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- PDB-8ukh: Crystal structure of Plasmodium falciparum CelTOS in complex with... -

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Basic information

Entry
Database: PDB / ID: 8ukh
TitleCrystal structure of Plasmodium falciparum CelTOS in complex with antibody 4h12
Components
  • 4h12 heavy chain
  • 4h12 light chain
  • Cell traversal protein for ookinetes and sporozoites
KeywordsCELL INVASION / transmission-blocking / membrane disruption
Function / homologyCell-traversal protein for ookinetes and sporozoites / Cell-traversal protein for ookinetes and sporozoites / Cell traversal protein for ookinetes and sporozoites
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsTang, W.K. / Tolia, N.H. / Urusova, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2024
Title: Multistage protective anti-CelTOS monoclonal antibodies with cross-species sterile protection against malaria.
Authors: Tang, W.K. / Salinas, N.D. / Kolli, S.K. / Xu, S. / Urusova, D.V. / Kumar, H. / Jimah, J.R. / Subramani, P.A. / Ogbondah, M.M. / Barnes, S.J. / Adams, J.H. / Tolia, N.H.
History
DepositionOct 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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: Cell traversal protein for ookinetes and sporozoites
B: Cell traversal protein for ookinetes and sporozoites
C: Cell traversal protein for ookinetes and sporozoites
D: Cell traversal protein for ookinetes and sporozoites
H: 4h12 heavy chain
I: 4h12 heavy chain
J: 4h12 heavy chain
K: 4h12 heavy chain
L: 4h12 light chain
M: 4h12 light chain
N: 4h12 light chain
O: 4h12 light chain


Theoretical massNumber of molelcules
Total (without water)259,71212
Polymers259,71212
Non-polymers00
Water19811
1
A: Cell traversal protein for ookinetes and sporozoites
B: Cell traversal protein for ookinetes and sporozoites
H: 4h12 heavy chain
I: 4h12 heavy chain
L: 4h12 light chain
M: 4h12 light chain


Theoretical massNumber of molelcules
Total (without water)129,8566
Polymers129,8566
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cell traversal protein for ookinetes and sporozoites
D: Cell traversal protein for ookinetes and sporozoites
J: 4h12 heavy chain
K: 4h12 heavy chain
N: 4h12 light chain
O: 4h12 light chain


Theoretical massNumber of molelcules
Total (without water)129,8566
Polymers129,8566
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.689, 59.728, 153.445
Angle α, β, γ (deg.)82.070, 82.200, 72.270
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Cell traversal protein for ookinetes and sporozoites


Mass: 18675.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1216600 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5P1
#2: Antibody
4h12 heavy chain


Mass: 23029.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody
4h12 light chain


Mass: 23222.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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

Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium acetate and 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 23861 / % possible obs: 97 % / Redundancy: 1.98 % / Biso Wilson estimate: 38.54 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.28
Reflection shellResolution: 3.52→3.62 Å / Num. unique obs: 2292 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→19.86 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 36.5628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2935 1212 5.08 %
Rwork0.2676 22645 -
obs0.269 23857 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.73 Å2
Refinement stepCycle: LAST / Resolution: 3.52→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14752 0 0 11 14763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002415080
X-RAY DIFFRACTIONf_angle_d0.648820511
X-RAY DIFFRACTIONf_chiral_restr0.06252358
X-RAY DIFFRACTIONf_plane_restr0.00472601
X-RAY DIFFRACTIONf_dihedral_angle_d6.63052042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.52-3.660.31121410.29792318X-RAY DIFFRACTION92.44
3.66-3.820.32631430.2932525X-RAY DIFFRACTION97.34
3.82-4.020.36621460.28432530X-RAY DIFFRACTION96.54
4.02-4.270.30341400.26912552X-RAY DIFFRACTION98.18
4.27-4.60.27331360.24532554X-RAY DIFFRACTION98.53
4.6-5.050.27531290.24772532X-RAY DIFFRACTION97.76
5.05-5.770.28861220.26582539X-RAY DIFFRACTION98.26
5.77-7.210.30091360.28952571X-RAY DIFFRACTION98.8
7.21-19.860.21841190.24412524X-RAY DIFFRACTION96.18
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)
10.03004570402460.00908996937691-0.03966673922170.0137769359845-0.02198061945850.06438332000610.06376267996840.00656135614716-0.0727434505206-0.107137647293-0.06527252664280.09728678137270.144322974477-0.09429483245220.0008325649230360.821428871699-0.06097239260520.03189407130491.035179486220.2042622968620.61576894714341.800618842226.6533389701-21.72333006
20.02461069865590.0120122863537-0.03472025399050.0273074625474-0.03723024889490.0647278628520.0234583456653-0.06073285856630.05723846881770.04012634304140.0378455088706-0.0501625768522-0.1235494070080.06936454409860.001371169289740.975472544110.001026877745630.03471266020161.02427652655-0.01221330229190.54516392680732.711446311720.2097158148-15.381522411
30.1971281266930.0367942211892-0.2554307370250.0145927557528-0.05808112767350.349710456061-0.1284164772230.20526534388-0.202098691475-0.166246363513-0.05759270397450.1281565867150.310095570964-0.134453975348-0.03758039592890.375773846988-0.0198094698709-0.09206996249580.2854590372160.08341587174740.873341842978-52.7585438813-29.4139512013-97.6316697327
40.04859116400330.0211069270813-0.1042245239850.0217820284233-0.0572736585210.230676777971-0.09908258088-0.1446553788050.07254168814960.121676195162-0.0575104621488-0.247222815508-0.1848285434480.349771257501-0.006267631094640.33343451745-0.02683845889640.0171187870530.29477481868-0.006171387330940.803055032311-61.3485791288-35.6794243393-90.7929665076
50.02941059361240.0127624398063-0.02700600688430.06685017527380.03101683816050.1077797878920.0202552179811-0.0335331784443-0.0573744192845-0.0298080578338-0.05631389217530.0213372845281-0.0200484548620.06229824434070.0005113811587560.909441715144-0.02880476690550.04679409038731.18665299966-0.03519733913710.26624390898471.078144631862.0853281079-3.09204240965
60.074068937188-0.0147778573153-0.0215977082710.100635343637-0.01131153849080.2128896617170.007409828534420.0309923627997-0.0117297984447-0.101848095291-0.0512612503337-0.06326726642940.08482147254970.111374201803-0.01118348571290.9432747133480.02701570417960.005575934867860.9999850295670.07043506866810.261447757913-9.473541912923.08808434931-33.9311089649
70.082228746191-0.0526265410259-0.03235152117550.2218949174020.02383224433530.06299053480770.03367026740110.0184870634997-0.04556902579740.0902679493333-0.01506107778170.09786250482680.01427377913290.07709888435290.1191729594670.138377012954-0.105440279458-0.114715488459-0.146191735066-0.1089667932181.04204956891-23.33435734185.62397767875-78.6451611725
80.313616202768-0.0483128336438-0.1408621556250.150187356547-0.1442694947810.2578976645220.06687872182660.3210993001960.0787126947623-0.09377221154710.0468678611317-0.100696693851-0.0741534245464-0.1793598511890.2384900456170.0278656986467-0.265538065946-0.143414544437-0.277295060808-0.07690656693171.06808966879-103.859024841-53.2022957184-109.741657578
90.05349114792630.03972576420450.004782648018440.108214603667-0.05021693138150.0113531190179-0.0895855640106-0.0393711257125-0.03537559413420.1448128539860.0326944986939-0.138771921159-0.02886314950440.1549699147290.007573898353111.124489781430.0790242292423-0.000900080749961.200528452760.03693237301630.23914297178381.842659317849.75806397453.42329093723
100.0314351264056-0.00106790826702-0.01309285669510.0369704031284-0.009413871202230.003765608327270.05021118917710.107624010514-0.0681898097772-0.0187737560732-0.07623490433830.02543177289260.137073884377-0.0285593891378-0.003871683232851.020803956120.06145064453810.026533449061.111764693450.01666235853980.243062815537-1.08803765195-11.0065589754-40.4876859289
110.172705649666-0.0603285248567-0.04052227354560.194083195241-0.09170866227990.05942839482840.0175432002238-0.154777093202-0.1420048067810.204831259370.015360683171-0.0735576847831-0.1174294416480.1032998118610.01211722702930.281494903676-0.121278587746-0.03669979176190.1456275787590.028701499890.887936339852-12.5824616463-6.65455552002-72.1955763308
120.268207048573-0.06632338255-0.2162154752050.239817479375-0.2110087997880.5428562662730.07332776262590.200655788647-0.172789743386-0.08347840188240.0375986754537-0.0372818135950.167103722404-0.2476687497570.1635358848110.195691082830.1013489756750.02547946733790.129485231778-0.08077248706581.04678889574-95.3081369128-67.160366984-116.067615369
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AA60 - 1161 - 57
22chain 'B'BB60 - 1151 - 56
33chain 'C'CC59 - 1161 - 58
44chain 'D'DD59 - 1161 - 58
55chain 'H'HE1 - 2171 - 217
66chain 'I'IF1 - 2171 - 217
77chain 'J'JG1 - 2171 - 217
88chain 'K'KH1 - 2181 - 218
99chain 'L'LI1 - 2101 - 210
1010chain 'M'MJ1 - 2101 - 210
1111chain 'N'NK1 - 2101 - 210
1212chain 'O'OL1 - 2101 - 210

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