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- PDB-7u9w: Pfs230 D1 domain in complex with 230AS-88 -

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Basic information

Entry
Database: PDB / ID: 7u9w
TitlePfs230 D1 domain in complex with 230AS-88
Components
  • 230AS-88
  • 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: 2.79 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: 230AS-88


Theoretical massNumber of molelcules
Total (without water)48,6912
Polymers48,6912
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.800, 129.820, 73.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11H-303-

HOH

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Components

#1: Protein Gametocyte surface protein P230


Mass: 21468.346 Da / Num. of mol.: 1 / 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 230AS-88


Mass: 27223.150 Da / Num. of mol.: 1
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.: 9 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.0, 1.0 M lithium chloride, 10% PEG 6000

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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: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→19.56 Å / Num. obs: 13052 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 70.98 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.08
Reflection shellResolution: 2.79→2.87 Å / Num. unique obs: 936 / CC1/2: 0.9

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Processing

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

7jum


Resolution: 2.79→19.56 Å / SU ML: 0.3707 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1174
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 653 5.01 %
Rwork0.224 12377 -
obs0.2256 13030 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.21 Å2
Refinement stepCycle: LAST / Resolution: 2.79→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 0 9 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263187
X-RAY DIFFRACTIONf_angle_d0.53934315
X-RAY DIFFRACTIONf_chiral_restr0.0452480
X-RAY DIFFRACTIONf_plane_restr0.0035551
X-RAY DIFFRACTIONf_dihedral_angle_d10.69541176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-3.010.3621270.29532413X-RAY DIFFRACTION98.72
3.01-3.310.28731290.27592447X-RAY DIFFRACTION99.61
3.31-3.790.3121300.25662452X-RAY DIFFRACTION99.61
3.79-4.760.22331300.20722479X-RAY DIFFRACTION99.62
4.76-19.560.22941370.19682586X-RAY DIFFRACTION99.67
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)
14.455631981790.8977330287841.42711735527.301434906594.419054467252.90870514704-0.312690632342-2.11463136169-1.248281388091.664425805670.2583988585091.606291286371.10966350502-1.685207175260.02354477804261.255057178-0.1844829038930.2328146661492.06731427369-0.0554359753821.589520031124.4743652439117.950204475140.1299543595
24.20944695775-3.074520719921.712638488782.71734993143-2.149321799183.10200735857-0.309116688824-1.244570114841.147586043211.102978559350.291638398899-1.05900245818-0.298073254285-0.0139557168437-0.01677056420260.6162173056030.0612337952918-0.004892590307441.19972218165-0.2635553276261.0982523406112.160270497730.623757042437.6589243031
38.74082592518-5.449920979771.224950717746.0598005451-0.3987405930553.68486749074-0.0789893164061-0.1788670300630.004596292285750.01255464119240.08665094888810.1464437724980.1696621965830.0833171527715-0.07304776067970.297843977092-0.01111749174440.06145061062910.813064519579-0.1047677683430.8950191993938.5282126916724.142111255628.9185545007
46.91719890815-3.66577373694-0.5083803366753.755075694160.003011762835054.00151436573-0.191170290129-0.669274153443-0.4856700003710.6483920274960.2814305897411.63184282766-0.462657587303-0.419088955435-0.1777945490030.3160909823140.2095403496890.09738122004041.28674805584-0.2138516330531.164770546290.32609076686733.12025232835.9897296425
