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- PDB-8fan: Crystal structure of Ky15.1 Fab in complex with circumsporozoite ... -

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Entry
Database: PDB / ID: 8fan
TitleCrystal structure of Ky15.1 Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky15.1 Antibody, heavy chain
  • Ky15.1 Antibody, light chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / external side of plasma membrane / cytoplasm
Similarity search - Function
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBurn Aschner, C. / Thai, E. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906 United States
CitationJournal: Cell Rep / Year: 2023
Title: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.
Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / ...Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / Huntwork, R.H.C. / Bolscher, J.M. / de Bruijni, M.H.C. / Sauerwein, R. / Dennison, S.M. / Tomaras, G.D. / Zavala, F. / Kellam, P. / Wardemann, H. / Julien, J.P.
History
DepositionNov 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ky15.1 Antibody, light chain
D: Ky15.1 Antibody, light chain
F: Ky15.1 Antibody, light chain
A: Ky15.1 Antibody, heavy chain
C: Ky15.1 Antibody, heavy chain
E: Ky15.1 Antibody, heavy chain
P: Circumsporozoite protein KQPA peptide
Q: Circumsporozoite protein KQPA peptide
R: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)147,6539
Polymers147,6539
Non-polymers00
Water00
1
D: Ky15.1 Antibody, light chain
C: Ky15.1 Antibody, heavy chain
Q: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,2183
Polymers49,2183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Ky15.1 Antibody, light chain
E: Ky15.1 Antibody, heavy chain
R: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,2183
Polymers49,2183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Ky15.1 Antibody, light chain
A: Ky15.1 Antibody, heavy chain
P: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)49,2183
Polymers49,2183
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.681, 181.681, 202.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Antibody Ky15.1 Antibody, light chain


Mass: 23467.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Ky15.1 Antibody, heavy chain


Mass: 24201.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein KQPA peptide / CS / PfCSP


Mass: 1549.577 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P19597

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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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4 M ammonium sulfate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 43443 / % possible obs: 98.1 % / Redundancy: 10 % / Biso Wilson estimate: 47.16 Å2 / CC1/2: 0.98 / Net I/σ(I): 7.7
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 2146 / CC1/2: 0.655

