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- PDB-8ezk: Pfs25 in complex with transmission-reducing antibody AS01-04 -

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Basic information

Entry
Database: PDB / ID: 8ezk
TitlePfs25 in complex with transmission-reducing antibody AS01-04
Components
  • 25 kDa ookinete surface antigen
  • Transmission-reducing antibody AS01-4, single-chain Fv
KeywordsIMMUNE SYSTEM / Pfs25 / transmission-blocking vaccine
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane
Similarity search - Function
Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
25 kDa ookinete surface antigen
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShukla, N. / Tang, 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)1ZIAAI001236 United States
CitationJournal: Npj Vaccines / Year: 2023
Title: A human antibody epitope map of the malaria vaccine antigen Pfs25.
Authors: Shukla, N. / Tang, W.K. / Coelho, C.H. / Long, C.A. / Healy, S.A. / Sagara, I. / Miura, K. / Duffy, P.E. / Tolia, N.H.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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: 25 kDa ookinete surface antigen
B: 25 kDa ookinete surface antigen
H: Transmission-reducing antibody AS01-4, single-chain Fv
I: Transmission-reducing antibody AS01-4, single-chain Fv


Theoretical massNumber of molelcules
Total (without water)95,1714
Polymers95,1714
Non-polymers00
Water34219
1
A: 25 kDa ookinete surface antigen
H: Transmission-reducing antibody AS01-4, single-chain Fv


Theoretical massNumber of molelcules
Total (without water)47,5852
Polymers47,5852
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 25 kDa ookinete surface antigen
I: Transmission-reducing antibody AS01-4, single-chain Fv


Theoretical massNumber of molelcules
Total (without water)47,5852
Polymers47,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.250, 91.720, 122.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 0 through 171)
d_1ens_2(chain "H" and resid 0 through 254)
d_2ens_2(chain "I" and (resid 0 through 123 or resid 144 through 254))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYTHRA1 - 172
d_21ens_1GLYTHRB1 - 172
d_11ens_2GLYTHRC1 - 235
d_21ens_2GLYGLYD2 - 125
d_22ens_2SERTHRD127 - 237

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.884638489217, -0.441966824218, -0.148593639453), (-0.456131234231, 0.754149950979, 0.472442746371), (-0.0967421343293, 0.485719237553, -0.868744946297)-32.163275608, -10.3187947746, -56.7319570988
2given(-0.87560398511, -0.468600487287, -0.117180393303), (-0.464883264267, 0.751665890423, 0.467848201642), (-0.131153390593, 0.464124953531, -0.876006173292)-30.5206628385, -10.7395313158, -57.324792199

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Components

#1: Protein 25 kDa ookinete surface antigen / Pfs25


Mass: 20033.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote)
Strain: isolate NF54 / Plasmid: pHL-Sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P13829
#2: Antibody Transmission-reducing antibody AS01-4, single-chain Fv


Mass: 27552.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-Sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium thiocyanate, 23% PEG 3350. Cryoprotected in 30% MPD

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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: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→38.06 Å / Num. obs: 34702 / % possible obs: 99.75 % / Redundancy: 7.9 % / Biso Wilson estimate: 50.85 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.04285 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 3380 / CC1/2: 0.694 / CC star: 0.905 / Rpim(I) all: 0.5615 / % possible all: 98.66

