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- PDB-8ezl: Pfs25 in complex with transmission-reducing antibody AS01-50 -

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Basic information

Entry
Database: PDB / ID: 8ezl
TitlePfs25 in complex with transmission-reducing antibody AS01-50
Components
  • 25 kDa ookinete surface antigen
  • Transmission-reducing antibody AS01-50, 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 NF54 (eukaryote)
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

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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 AS01-50, single chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9763
Polymers49,7552
Non-polymers2211
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-2 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.610, 55.750, 86.090
Angle α, β, γ (deg.)90.000, 103.629, 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 NF54 (eukaryote) / Strain: isolate NF54 / Plasmid: pHLSec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P13829
#2: Antibody Transmission-reducing antibody AS01-50, single chain Fv


Mass: 29721.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum NF54 (eukaryote) / Strain: isolate NF54 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M lithium chloride, 0.1M HEPES pH 7.5, and 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033132 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033132 Å / Relative weight: 1
ReflectionResolution: 2.3→46.8 Å / Num. obs: 18026 / % possible obs: 98.29 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.35 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.03684 / Net I/σ(I): 14.13
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1731 / CC1/2: 0.815 / Rpim(I) all: 0.3006 / % possible all: 94.75

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Processing

Software
NameVersionClassification
PHENIX1.14.3260refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PHB

6phb


Resolution: 2.3→46.8 Å / SU ML: 0.3389 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.6157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 1802 10 %
Rwork0.2155 16223 -
obs0.2195 18025 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 14 54 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223326
X-RAY DIFFRACTIONf_angle_d0.51474500
X-RAY DIFFRACTIONf_chiral_restr0.043510
X-RAY DIFFRACTIONf_plane_restr0.0034577
X-RAY DIFFRACTIONf_dihedral_angle_d9.4761224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.38031300.36071165X-RAY DIFFRACTION93.5
2.36-2.430.36121380.30241249X-RAY DIFFRACTION99.28
2.43-2.510.32131400.28251257X-RAY DIFFRACTION99.22
2.51-2.60.28761390.27351255X-RAY DIFFRACTION99.36
2.6-2.70.33391370.28641229X-RAY DIFFRACTION98.34
2.7-2.830.3751370.28611238X-RAY DIFFRACTION98.5
2.83-2.980.29261400.28141252X-RAY DIFFRACTION99
2.98-3.160.3091380.24711246X-RAY DIFFRACTION97.95
3.16-3.410.25361390.24481254X-RAY DIFFRACTION99.43
3.41-3.750.24411420.19551274X-RAY DIFFRACTION98.61
3.75-4.290.21941370.17491234X-RAY DIFFRACTION97.23
4.29-5.40.1931390.15621259X-RAY DIFFRACTION98.59
5.41-46.80.24261460.19191311X-RAY DIFFRACTION98.85
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)
17.54624410069-2.81928942286-0.3690087394983.432776375463.88590646436.563079308580.174125256584-0.424491831421-0.1415408627560.200521310647-0.07401358347570.2438997222490.348580564739-0.3545823501230.2075655744160.348975920723-0.033191737090.04671928190790.537631490364-0.02414273959970.515083912442-4.35011573956-30.708376122729.3669751394
20.811365770417-0.6244340742561.80956103391.207895599682.248933708437.48600647348-0.176279207405-0.1361440606880.0523461749733-0.0168417101072-0.04447659961140.0815355146058-0.506034143974-0.3385499109560.1848350727570.3882740093260.004604370465160.02323121402210.4185447735430.02540930692760.5152397763930.563451631929-19.770258077540.4879940205
35.83208248635-2.337739148030.2401991981484.26705942594.938336586957.784755493320.0621578604523-0.187352879682-0.8700714320870.2418468110480.15729933527-0.2710756140970.556356570410.715656999946-0.1837077607590.5456580572470.02347950399060.001463942572040.549141259994-0.002265288013560.42759491131412.1951283072-23.438564759839.9572296696
47.42109645126-1.287000733622.479404233242.32312830483-0.2487424649053.70363997575-0.1394681225780.335869321470.0354168079363-0.1736734916980.0250443991606-0.114339041637-0.1064562143910.03480455734110.06760252038070.331683902023-0.03819210185770.06150383119360.25752830365-0.03307554169630.4722622338739.38181526023-28.016685621220.9418224072
55.53831931456-6.145872576686.894464669357.04456057801-7.812072607738.86434287843-0.2074988371471.22376423769-0.00490179593519-0.4561639865790.105435557847-0.265407331443-1.000361781880.07355864701040.1638502294460.8619578636490.016430481207-0.09138248342210.7736044975160.03480644743280.736961911113-13.2156042914-13.736568011912.6278803129
65.54464132292-0.9355387565250.2570010470044.30680413813-0.9877199114523.057925111050.06930331591530.240681811922-0.103340792991-0.074489418875-0.0426504206841-0.1038481531910.1306112657370.1537727115040.04038122280780.277676731970.008928512145530.03149031190530.34459469264-0.0001425940400650.31837963756828.6596639555-21.661026354861.8081313714
76.45415165681-1.295849984543.36822315721.67668960304-0.8172299682134.260699362060.0693076092207-0.0475660484586-0.223908563862-0.126314290759-0.02016670089680.03094628216880.115570761561-0.0257684535083-0.08158500642790.324323768106-0.008754600792150.05268746630080.278592924271-0.01675367671970.29713936776617.7575777901-25.864376597662.6863615776
83.495911317850.7365454104710.7548626176812.35437586532-1.410242232322.967902830550.0343991372735-0.228885747421-0.0583790220617-0.01372639061490.004378664689650.02352334677550.155198982292-0.221981472225-0.08673377807120.3048330187360.02731496547130.01926749531790.424113466358-0.03758548677690.33930653406111.4047022305-30.488151171472.6148021889
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 10 )AA-1 - 101 - 12
22chain 'A' and (resid 11 through 72 )AA11 - 7213 - 74
33chain 'A' and (resid 73 through 88 )AA73 - 8875 - 90
44chain 'A' and (resid 89 through 163 )AA89 - 16391 - 165
55chain 'A' and (resid 164 through 174 )AA164 - 174166 - 176
66chain 'H' and (resid 1 through 84 )HB1 - 841 - 84
77chain 'H' and (resid 85 through 128 )HB85 - 12885 - 128
88chain 'H' and (resid 129 through 270 )HB129 - 270129 - 254

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