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Basic information

Entry
Database: PDB / ID: 9bjg
TitleCrystal structure of broadly neutralizing human monoclonal antibody 75B10 in complex with AMA1
Components
  • 75B10 Fab Heavy Chain
  • 75B10 Fab Light Chain
  • Apical membrane antigen 1
KeywordsSTRUCTURAL PROTEIN / Apical membrane antigen 1 / Plasmodium / Malaria / Antigen-Antibody complex
Function / homology
Function and homology information


apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Domain/homology
Apical membrane antigen 1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPatel, P.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)1ZIAAAI001236 United States
CitationJournal: Cell Rep Med / Year: 2025
Title: A strain-transcending anti-AMA1 human monoclonal antibody neutralizes malaria parasites independent of direct RON2L receptor blockade.
Authors: Patel, P.N. / Diouf, A. / Dickey, T.H. / Tang, W.K. / Hopp, C.S. / Traore, B. / Long, C.A. / Miura, K. / Crompton, P.D. / Tolia, N.H.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apical membrane antigen 1
H: 75B10 Fab Heavy Chain
L: 75B10 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)89,9683
Polymers89,9683
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-21 kcal/mol
Surface area31550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.236, 93.236, 228.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Apical membrane antigen 1 / Merozoite surface antigen


Mass: 39655.469 Da / Num. of mol.: 1 / Mutation: T64A, T188A, S273A, S323A, S324A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1133400 / Plasmid: pHL-sec / Cell (production host): Kidney (Embryonic) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q7KQK5
#2: Antibody 75B10 Fab Heavy Chain


Mass: 26511.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-sec / Cell (production host): Kidney (Embryonic) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody 75B10 Fab Light Chain


Mass: 23800.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHL-sec / Cell (production host): Kidney (Embryonic) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe author states that all N-linked glycosylation sites (NXS/T) were modified by substituting the ...The author states that all N-linked glycosylation sites (NXS/T) were modified by substituting the serine or threonine residue with an alanine residue to prevent N-linked glycosylation.

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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M calcium acetate, 0.1 M Imidazole, 20% PEG 1000

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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 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→19.88 Å / Num. obs: 26126 / % possible obs: 92.3 % / Redundancy: 10.1 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.2585 / Rpim(I) all: 0.08541 / Rrim(I) all: 0.2725 / Net I/σ(I): 4.5
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 10 % / Rmerge(I) obs: 1.594 / Mean I/σ(I) obs: 0.59 / Num. unique obs: 1954 / CC1/2: 0.573 / CC star: 0.854 / Rpim(I) all: 0.5225 / Rrim(I) all: 1.679 / % possible all: 77.49

