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- PDB-8fb7: Crystal structure of Ky15.10 Fab in complex with circumsporozoite... -

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Basic information

Entry
Database: PDB / ID: 8fb7
TitleCrystal structure of Ky15.10 Fab in complex with circumsporozoite protein NPDP peptide
Components
  • Circumsporozoite protein NPDP peptide
  • Ky15.10 Antibody, Heavy Chain
  • Ky15.10 Antibody, Light chain
KeywordsIMMUNE SYSTEM / Malaria
Function / homology
Function and homology information


side of membrane / cell surface / 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: 1.75 Å
AuthorsPrieto, K. / 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 29, 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

Downloads & links

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Assembly

Deposited unit
A: Ky15.10 Antibody, Heavy Chain
B: Ky15.10 Antibody, Light chain
H: Ky15.10 Antibody, Heavy Chain
L: Ky15.10 Antibody, Light chain
P: Circumsporozoite protein NPDP peptide
Q: Circumsporozoite protein NPDP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,97914
Polymers99,4826
Non-polymers4978
Water16,412911
1
A: Ky15.10 Antibody, Heavy Chain
B: Ky15.10 Antibody, Light chain
Q: Circumsporozoite protein NPDP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0528
Polymers49,7413
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-24 kcal/mol
Surface area20550 Å2
MethodPISA
2
H: Ky15.10 Antibody, Heavy Chain
L: Ky15.10 Antibody, Light chain
P: Circumsporozoite protein NPDP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9276
Polymers49,7413
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-25 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.432, 67.945, 83.233
Angle α, β, γ (deg.)90.000, 105.180, 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
Components on special symmetry positions
IDModelComponents
11H-422-

HOH

21L-573-

HOH

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Components

#1: Antibody Ky15.10 Antibody, Heavy Chain


Mass: 24547.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Ky15.10 Antibody, Light chain


Mass: 23534.154 Da / Num. of mol.: 2
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 NPDP peptide / CS