51.06978302652-0.7486200602170.1951391727694.12435283585-0.08619833597372.51293896295-0.371686664938-1.097180419160.0600960199815-0.3478822178530.8847847097240.0927273216985-0.157297462248-0.230819879653-0.4756951926710.350184830854-0.0771290428875-0.2715864261180.991289798256-0.03597136519931.3594013054250.223457181918.150821179423.3239161412
64.249572214270.1387928229950.7097364103511.34424090891-0.573171011172.52479637385-0.0534349756283-0.8977461130710.7024976755290.2344036221130.150372912899-0.337392700936-0.603387659830.01628741198510.1071747694640.2311931128730.00657408866866-0.1104134417630.975601670457-0.1897342564931.108947640139.041943118718.954214253227.5361524389
74.680815443470.5736324172460.046327150152.26442901587-0.3813982594491.151603083650.130730032019-0.508920600570.1193307054310.113850507541-0.0744675707849-0.146176422791-0.005428543881540.01866881616590.2072330885240.231834486023-0.0697937488321-0.2397343882351.01543078086-0.1462692509291.3005639919143.573219125918.18811380132.632365099
85.93295869039-0.7511933660070.8100997180893.82934125831-0.1195562440873.48436858360.0970468698489-0.3723319022990.2345265157830.551884195588-0.338505611802-0.388707267383-0.03097026160330.143199458172-0.08373137574340.298812467541-0.0814366623401-0.1291618873510.870072206298-0.1578468552741.0296018724846.043103468510.957892143125.2872396975
94.507009593880.0860005141175-0.1370628141451.637532995010.3611343849482.11556286488-0.051207348156-0.379336307810.3012054794080.27739165367-0.03770576873290.1696061399580.0225584524791-0.1014708150170.1119191859880.1031952779380.009539213908640.0142201945570.806344155435-0.1019208721931.0479897048535.287065537712.462445224919.5908745528
101.228091224850.679013576816-0.3323391232710.412675993639-0.3336343983980.814555733881-0.02543765940060.230303654659-0.478338686794-0.09698747971710.0112902691643-0.07237134400090.214703461944-0.07581232392560.07358398474010.1193681179580.045416938712-0.01978207675140.947278024981-0.1578773046671.2293174909927.78186976566.875031518378.74414310559
113.72769506973-0.9524423758191.99242462060.4518795477530.1590274452843.227978359140.3150148105320.2157640383180.263595471067-0.2042615335140.008923845732960.0697333880161-0.241251008563-0.0857383703602-0.1024654268760.267695852938-0.0408547681833-0.02148593308330.887463956846-0.1607392650881.1270488908926.745459093213.98567669478.15398727511
122.50013700952-2.38806749264-1.257687224282.275678390051.182523101942.315917085260.3176607539310.843901100588-0.0683956790118-0.525540976588-0.00761519845449-0.660082188837-0.506057926490.2342314264380.1042077627880.302657431555-0.17788261978-0.09578332711690.765209226995-0.1001648887330.93041928046932.803619153511.69437267364.32540374687
130.1697287284580.0194886933293-0.6912392633440.247689112655-0.0320850309612.7858294448-0.1724408517870.139273459266-0.520868710622-0.0592450559987-0.122619812106-0.2315430901430.2413338057360.8222944470350.327708331780.1645955288470.0694020881837-0.03818369202510.77961492598-0.1730569153880.89582163686533.1783100637.2229489262913.6633602245
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 562 through 583 )AA562 - 5831 - 22
22chain 'A' and (resid 584 through 625 )AA584 - 62523 - 64
33chain 'A' and (resid 626 through 719 )AA626 - 71965 - 158
44chain 'A' and (resid 720 through 732 )AA720 - 732159 - 171
55chain 'H' and (resid 1 through 17 )HB1 - 171 - 17
66chain 'H' and (resid 18 through 60 )HB18 - 6018 - 60
77chain 'H' and (resid 61 through 83 )HB61 - 8361 - 83
88chain 'H' and (resid 84 through 98 )HB84 - 9884 - 98
99chain 'H' and (resid 99 through 151 )HB99 - 15199 - 133
1010chain 'H' and (resid 152 through 180 )HB152 - 180134 - 162
1111chain 'H' and (resid 181 through 217 )HB181 - 217163 - 199
1212chain 'H' and (resid 218 through 232 )HB218 - 232200 - 214
1313chain 'H' and (resid 233 through 249 )HB233 - 249215 - 231

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