (resid 1 through 17 or resid 19...BB170 - 206171 - 207
192SERSERASNASN(chain 'B' and (resid 1 through 17 or resid 19...BB208 - 210209 - 211
212GLUGLUGLUGLU(chain 'E' and (resid 1 through 17 or resid 19...EE1 - 171 - 17
222ALAALACYSCYS(chain 'E' and (resid 1 through 17 or resid 19...EE19 - 2319 - 23
232THRTHRSERSER(chain 'E' and (resid 1 through 17 or resid 19...EE25 - 4925 - 49
242ARGARGTRPTRP(chain 'E' and (resid 1 through 17 or resid 19...EE54 - 14854 - 149
252VALVALASNASN(chain 'E' and (resid 1 through 17 or resid 19...EE150 - 152151 - 153
262GLNGLNTHRTHR(chain 'E' and (resid 1 through 17 or resid 19...EE155 - 164156 - 165
272GLNGLNSERSER(chain 'E' and (resid 1 through 17 or resid 19...EE166 - 168167 - 169
282ASPASPTHRTHR(chain 'E' and (resid 1 through 17 or resid 19...EE170 - 206171 - 207
292SERSERASNASN(chain 'E' and (resid 1 through 17 or resid 19...EE208 - 210209 - 211
113TYRTYRGLUGLU(chain 'C' and (resid 579 through 633 or resid 635...CC579 - 63328 - 82
123LEULEUPROPRO(chain 'C' and (resid 579 through 633 or resid 635...CC635 - 64384 - 92
133LYSLYSGLUGLU(chain 'C' and (resid 579 through 633 or resid 635...CC645 - 65494 - 103
143THRTHRASNASN(chain 'C' and (resid 579 through 633 or resid 635...CC656 - 677105 - 126
153LYSLYSPHEPHE(chain 'C' and (resid 579 through 633 or resid 635...CC679 - 683128 - 132
163GLUGLULYSLYS(chain 'C' and (resid 579 through 633 or resid 635...CC685 - 716134 - 165
173GLYGLYTYRTYR(chain 'C' and (resid 579 through 633 or resid 635...CC718 - 730167 - 179
213TYRTYRGLUGLU(chain 'F' and (resid 579 through 633 or resid 635...FF579 - 63328 - 82
223LEULEUPROPRO(chain 'F' and (resid 579 through 633 or resid 635...FF635 - 64384 - 92
233LYSLYSGLUGLU(chain 'F' and (resid 579 through 633 or resid 635...FF645 - 65494 - 103
243THRTHRASNASN(chain 'F' and (resid 579 through 633 or resid 635...FF656 - 677105 - 126
253LYSLYSPHEPHE(chain 'F' and (resid 579 through 633 or resid 635...FF679 - 683128 - 132
263GLUGLULYSLYS(chain 'F' and (resid 579 through 633 or resid 635...FF685 - 716134 - 165
273GLYGLYTYRTYR(chain 'F' and (resid 579 through 633 or resid 635...FF718 - 730167 - 179

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules CF

#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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Antibody , 2 types, 4 molecules ADBE

#1: Antibody RUPA-32 Fab Heavy Chain


Mass: 23767.695 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-32 Fab Light Chain


Mass: 23535.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 105 molecules

#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate, 30 % (w/v) PEG 8000, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.59→29.43 Å / Num. obs: 44577 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 61.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.065 / Rrim(I) all: 0.226 / Net I/σ(I): 9.5
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.718 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4638 / CC1/2: 0.701 / Rpim(I) all: 0.523 / Rrim(I) all: 1.833 / % possible all: 100

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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: 2.59→29.43 Å / SU ML: 0.3194 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 1999 4.49 %
Rwork0.1959 42561 -
obs0.1975 44560 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.62 Å2
Refinement stepCycle: LAST / Resolution: 2.59→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9254 0 40 88 9382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01089480
X-RAY DIFFRACTIONf_angle_d1.386512867
X-RAY DIFFRACTIONf_chiral_restr0.07251459
X-RAY DIFFRACTIONf_plane_restr0.01111641
X-RAY DIFFRACTIONf_dihedral_angle_d19.1223486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.33611420.29213021X-RAY DIFFRACTION100
2.65-2.730.32471410.27453007X-RAY DIFFRACTION100
2.73-2.810.26561430.26293042X-RAY DIFFRACTION99.94
2.81-2.90.28671410.26213007X-RAY DIFFRACTION100
2.9-30.2741430.25383031X-RAY DIFFRACTION100
3-3.120.3181420.24973028X-RAY DIFFRACTION99.94
3.12-3.260.30321410.23473002X-RAY DIFFRACTION99.87
3.26-3.430.26591420.21783027X-RAY DIFFRACTION99.94
3.43-3.650.25731440.20383066X-RAY DIFFRACTION99.94
3.65-3.930.24361410.19313023X-RAY DIFFRACTION99.97
3.93-4.320.2021430.16663042X-RAY DIFFRACTION100
4.32-4.950.18271440.14813057X-RAY DIFFRACTION99.94
4.95-6.220.18881450.17443077X-RAY DIFFRACTION99.85
6.22-29.430.20561470.18063131X-RAY DIFFRACTION99.82

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