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PHB

6phb


Resolution: 2.3→38.06 Å / SU ML: 0.3172 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 1998 5.76 %
Rwork0.2291 32689 -
obs0.2308 34687 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.26 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6157 0 0 19 6176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416269
X-RAY DIFFRACTIONf_angle_d0.80448492
X-RAY DIFFRACTIONf_chiral_restr0.0503956
X-RAY DIFFRACTIONf_plane_restr0.00511097
X-RAY DIFFRACTIONf_dihedral_angle_d10.82572298
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.46190296923
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.809807968422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.39621390.41032272X-RAY DIFFRACTION98.29
2.36-2.420.38981400.35382285X-RAY DIFFRACTION99.51
2.42-2.490.34821410.3152295X-RAY DIFFRACTION99.84
2.49-2.570.28991400.29712304X-RAY DIFFRACTION99.92
2.57-2.660.33531410.28782303X-RAY DIFFRACTION99.92
2.66-2.770.30121410.2882316X-RAY DIFFRACTION99.88
2.77-2.90.27371420.28692316X-RAY DIFFRACTION99.88
2.9-3.050.33171420.26692326X-RAY DIFFRACTION99.96
3.05-3.240.26741420.26812317X-RAY DIFFRACTION99.84
3.24-3.490.30921430.25392345X-RAY DIFFRACTION100
3.49-3.840.26591440.2242347X-RAY DIFFRACTION100
3.84-4.40.2421450.18732372X-RAY DIFFRACTION99.88
4.4-5.540.19431450.17572380X-RAY DIFFRACTION99.92
5.54-38.060.21961530.19342511X-RAY DIFFRACTION99.89
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)
11.24960285547-0.327403023558-0.9081448670991.77040416936-0.9099721334322.479143771330.00238478774728-0.04299755656260.1742506512450.11636450712-0.0199053833287-0.102317154447-0.2505652414850.186160653624-0.165190984320.408830180149-0.0255957186185-0.007581207693180.5220734525660.06401139725920.603150858299-35.435451057328.6509555642-27.3764827582
22.490279548120.988013498203-0.2112060609982.52726237261-0.3560987128072.13510022331-0.008000761087920.347060849319-0.207662836229-0.457083893423-0.02745341239880.03097017038690.1829556206550.260375180356-0.05938261305460.5530885907880.07979216911610.130723133090.723257162620.1044602956720.660863753566-28.628518869522.1352646172-45.5636022496
31.074357308421.01767847764-1.358856971440.881415395578-1.16830292971.49398700858-0.957625244404-0.296355649973-0.996920595230.02509072854120.125359444436-0.3657103861860.921885699285-0.3150843421330.04372201864390.8279975221880.0981781199040.2567899319320.757435393189-0.03121983362241.07737763428-39.65081138035.98824809378-35.9373770128
41.074347644921.16685787497-1.453392192511.14309842481-1.161994273272.88117342097-0.182983549328-0.09598217524650.2604331967480.3663300481680.151257215294-0.0712846367046-0.271820182646-0.506410885920.08303204338650.4978206901830.02117229471720.04414866957740.4865094143430.01293265154460.511525478694-10.36539904970.292455862544-15.6630866877
52.548416314060.0489688453920.06063466701032.70831989089-0.2726463253492.791118294510.07644782431840.01398974898860.0792136297852-0.30190392038-0.0721842073185-0.0658877749011-0.493827452193-0.325376953869-0.03541918528420.6006047661180.04742675381760.009821177974670.4986509493610.01414405659050.567710628721-7.5046452204618.6569163224-19.8639824323
60.2467541554250.6898988141740.008916049071493.047903092590.3586953827280.01184052871410.2355634046990.2590625895570.382178067451-0.424219358455-0.1090068557870.493087097274-0.72085680074-0.376560943059-0.1742136761661.113520699470.2978897022280.04610939530140.699553550069-0.02373965958060.852652158844-9.4297839920832.8684597764-14.6686552244
70.141876056430.35423337707-0.09220265910162.92988371027-0.8442274542350.1348874700780.360545011428-0.125424741330.5816139234621.50345483640.03568397977090.539747778671-0.63973189143-0.5109161820510.07191088467050.6496859360170.1206706388540.239400467740.6961367385760.03751176869820.802053035001-11.716735239312.8104974058-3.48368961685
81.825851826371.422002327960.1467622535121.088460596280.1140619050570.004995591030310.5365481678030.696812257192-0.61474178709-0.1823365394170.3669666000460.09544619462790.72754243678-0.7430504304610.08074698659590.6062817931910.0805836497327-0.1271280092881.028779723390.00919318129351.08794462731-21.60801808311.35383186461-4.7486074195
92.372168591380.751538336566-0.8221447076792.552503877931.103689176682.207883683050.127450421709-0.449014549874-0.07624095395990.2515088262370.125878640514-0.04614363876030.5045173239730.5360088193640.1706069516390.6553427268610.00909483606721-0.07747507056040.560427189380.08934016200970.658077453339-5.63048981414-5.70375663007-5.96653890399