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Processing

Software
NameVersionClassification
SERGUIdata collection
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487phasing
Cootmodel building
PHENIX1.21_5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.88 Å / SU ML: 0.3643 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 22.8581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 1843 7.64 %
Rwork0.1987 22288 -
obs0.2013 24131 92.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 0 15 5593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385714
X-RAY DIFFRACTIONf_angle_d0.58747757
X-RAY DIFFRACTIONf_chiral_restr0.0448841
X-RAY DIFFRACTIONf_plane_restr0.00451011
X-RAY DIFFRACTIONf_dihedral_angle_d5.1523768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.36511180.31741400X-RAY DIFFRACTION77.49
2.98-3.070.32281200.29451490X-RAY DIFFRACTION81.89
3.07-3.160.3221320.28191570X-RAY DIFFRACTION85.06
3.16-3.280.311440.25971599X-RAY DIFFRACTION88.52
3.28-3.410.29331380.25291695X-RAY DIFFRACTION92.86
3.41-3.560.25691400.22651740X-RAY DIFFRACTION93.86
3.56-3.750.25181410.20071734X-RAY DIFFRACTION94.27
3.75-3.980.24741480.19311784X-RAY DIFFRACTION96.6
3.98-4.290.2141440.16791802X-RAY DIFFRACTION96.91
4.29-4.710.18051540.14591805X-RAY DIFFRACTION97.46
4.71-5.380.16791540.15211857X-RAY DIFFRACTION98.24
5.38-6.730.1941520.18651858X-RAY DIFFRACTION97.48
6.74-19.880.20941580.18881954X-RAY DIFFRACTION97.82
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)
13.117381746521.1734867941-1.630153516025.95496340225-1.864838669524.872143265970.0243139499294-0.451015509379-0.02584897032560.531609753808-0.227552572544-0.344741012149-0.01985374573611.003715204910.1715967703580.3899250369350.0385714158047-0.05822623769690.671136123964-0.06458168139020.336217245262-39.29434.41235.296
24.21865881102-0.2543705596020.240751640096.22495765631.372283911076.48588553501-0.07606877083880.05156042377390.708636183161-0.3659097669540.0181661161042-0.141228210391-0.8409365739940.01074851820360.02951681400170.302014404918-0.0402482146897-0.09947445055990.471258850207-0.02168523378130.327206985941-43.31338.58214.674
32.995593257710.08657806013160.6925899668025.22279970319-0.3244602801933.08824963538-0.1587055419830.184815955004-0.199502417357-0.06611025694310.100061930845-0.236755644866-0.1509730231390.2422739932670.02277032072820.264844320136-0.00594172543840.01341504989090.504342121115-0.05813464278810.27999273603-39.84334.51619.808
42.991780127880.0566539556724-1.192544376924.542293149280.08276318781964.218824608310.0600400849227-0.4999135570680.04636049469560.671324483848-0.1035610294560.1028978971380.1941860199470.01082950554730.0727027902670.4023384563590.00199827654226-0.02394266887660.576449409598-0.0640316657480.274196920425-54.06331.93439.731
55.705142665874.87654101931.493075834056.342234241962.086188382181.81906082236-0.005437279769170.0854305448401-0.3634454016790.14625023176-0.0810553589997-0.3546621154850.0976607498704-0.05397174923640.0536005599350.444246649270.04407758894880.02476837797870.4108985109410.055068183710.303854434714-52.4826.8416.682
68.22166797798-0.3014633354471.926929508117.4038045860.05610176211365.592582731610.452935615472-0.4350172615010.0296144596280.11897709231-0.2614633750330.4232350909360.866161618922-0.184940674638-0.2257043714550.3816568012810.0004441887970960.08470195453910.3210795257320.01876795214450.306969798895-61.35611.99311.054
71.061923510330.304297840790.4683459466382.183022743692.32381774313.048391613390.111841252073-0.0627029325156-0.102669326680.115818646567-0.1141073311140.1006530197930.239023795877-0.1339908296640.0274816015120.2808715371530.02167440772860.03742718004630.292051789330.07588438163660.358617067556-61.4436.17-2.098
82.390369373621.16036515729-0.4360404598583.85664007114-1.162472137834.94094590444-0.07031737391690.319544936731-0.347330307339-0.455322946661-0.0938437671253-0.3099482589150.4519720164460.3445470286550.07988907747140.4832705828080.083678315858-0.004130098154020.380407308387-0.01450195918030.435311200728-62.265-0.807-23.389
94.85410712849-2.781622187231.253530885082.388053481461.488921483685.95455434492-0.253191463363-0.173561774399-0.0465914001154-0.0719076919705-0.2529769849760.344959770044-0.253222693663-0.5022123328790.5418333824050.29213328731-0.0420629203416-0.03585599742770.268444861433-0.0512981216530.387423764892-67.91528.4550.725
103.288107304661.104487300291.638789096523.86002351453-0.8590261404994.22999723739-0.08302390886840.4316907140720.319399503242-0.733712401652-0.0307171910286-0.428379486282-0.2685969038090.8446525186650.1390820892190.3510057738880.003094265651180.03278486812070.4484129800870.05230609634890.358981206717-55.42426.553-1.737
112.37399637455-0.2910182271570.2080044584963.674517375241.339257020335.42310961498-0.04074331972790.0488822894920.395524942672-0.20722632401-0.3327351198220.0976938618295-0.789434138214-0.03687879597450.3970642005030.3608885521970.0171361900496-0.0323115269950.306026765938-0.01802081742890.391643719928-62.97230.021-3.101
122.935034071370.33909518132-0.9703291823096.366708923580.2585047440372.0373410515-0.08590776067120.0968914464116-0.00096704586980.12692825018-0.2886211525320.8255730365470.273849276509-1.434969512810.4080893022970.2533331592180.002335926171930.05909583983720.6192131224680.001560275640590.360050140914-67.06921.5138.915
135.03498100841.724145991210.2980798721794.706295273533.473094858834.69786325638-0.38439191951-0.554492992441.19601986855-0.5781439197090.1960096006940.548923869741-0.513619991179-0.3703435443430.1524782744350.7058817945750.165889579231-0.181083508110.478925530632-0.06494979220330.631895868109-69.10124.658-22.003
142.851004867343.072311870340.9520638624744.098163495691.439433519852.10268718335-0.0249663008870.237546451940.196999471766-0.533876302241-0.01954893601740.647201952093-0.0202628763966-0.01206829241020.09743078452780.5222869901790.0785026322827-0.107451790750.570577294050.008702365183090.445699055333-75.1514.356-27.568
153.403179281742.450907310880.5024032524817.10116304050.133467185813.33904590299-0.04372900115010.4939500451860.157729721938-0.9601409457020.005144316406660.9710215981410.258300567211-0.482139516790.03038992154720.5113680364930.0998590756272-0.1013442009150.614958801345-0.03413858314310.483599594586-78.5495.986-28.016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 108:144 )A108 - 144
2X-RAY DIFFRACTION2( CHAIN A AND RESID 145:201 )A145 - 201
3X-RAY DIFFRACTION3( CHAIN A AND RESID 202:297 )A202 - 297
4X-RAY DIFFRACTION4( CHAIN A AND RESID 298:438 )A298 - 438
5X-RAY DIFFRACTION5( CHAIN H AND RESID 1:33 )H1 - 33
6X-RAY DIFFRACTION6( CHAIN H AND RESID 34:60 )H34 - 60
7X-RAY DIFFRACTION7( CHAIN H AND RESID 61:178 )H61 - 178
8X-RAY DIFFRACTION8( CHAIN H AND RESID 179:229 )H179 - 229
9X-RAY DIFFRACTION9( CHAIN L AND RESID 1:38 )L1 - 38
10X-RAY DIFFRACTION10( CHAIN L AND RESID 39:61 )L39 - 61
11X-RAY DIFFRACTION11( CHAIN L AND RESID 62:90 )L62 - 90
12X-RAY DIFFRACTION12( CHAIN L AND RESID 91:102 )L91 - 102
13X-RAY DIFFRACTION13( CHAIN L AND RESID 103:113 )L103 - 113
14X-RAY DIFFRACTION14( CHAIN L AND RESID 114:150 )L114 - 150
15X-RAY DIFFRACTION15( CHAIN L AND RESID 151:212 )L151 - 212

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