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- PDB-7ua8: Pfs230 D1 domain in complex with 230AL-20 -

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Basic information

Entry
Database: PDB / ID: 7ua8
TitlePfs230 D1 domain in complex with 230AL-20
Components
  • 230Al-20
  • Gametocyte surface protein P230
KeywordsCELL INVASION / antibody / Plasmodium falciparum / Pfs230 / transmission blocking
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
Gametocyte surface protein P230
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, W.K. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2023
Title: A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine.
Authors: Tang, W.K. / Coelho, C.H. / Miura, K. / Nguemwo Tentokam, B.C. / Salinas, N.D. / Narum, D.L. / Healy, S.A. / Sagara, I. / Long, C.A. / Duffy, P.E. / Tolia, N.H.
History
DepositionMar 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P230
H: 230Al-20
B: Gametocyte surface protein P230
I: 230Al-20


Theoretical massNumber of molelcules
Total (without water)97,6094
Polymers97,6094
Non-polymers00
Water1267
1
A: Gametocyte surface protein P230
H: 230Al-20


Theoretical massNumber of molelcules
Total (without water)48,8052
Polymers48,8052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gametocyte surface protein P230
I: 230Al-20


Theoretical massNumber of molelcules
Total (without water)48,8052
Polymers48,8052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.470, 165.120, 44.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2(chain "H" and resid 1 through 245)
d_2ens_2(chain "I" and (resid 1 through 119 or resid 140 through 245))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUASNA1 - 176
d_21ens_1LEUASNC1 - 176
d_11ens_2GLNILEB1 - 225
d_21ens_2GLNSERD1 - 119
d_22ens_2ASPILED122 - 227

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein Gametocyte surface protein P230


Mass: 21468.346 Da / Num. of mol.: 2 / Mutation: N585Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Komagataella pastoris (fungus) / References: UniProt: P68874
#2: Antibody 230Al-20


Mass: 27336.229 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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 Matthews: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.16 M ammonium citrate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→19.82 Å / Num. obs: 27889 / % possible obs: 97 % / Redundancy: 6.9 % / Biso Wilson estimate: 62.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.33
Reflection shellResolution: 2.8→2.96 Å / Num. unique obs: 4376 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JUM

7jum


Resolution: 2.8→19.82 Å / SU ML: 0.441 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.2422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2742 1386 5.01 %
Rwork0.2494 26271 -
obs0.2506 27657 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6332 0 0 7 6339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046468
X-RAY DIFFRACTIONf_angle_d0.83218761
X-RAY DIFFRACTIONf_chiral_restr0.0528973
X-RAY DIFFRACTIONf_plane_restr0.00611114
X-RAY DIFFRACTIONf_dihedral_angle_d16.23882399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.316561783842
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.491240565173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.40781370.38242586X-RAY DIFFRACTION96.46
2.9-3.010.36651360.36852564X-RAY DIFFRACTION96.88
3.01-3.150.36211400.33012634X-RAY DIFFRACTION97.47
3.15-3.320.32741360.30242579X-RAY DIFFRACTION97.63
3.32-3.520.31111390.28132624X-RAY DIFFRACTION97.46
3.52-3.790.30031380.25292629X-RAY DIFFRACTION97.46
3.79-4.170.27881300.23462481X-RAY DIFFRACTION91.33
4.17-4.770.24821400.19882678X-RAY DIFFRACTION98.22
4.77-5.980.21771440.20362723X-RAY DIFFRACTION98.42
5.98-19.820.21911460.23322773X-RAY DIFFRACTION95.27
Refinement TLS params.Method: refined / Origin x: -38.1071901892 Å / Origin y: 26.5556772594 Å / Origin z: -17.4629332926 Å
111213212223313233
T0.550001893658 Å2-0.0117521210015 Å20.0999521886608 Å2-0.51056114125 Å20.0558967910447 Å2--0.425956430123 Å2
L0.652359726454 °2-0.423722703864 °20.0260991588714 °2-2.78260279858 °20.674517632589 °2--2.29427997622 °2
S-0.0784618158456 Å °-0.0917974474027 Å °-0.0185029757852 Å °0.163041486417 Å °0.110440205451 Å °0.0348540302226 Å °0.0387656351166 Å °0.0562280351824 Å °-0.0603505461526 Å °
Refinement TLS groupSelection details: all

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