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- PDB-7ua2: Pfs230 D1 domain in complex with 230AL-18 -

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Basic information

Entry
Database: PDB / ID: 7ua2
TitlePfs230 D1 domain in complex with 230AL-18
Components
  • 230AL-18
  • Gametocyte surface protein P230
  • LMIV230-01
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: 2.19 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 1.3Oct 23, 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
B: LMIV230-01
H: 230AL-18


Theoretical massNumber of molelcules
Total (without water)76,5313
Polymers76,5313
Non-polymers00
Water1,24369
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)152.650, 77.930, 58.780
Angle α, β, γ (deg.)90.000, 99.218, 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

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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: Pichia (fungus) / References: UniProt: P68874
#2: Antibody LMIV230-01


Mass: 27470.537 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: Antibody 230AL-18


Mass: 27592.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium formate, 20% 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: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→36.56 Å / Num. obs: 34043 / % possible obs: 97.2 % / Redundancy: 3 % / Biso Wilson estimate: 44.29 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.89
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 2344 / CC1/2: 0.87

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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: 2.19→36.56 Å / SU ML: 0.2895 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.7751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 1701 5 %
Rwork0.2216 32289 -
obs0.2233 33990 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.28 Å2
Refinement stepCycle: LAST / Resolution: 2.19→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 0 69 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054982
X-RAY DIFFRACTIONf_angle_d0.70876747
X-RAY DIFFRACTIONf_chiral_restr0.0493747
X-RAY DIFFRACTIONf_plane_restr0.006856
X-RAY DIFFRACTIONf_dihedral_angle_d21.9141824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.260.35561340.33352518X-RAY DIFFRACTION90.79
2.26-2.330.36841410.32012674X-RAY DIFFRACTION98.36
2.33-2.410.32511420.30552699X-RAY DIFFRACTION97.76
2.41-2.510.33681400.30792658X-RAY DIFFRACTION96.09
2.51-2.620.36361430.31232715X-RAY DIFFRACTION99
2.62-2.760.31011460.27662750X-RAY DIFFRACTION98.74
2.76-2.940.29391440.25962736X-RAY DIFFRACTION99.04
2.94-3.160.27611420.26442720X-RAY DIFFRACTION98.62
3.16-3.480.27421420.21972693X-RAY DIFFRACTION97.32
3.48-3.980.22191410.19592694X-RAY DIFFRACTION97.02
3.98-5.020.20391440.15882732X-RAY DIFFRACTION97.82
5.02-36.560.21091420.18752700X-RAY DIFFRACTION94.89
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)
12.740230951650.5252122737911.070988318332.35111037172-0.5209831488923.456371426610.19511590988-0.1216314228910.03183130300290.102991547736-0.1237766554030.00511116499403-0.0454748801282-0.0119427995319-0.09584994079780.455925152766-0.05832899549440.1223506329780.499620764903-0.1466175657470.322851991355-42.5274007784-21.588521845512.8900731221
25.86570551592-0.1794965866641.018578150652.85120118435-0.6916916633116.258491004120.122755041637-0.591788757771-0.1590521203080.0188998674670.2131632937930.5585585405610.453616408812-0.248545642745-0.3533439389730.566190427693-0.1315691325210.1279597796840.576903149929-0.09922399320120.401702161521-50.7811613439-27.456128576323.2132290449
31.986840248010.638576332060.1466253803092.30396464432-1.473377671594.044595103560.15679881172-0.5127248573040.2790537815050.492945719798-0.1289279002630.0369819307525-0.260571251875-0.0640477530465-0.1971812911980.466689309563-0.07397810898880.1061217649730.360563556023-0.09137622180810.390283164683-50.130658426-18.186361878215.3879400958
43.1413270643-1.647748112460.03177294424615.45780960921-0.4401157714814.760068709260.0737372213859-0.5491127558080.1010057002080.624887726836-0.0265431277121-0.675769184274-0.3965906592450.842545226449-0.009429790561260.43945622272-0.1701294585550.01430368396830.406776225783-0.1176436454450.634583419251-37.2220634057-13.023878808914.5826309753
51.45737984658-0.4261975862551.377842355443.45001108534-1.658225904243.719219392990.1110804472880.04513274928060.9113663960740.184078869187-0.268184056221-0.503998516328-0.3394544679180.2832932788160.1283024743150.468055365842-0.1293859843620.1283558722170.407220151816-0.1209535061650.531300541814-39.4723193873-7.895518029567.31757365025