Mass: 1659.668 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P08307
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium chloride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 108854 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 5402 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.27 Å / SU ML: 0.2035 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1982 1998 1.84 %
Rwork0.1631 106799 -
obs0.1637 108797 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.88 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6860 0 32 911 7803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01247202
X-RAY DIFFRACTIONf_angle_d1.17199834
X-RAY DIFFRACTIONf_chiral_restr0.07781100
X-RAY DIFFRACTIONf_plane_restr0.00871264
X-RAY DIFFRACTIONf_dihedral_angle_d13.44272606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.29691430.26647611X-RAY DIFFRACTION99.79
1.79-1.840.30871410.24867520X-RAY DIFFRACTION99.93
1.84-1.90.24881430.22277650X-RAY DIFFRACTION99.9
1.9-1.960.21511410.19657559X-RAY DIFFRACTION99.79
1.96-2.030.21391420.18137603X-RAY DIFFRACTION99.91
2.03-2.110.22921420.18697591X-RAY DIFFRACTION99.95
2.11-2.20.24271420.18067630X-RAY DIFFRACTION99.91
2.2-2.320.21711420.17587579X-RAY DIFFRACTION99.91
2.32-2.470.2191430.1787611X-RAY DIFFRACTION99.91
2.47-2.660.24661420.18187661X-RAY DIFFRACTION99.97
2.66-2.920.21141430.1767626X-RAY DIFFRACTION99.94
2.92-3.350.18971440.16297672X-RAY DIFFRACTION99.95
3.35-4.210.17141440.13617673X-RAY DIFFRACTION99.72
4.21-29.270.15931460.1367813X-RAY DIFFRACTION99.66
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)
11.816982039150.007864106309940.6325688791731.33861995366-0.1122951180644.58388258048-0.0234933740546-0.0106201680982-0.122362483779-0.03146920402320.0475872469456-0.07071298571490.005437487302170.07018783929940.004678039719520.169625442902-0.005981278373050.02746131087160.169779606246-0.01376398137820.234433020223-42.5058453896-2.2476771464837.2736784747
23.786936350233.34800425739-0.8766500633013.68366659078-1.348988419581.78841706619-0.0320490409406-0.127648194433-0.2224706397830.0997748597416-0.0536789032949-0.03848952216970.1938653788660.002048842580090.08486370563260.2450958817250.04607622658620.05354602204260.1588275847120.007092195347730.238230839019-57.4075966726-14.350695096969.8236552862
33.99788053651.18561690378-0.9984609479842.11102392746-0.6201422799513.03269612650.0202761520581-0.1158186348740.0918062035421-0.01898417722520.006088462843340.207887300098-0.0695642031308-0.262895856097-0.03258169307610.1795124902370.0161830151703-0.02146617892310.1620018186-0.002630527873420.179838642507-64.3531541984-0.0072332564256734.6096551211
41.696131633670.9967217024771.562398805721.904638072292.263367517775.489923178730.0141079386155-0.07154523827420.004188005734910.0960167147887-0.06160709105750.05373173083410.193505828799-0.06053471489060.03426482303640.1824121235630.01190756197120.05604857087210.1362020345560.01857025733060.204776454731-66.2154572001-1.0086884975469.8966696464
50.814790035148-0.1299791604370.3099236176371.68322453335-1.12947186463.548095498680.1951271653030.14010929981-0.0978384188336-0.314812338922-0.39880998442-0.2716271379860.4332737825240.8391950219250.1548543662940.2775624125390.1666869185660.0009766704858060.5498632981710.0531939841980.282949793986-8.17379896358-4.3981287122514.5970917358
62.21251777541-0.0534483203326-0.140195338915.5048762699-0.6910819873853.1612259761-0.0759498145780.1653833146630.417850725840.0404202160356-0.00787059187305-0.570684623855-0.3306140957150.5589777667160.07597317380960.211157464298-0.063105489199-0.0431669933630.3769754817650.01917048466040.342470207685-14.272980356222.9419444916-8.68433928686
71.17222658326-0.01915219623230.8822298367224.79267969736-0.3613490429472.78778604809-0.06638009431560.07124201095780.125891413122-0.0321025320549-0.149107021008-0.0685089587697-0.4231872047550.08638905765390.2160931518890.203318339702-0.0230321521999-0.0261579041820.3260022000860.00638235618390.203653502756-19.106514918610.199872167726.7164765783
81.58427609289-0.0949885899771.797995641242.495185752560.2708627105736.8242632849-0.114644580344-0.09393838037630.1402266520730.2196786854860.0878856831106-0.0842216737709-0.449705392532-0.01007091224630.0178352289880.2342672377730.0101537123839-0.0005529971225560.1538039565420.0221770664490.206849098894-30.073139078924.7258290101-5.01059024125
93.93282531365-3.809321844814.836418940258.25454697668-1.122450180988.724232050560.304870316733-0.766920169297-1.277676477970.02300159515230.006524139756230.029441588211.120163067210.494351497537-0.3239575253570.30648053350.0690820257793-0.02384043741420.4035125794480.06683572529320.267304038711-8.90826241629-10.551607953428.4852439501
108.24546682899-1.00333148134-6.333932563341.82775462914-0.2781510247457.123941483750.2789915221961.484016842070.0875384480629-1.40314098995-0.666800376361-0.00435661343357-0.594386833288-0.2333463484240.2109733287720.4124056941710.03500682721140.01495187828870.4747451485880.01179219986770.196091353225-43.21928137731.2686313946119.1987802239
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 113 )AA1 - 1131 - 125
22chain 'A' and (resid 114 through 216 )AA114 - 216126 - 228
33chain 'B' and (resid 1 through 107 )BD1 - 1071 - 106
44chain 'B' and (resid 108 through 213 )BD108 - 213107 - 212
55chain 'H' and (resid 1 through 113 )HH1 - 1131 - 125
66chain 'H' and (resid 114 through 214 )HH114 - 214126 - 223
77chain 'L' and (resid 1 through 107 )LK1 - 1071 - 106
88chain 'L' and (resid 108 through 214 )LK108 - 214107 - 213
99chain 'P' and (resid 2 through 10 )PM2 - 101 - 9
1010chain 'Q' and (resid 3 through 15 )QN3 - 151 - 13

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