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- PDB-8ezm: Pfs25 in complex with transmission-reducing antibody AS01-63 -

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Basic information

Entry
Database: PDB / ID: 8ezm
TitlePfs25 in complex with transmission-reducing antibody AS01-63
Components
  • 25 kDa ookinete surface antigen
  • Transmission-reducing antibody AS01-63, Single-chain Fv
KeywordsIMMUNE SYSTEM / Pfs25 / transmission-blocking vaccine
Function / homologyOokinete surface antigen, EGF domain / Pvs28 EGF domain / side of membrane / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / cell surface / plasma membrane / 25 kDa ookinete surface antigen
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Oct 23, 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: 25 kDa ookinete surface antigen
H: Transmission-reducing antibody AS01-63, Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5425
Polymers48,1292
Non-polymers4133
Water36020
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)101.890, 84.710, 65.870
Angle α, β, γ (deg.)90.000, 96.570, 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 25 kDa ookinete surface antigen / Pfs25


Mass: 20033.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate NF54 / Plasmid: pHLSec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P13829
#2: Antibody Transmission-reducing antibody AS01-63, Single-chain Fv


Mass: 28096.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLSec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 2.2M ammonium sulfate, 0.1M sodium citrate pH 5.4

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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: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.5 Å / Num. obs: 30366 / % possible obs: 93.21 % / Redundancy: 3.5 % / Biso Wilson estimate: 59.38 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.02691 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.5 % / Num. unique obs: 2543 / CC1/2: 0.783 / Rpim(I) all: 0.3575 / % possible all: 77.68