62.97246257829-0.508306814886-0.1367794872982.50561770872-1.48769515496.35906895730.119395194124-0.5200051334830.4425476157710.3894957818430.003043882487580.068397446315-0.141146009007-0.192018504196-0.1411341588140.454372808153-0.1767054637580.1140753559720.452672354667-0.1730438698440.433026985619-46.4347561845-15.161559800615.0672824327
72.88607149875-0.3767969439280.4541604116124.26406538691-3.584873250743.008735065030.3301875630040.0202858945016-0.11992179729-0.218046808752-0.0120524144714-0.04973560883580.6030147541750.281356812683-0.03581777588950.437279653033-0.09179450941120.1031707034280.373356145313-0.07935884940740.426737535174-41.9829894054-19.54062889332.87820806143
83.47654032785-0.671174288414-0.8846582948523.648305793960.2991598288223.60074417582-0.0325897319447-0.4906122487050.09365541430560.0592952594036-0.142958052935-1.039973588240.0585725742570.7187383692880.139941996380.344474452436-0.02100291115370.0446448214540.5336763133630.08092311350340.682261441929-19.3360424011-33.40162171163.87428194809
95.13911591974-1.90406232872-3.216323558088.39415335163-2.744531844114.003492313240.153613199917-1.275258215440.4410931672421.155932917570.745619961188-0.7933131460650.3190429848160.1835463336880.7296582366831.23512902330.0963577280877-0.7568699784261.638860359260.112943768310.770825582386-12.5185123434-37.469497706531.5222148365
106.01936419769-0.8761726731-2.353277729573.823459844452.280789338625.41319463454-0.229426241025-1.49619464677-0.1205913838521.15791996460.227697961614-0.5571852349340.4703719705940.550099985779-0.05750583201260.7956616301180.0130194385717-0.298476678731.012719972850.04165051839930.674560143651-21.1870722662-32.999594492524.1210845497
113.124809627791.2163709489-3.809129022280.550247802984-1.463589604368.00152700379-0.454511956171-0.986286332413-0.2345161917250.611842176547-0.00333428511715-0.62976433440.589191066241.66958815320.4306421636331.177484270890.184460213537-0.3420876693981.135261506590.120698817530.88577151993-17.0314141423-41.262970393524.7039740661
128.00234663582-6.621132728835.615135305638.98241616102-5.693791564459.00865919108-0.2637972368060.4248771365121.271627127440.480821179575-0.642150378067-1.34191790383-0.3250123248291.556710474140.730866260440.477498297536-0.0503606388942-0.04566470991670.851375910501-0.1016229456360.641638045941-14.5491223837-31.727664912117.9464737944
134.402846386960.137486105076-0.25477120964.22686702268-0.2167795651122.38035725449-0.04934941838320.0145121989387-0.3239946967190.1190794000090.0617344559569-0.152552973494-0.0946100106272-0.0110850361729-0.04358576073810.3249367788160.01686983904030.121264234030.284815289169-0.01743807222540.257677129472-57.7129014392-44.12739902885.16717412337
146.75326817651-2.294815352020.4981390721077.58926943179-3.555614956562.44675183082-0.227553783379-0.0857284035791-0.5373717315460.0338436749641-0.474867817088-0.7571918317630.2117310300130.4807908616780.4009472024760.499484415379-0.01176256851460.1231458687280.323340959792-0.0356850762880.456249663934-54.4143174512-51.62566689028.54746915634
152.894253632570.540187740078-0.9449717994991.36661891122-0.09965587684241.843812276960.114655201988-0.1747699335470.1292357276340.1699680208789.51302404283E-50.0584467804345-0.133691042347-0.102473623375-0.1093155812420.419134500324-0.0035252699560.1104010368760.382838097949-0.002814835757150.209431507489-71.1681124532-36.630475464316.5828369275
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 559 through 594 )AA559 - 5941 - 36
22chain 'A' and (resid 595 through 607 )AA595 - 60737 - 49
33chain 'A' and (resid 608 through 639 )AA608 - 63950 - 81
44chain 'A' and (resid 640 through 656 )AA640 - 65682 - 98
55chain 'A' and (resid 657 through 676 )AA657 - 67699 - 118
66chain 'A' and (resid 677 through 719 )AA677 - 719119 - 161
77chain 'A' and (resid 720 through 732 )AA720 - 732162 - 174
88chain 'B' and (resid 1 through 155 )BB1 - 1551 - 130
99chain 'B' and (resid 156 through 168 )BB156 - 168131 - 143
1010chain 'B' and (resid 169 through 218 )BB169 - 218144 - 193
1111chain 'B' and (resid 219 through 233 )BB219 - 233194 - 208
1212chain 'B' and (resid 234 through 249 )BB234 - 249209 - 224
1313chain 'H' and (resid 1 through 76 )HC1 - 761 - 76
1414chain 'H' and (resid 77 through 91 )HC77 - 9177 - 91
1515chain 'H' and (resid 92 through 250 )HC92 - 25092 - 229

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