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U6V

4u6v


Resolution: 2.9→39.34 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1403
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1999 4.6 %
Rwork0.2154 41438 -
obs0.217 43437 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9902 0 0 0 9902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002210139
X-RAY DIFFRACTIONf_angle_d0.546113798
X-RAY DIFFRACTIONf_chiral_restr0.04271549
X-RAY DIFFRACTIONf_plane_restr0.00491766
X-RAY DIFFRACTIONf_dihedral_angle_d11.14423582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39051410.31112921X-RAY DIFFRACTION99.13
2.97-3.050.33811410.29222918X-RAY DIFFRACTION99
3.05-3.140.35081410.29212934X-RAY DIFFRACTION98.97
3.14-3.240.31971430.28082950X-RAY DIFFRACTION98.94
3.24-3.360.31271410.25892927X-RAY DIFFRACTION98.74
3.36-3.490.27871410.23622938X-RAY DIFFRACTION98.59
3.49-3.650.26631400.22242921X-RAY DIFFRACTION98.84
3.65-3.850.2711430.21212948X-RAY DIFFRACTION98.44
3.85-4.090.23351410.20242932X-RAY DIFFRACTION98.15
4.09-4.40.21431440.17142967X-RAY DIFFRACTION98.14
4.4-4.840.17021430.1582965X-RAY DIFFRACTION98.01
4.84-5.540.19611440.16942975X-RAY DIFFRACTION97.65
5.54-6.980.24481440.22433009X-RAY DIFFRACTION96.9
6.98-39.340.2341520.21333133X-RAY DIFFRACTION95.94
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)
15.925627002121.14104694542-0.8997002998293.38678605512-0.9025455410664.85794518501-0.351372078429-0.802644965647-0.7165762085090.2465408047920.181284216639-0.1787986435060.7134431258670.3212638828480.1662705483420.54188342410.1053757945370.06314872351270.6503114865440.19561585170.75217477239228.38-23.453-18.773
26.18977730661-0.3202112847750.0887401085232.79936437679-1.10639619973.02584265095-0.0116430640784-0.2251087136030.773902591583-0.0680897439101-0.0589342696920.245039086469-0.3432432447580.3136401944170.04000538100110.4624934388550.0470829061006-0.02337633504520.569500645408-0.09089631905170.5445094834345.9793.945-34.872
33.654275882860.3273056784470.1426328999682.72874830463-1.172015795542.13939902902-0.0515735970832-0.04795024346030.0399157032322-0.1765675653080.1310204799120.373445053580.037171023046-0.147091597592-0.09125751971990.3399684291350.0131755975819-0.02843896461960.249723477918-0.02119491549210.23739386348487.172-16.3852.328
43.1146584603-1.380243847661.348261509093.15025786475-1.492957516452.536863709810.2790154895760.0868293391945-0.07039456453830.257177054133-0.624460077004-1.640897471290.1967779939010.6944229294320.2186311102790.4709834468920.00500583494269-0.05222723933130.4365644322360.0732400581761.06482083641120.055-17.16117.132
52.536651109531.997988688950.2170915053953.71436965901-1.383270136231.127024986180.190052134903-0.330738782890.1921311088430.296061031828-0.1081771546430.378836985334-0.272387781522-0.0117450748116-0.06235746849420.366253322638-0.06038479851730.1451315048420.350152484969-0.05745515659730.32277150039355.973-56.172-11.783
64.24898645932-1.80166692442-1.723493832423.655799180761.253031622591.94956617368-0.070337494739-0.121598640744-0.1909219728070.2390396770410.0579183030722-0.1973444659770.505570012064-0.02809577974140.03152354002760.384830266978-0.0356551513361-0.002064434492810.2627696246350.009695351213870.19695442637561.752-88.321-28.82
72.493945810740.039391529399-0.8039218135680.0982129290043-0.1663356521851.569340380260.01179795829-0.281889385278-0.2381614198460.209995337442-0.1212791079560.06392595969220.1920920572070.06627182170320.1434443150020.4849913735160.01177807198360.02196044683920.4392807493130.007659399892140.79193050508111.771-15.278-31.591
80.08259074115350.310725500334-0.2989554595173.664577277560.10515560752.99363258502-0.1828661315710.3521098953140.125029984189-0.2945022350080.01907504173720.1000743629760.3816226051730.2745505083760.130061884430.4368126743960.103468365415-0.03023496908020.609525806398-0.01060277146890.6874680019337.847-2.65-47.691
92.530569733250.7772123590420.1923611745512.70685184045-0.273467238281.31444696566-0.2214467827720.1290162776350.09013290875820.08434834221070.1932312111760.489824033372-0.0304460818399-0.1570488697690.05986969012120.3285558754260.002635036229210.02356954977090.269183204422-0.04721752609580.34074541612784.786-34.34915.765
100.7138369737430.08863611999460.274835507554.67629211332.533007732791.49529654032-0.184787585691-0.220209952399-0.05327102701451.754632191350.127988287534-0.268756334162-0.263937258712-0.03169934996660.09814279236121.024932900020.0869584914645-0.1851617308960.37480151029-0.08786564437270.613141896352110.413-20.06630.206
111.317999398971.167732268870.04236230421782.755861597-0.01904373385240.4366356931530.13493066874-0.05783034094970.241216157780.207404980342-0.1654103179330.0934032094161-0.1238853932480.00105678010470.04782788156940.285779847948-0.01397271075420.003531815404080.3073860729470.05966701404380.34039634710171.843-50.101-26.585
125.849933464160.06698887803972.230118595142.635988996440.558395239141.96833081218-0.1408177252750.2707194413070.0900755429338-0.289489431285-0.03730759899630.0232302711376-0.0511341278953-0.06755343038070.1603862326810.30038849843-0.01635017233930.02196601614310.3113937906060.01649194307980.12013074365661.818-77.484-41.381
137.281002919462.585038234714.195574112110.9273971236241.500765874982.43070905728-0.4039510796382.14883144006-1.38554608828-1.158373575310.535070565837-0.427645964155-0.3114594486930.73468640773-0.1230017676571.052256116170.2616157052130.3687740330130.887741947299-0.04051226087240.6425919430845.786-29.275-22.113
147.972892293883.89086990981-3.139792027469.41222417384-4.068722948582.36553641557-0.5456433722191.571041481730.0563148006181-0.6170620114960.5021540348481.73058680461.0732176089-0.3880400082530.03354552790560.567473158355-0.0460119566788-0.263656862480.569235560734-0.0245290980130.65412367600270.739-31.6974.963
153.92371511834-3.207407134433.532361652525.88644939032-2.756393552953.36217013034-0.291091288285-0.1902648312660.715876515930.6824336827590.1029256054780.246097234188-0.285471216205-0.2171544241210.01459853873240.393740312391-0.06753582016410.1405492549250.543644880277-0.05783713260380.47214180795666.211-36.254-14.416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:106 )B1 - 106
2X-RAY DIFFRACTION2( CHAIN B AND RESID 107:212 )B107 - 212
3X-RAY DIFFRACTION3( CHAIN D AND RESID 1:106 )D1 - 106
4X-RAY DIFFRACTION4( CHAIN D AND RESID 107:211 )D107 - 211
5X-RAY DIFFRACTION5( CHAIN F AND RESID 1:106 )F1 - 106
6X-RAY DIFFRACTION6( CHAIN F AND RESID 107:212 )F107 - 212
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1:122 )A1 - 122
8X-RAY DIFFRACTION8( CHAIN A AND RESID 123:213 )A123 - 213
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:122 )C1 - 122
10X-RAY DIFFRACTION10( CHAIN C AND RESID 123:213 )C123 - 213
11X-RAY DIFFRACTION11( CHAIN E AND RESID 1:122 )E1 - 122
12X-RAY DIFFRACTION12( CHAIN E AND RESID 123:214 )E123 - 214
13X-RAY DIFFRACTION13( CHAIN P AND RESID 8:12 )P8 - 12
14X-RAY DIFFRACTION14( CHAIN Q AND RESID 7:12 )Q7 - 12
15X-RAY DIFFRACTION15( CHAIN R AND RESID 5:13 )R5 - 13

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