102.213990668630.329754412921-0.1162064105053.0117653505-0.7260482824361.76572887914-0.319504876512-0.05442938815770.894950793887-0.5386689930190.226621574185-0.30104335509-0.2308109600711.191128167630.1811892761780.9549642161820.06586939082820.02203204241370.7385451162840.03077954075580.8442523342678.78582400876-4.97513103988-22.2754334551
112.69589659065-0.03242639068920.9519395781421.68352983917-0.3288230248472.620500126050.121829053622-0.1671995341520.0583021572180.100885566166-0.169128317250.04686667504590.246336640751-0.3139720586750.04625309943670.491214041073-0.02217024260950.03003733581150.435046983017-0.01760506928680.548882464829-35.91980620976.18935886256-7.28249164838
122.752304529250.04637432581190.2154717732520.8525990123690.1348239941470.5879423225860.110673645636-0.2342549151640.1649055358870.0257433553193-0.1394812409110.05518646597840.0371253524579-0.111854661072-0.01050752892250.400269671587-0.02635987271740.03460846709250.461482886918-0.04049517504340.452761874853-47.766658223412.5191331415-6.07006574259
133.07096695898-0.4234155545440.159005684282.02232404331-0.2015048294281.93442773306-0.4262976636530.7301837830350.39413153467-0.635291269904-0.35172885566-0.2440291967340.8617446215510.09199611475080.06947457523480.86212655687-0.1037065499810.06710806921070.529710196541-0.08456491800480.68940716725-2.040840253453.45416003915-47.4433123631
142.086115779760.72142218360.3231492525970.902960238681-0.1853693738332.04456549866-0.0276802825101-0.0235520939712-0.09564495794580.07091391162070.05397282531320.08145626071210.144263299765-0.09777729173370.03292378656730.594281989904-0.0100892787196-0.00655393186670.410519536587-0.02499680496160.499068526477-4.022072107999.80459738575-37.9845914603
150.5316118579510.5830444647030.4323281866310.5847973774740.0560617822722.18152050804-0.05194933226610.0992376926235-0.0971675311114-0.1776041509910.0387367841589-0.02142415657150.3818792214520.0508347772550.0401685662350.674142766578-0.03718734183850.04701740676330.488768766192-0.04964619557270.498667082206-0.7001137265348.87782467235-41.3465558014
160.4548521319730.00434767091935-0.245541410890.258742163704-0.08361345726570.08839235362470.2845407163060.344685787968-0.2552780796860.09768672593190.27168369743-0.648302040720.256333966255-0.250648622241-0.01142671292930.61243090776-0.04425684106150.02158250101990.628187345053-0.008269971536250.576865071702-1.215538399923.8669002972-48.5484365895
173.84957316956-0.00956139474084-1.11913512560.438512131721-0.03211920630811.101200349790.402766182859-0.2634305888970.6416744413260.235309412453-0.240556434811-0.290806337215-0.6330541016180.35384727919-0.1200668770360.727274471579-0.0847278504678-0.02522532440470.6373590038590.08481924836070.50253651199918.324792368330.8589466342-44.163476632
182.659452583570.697026371718-0.4343846777672.13975660671-0.962556553642.127753326920.131656551233-0.0355443095341-0.136463487592-0.2379091863540.0557482766184-0.0489851143542-0.2970490202120.0394560983832-0.04489125335860.5451885036090.03011290962960.01442268520950.435049805296-0.01861995426390.4293554644439.0067564756520.4896356471-36.5403064973
191.999687378540.656167327375-0.2491921269590.945293591981-1.098109807681.90552229741-0.1436414184040.130801225364-0.0133189913035-0.151608477427-0.1087088118280.07659085855280.1584690751170.365868492851-0.02998393192860.5673311628870.005346161887510.008270990301450.537428237842-0.004570911874610.5445401394413.806333925423.0276486032-38.9171403704
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 88 )AA0 - 881 - 89
22chain 'A' and (resid 89 through 149 )AA89 - 14990 - 150
33chain 'A' and (resid 150 through 171 )AA150 - 171151 - 172
44chain 'B' and (resid 0 through 24 )BB0 - 241 - 25
55chain 'B' and (resid 25 through 61 )BB25 - 6126 - 62
66chain 'B' and (resid 62 through 72 )BB62 - 7263 - 73
77chain 'B' and (resid 73 through 99 )BB73 - 9974 - 100
88chain 'B' and (resid 100 through 109 )BB100 - 109101 - 110
99chain 'B' and (resid 110 through 157 )BB110 - 157111 - 158
1010chain 'B' and (resid 158 through 172 )BB158 - 172159 - 173
1111chain 'H' and (resid 0 through 52 )HC0 - 521 - 53
1212chain 'H' and (resid 53 through 255 )HC53 - 25554 - 236
1313chain 'I' and (resid -1 through 25 )ID-1 - 251 - 27
1414chain 'I' and (resid 26 through 73 )ID26 - 7328 - 75
1515chain 'I' and (resid 74 through 118 )ID74 - 11876 - 120
1616chain 'I' and (resid 119 through 150 )ID119 - 150121 - 133
1717chain 'I' and (resid 151 through 165 )ID151 - 165134 - 148
1818chain 'I' and (resid 166 through 191 )ID166 - 191149 - 174
1919chain 'I' and (resid 192 through 254 )ID192 - 254175 - 237

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