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PHB

6phb


Resolution: 2.1→44.5 Å / SU ML: 0.3123 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.2117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 2010 6.62 %
Rwork0.2045 28342 -
obs0.2066 30352 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 24 20 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323097
X-RAY DIFFRACTIONf_angle_d0.54114181
X-RAY DIFFRACTIONf_chiral_restr0.047465
X-RAY DIFFRACTIONf_plane_restr0.0036537
X-RAY DIFFRACTIONf_dihedral_angle_d10.64811136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.37531130.33021588X-RAY DIFFRACTION73.07
2.15-2.210.30711440.29421997X-RAY DIFFRACTION91.73
2.21-2.280.35261610.29692037X-RAY DIFFRACTION95.36
2.28-2.350.38071310.29162099X-RAY DIFFRACTION96.5
2.35-2.430.33771500.28062068X-RAY DIFFRACTION95.98
2.43-2.530.30731450.25842090X-RAY DIFFRACTION96.67
2.53-2.650.2751380.24562078X-RAY DIFFRACTION95.39
2.65-2.790.29151400.2691922X-RAY DIFFRACTION88.84
2.79-2.960.3291470.2952073X-RAY DIFFRACTION96.56
2.96-3.190.31731520.24792100X-RAY DIFFRACTION96.12
3.19-3.510.24061450.21972070X-RAY DIFFRACTION95.56
3.51-4.020.1961430.18611975X-RAY DIFFRACTION91.49
4.02-5.060.16831470.15032122X-RAY DIFFRACTION96.47
5.06-44.50.22251540.18132123X-RAY DIFFRACTION95.51
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)
19.22960043563.95158295697-0.9592649489516.81459863262-3.088901945775.297050096010.202451072371-0.0521011500027-0.837190420083-0.4227856824570.311333163352-0.03646209406580.755031061654-0.218740962518-0.3378860985120.7856961508770.053411889392-0.1575662630330.677137303840.05706261821610.666824818633-36.2988891558-1.9091688917814.8469873847
29.64095124392-2.73045268725-3.851590179962.156822675490.7254092226022.127174516040.5082661911960.0407906559398-0.578813065177-0.480117367872-0.1968925900610.4290079656580.446223463809-1.2876474329-0.6457715695440.8250936588160.0163441275703-0.1519751827220.9549116905470.1841986171331.01640632506-39.0475868572-5.3888742886424.4914407427
34.39475497346-2.286421864943.250377854724.77051018245-2.530844726092.64652014780.886856542341-0.86836566123-0.7462300581430.3362269613890.3924645305160.2930394340460.607676128054-1.26263759717-0.947433643940.7798051137040.0122143318408-0.05413406362671.31195938160.07491030808970.961590105809-39.2643251006-8.7204473848740.3952048388
40.715386218965-0.4972604514481.301541054451.6713191956-3.460916401148.200113268410.3286323992420.1233544679060.159076754127-0.3613498389120.08633823257890.3558972816550.391129039720.0509403199438-0.1975320849760.5811041241920.0263899306576-0.03698791356370.7857060529820.1287366189410.615343984088-27.9189167373-5.3311452981835.4644925497
59.3996050638-2.429717322471.470432504414.59227377019-0.3858184456921.347708601470.0257944579317-0.367098903090.3493800597130.1133890189240.139324987749-0.587878036015-0.00499485395857-0.204914934235-0.1100886980160.5922170362540.06314770992950.001939337789230.60437426153-0.009810226904930.600513128879-21.52381738838.8265906360216.2160579335
62.708972483072.932925376991.385375558069.279723310930.9642367505821.10173152711-0.6198648669230.6315684702640.422485928719-1.229598577470.8285052178440.3752450040890.378325315236-0.473660452631-0.1075942174140.9655270461150.105892182584-0.05464723364750.7681764433820.106023541220.697768734557-33.80359114199.59681235585.86126970566
72.02643951068-1.939506811220.9816076303795.85392380601-0.3569990016861.659123348940.253425408880.300489345666-1.23870961284-0.0905879023258-0.3502975545041.686217331530.552934698555-0.576673963391-0.131471100340.8728779495870.0111122063369-0.1832537784530.93276885442-0.1337749308391.08969489824-47.83575386835.63015324059.84631286966
84.651975442161.861106313525.484492295582.192201761553.281220447836.11604277553-0.1640603980570.6514946484230.555801058899-0.1525541976690.1331996073190.147054519782-0.5948334179010.5827099417080.03112124808360.732433271794-0.1224127841820.06403671069780.8054177307220.2446511065950.6574279443-7.795514063395.0057385508943.0820526693
93.862164289130.9804642302331.482784397693.743571109540.1516861132922.67696817603-0.03426239305630.4680552816080.448193414588-0.00306333372724-0.1387977629610.0352173101695-0.3063293126010.2886321759770.1962971002480.49043040409-0.05130576546510.03406518408470.5232396512430.148832229860.521442612762-12.35447372.0130179173849.3505937858
103.519264704942.307431362331.020139287635.98287668346-1.538736881721.379481641430.2795520119150.2076852761250.01032390689970.016284281781-0.2507542984130.0052565227012-0.03416646970830.457105024046-0.09730269603210.5180135829960.07548469730840.05909154058440.592950204406-0.08390511975630.302671243271-2.05665095082-11.358097078157.5639799161
114.695415366360.129251180206-0.2332642838463.68752090923-1.304927298363.334922905390.07897439127990.1592396710330.124999760672-0.0442404736048-0.0535426301528-0.2044389279440.05219162482360.0235187868506-0.0185106426210.4066189248740.00465687451171-0.01834579023010.465801169002-0.001211870714810.345985606281-10.4956163434-16.440284107452.8487644726
125.3913864392-1.05442706298-0.2646982076375.307654897670.09945353872911.709270850630.07115632515480.869013339352-0.293881543169-0.391229373775-0.0191622473375-0.1302696949490.1291801324220.328091459967-0.06666796182030.5042001893590.00609234291722-0.03790955221920.637787240502-0.03385249253940.356539781774-8.29882946889-21.467052182149.4574055336
138.13423096995-6.83394735449-2.866430876655.457111029672.537428523093.03878569538-0.0182255438828-0.5755675947520.8072055898850.2796208661670.213907085461-0.305521418176-0.0601300434080.0308401972614-0.04309257576540.483880423918-0.05603458317060.02967243061960.5303535138130.03584229056910.570418453702-9.59855788722-11.279238975156.1562732714
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 24 )AA1 - 241 - 24
22chain 'A' and (resid 25 through 37 )AA25 - 3725 - 37
33chain 'A' and (resid 38 through 47 )AA38 - 4738 - 47
44chain 'A' and (resid 48 through 88 )AA48 - 8848 - 88
55chain 'A' and (resid 89 through 128 )AA89 - 12889 - 128
66chain 'A' and (resid 129 through 138 )AA129 - 138129 - 138
77chain 'A' and (resid 139 through 162 )AA139 - 162139 - 162
88chain 'H' and (resid 1 through 33 )HB1 - 331 - 33
99chain 'H' and (resid 34 through 112 )HB34 - 11234 - 112
1010chain 'H' and (resid 113 through 156 )HB113 - 156113 - 136
1111chain 'H' and (resid 157 through 190 )HB157 - 190137 - 170
1212chain 'H' and (resid 191 through 236 )HB191 - 236171 - 216
1313chain 'H' and (resid 237 through 256 )HB237 - 256217 - 236

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