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- PDB-8f9s: Crystal structure of Ky15.2 Fab in complex with circumsporozoite ... -

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Basic information

Entry
Database: PDB / ID: 8f9s
TitleCrystal structure of Ky15.2 Fab in complex with circumsporozoite protein NDN peptide
Components
  • Circumsporozoite protein NDN peptide
  • Ky15.2 Antibody, heavy chain
  • Ky15.2 Antibody, light chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody
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: 2.1 Å
AuthorsThai, 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 24, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ky15.2 Antibody, heavy chain
L: Ky15.2 Antibody, light chain
A: Ky15.2 Antibody, heavy chain
B: Ky15.2 Antibody, light chain
C: Circumsporozoite protein NDN peptide
P: Circumsporozoite protein NDN peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,22618
Polymers97,4816
Non-polymers74512
Water5,747319
1
H: Ky15.2 Antibody, heavy chain
L: Ky15.2 Antibody, light chain
P: Circumsporozoite protein NDN peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1139
Polymers48,7403
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ky15.2 Antibody, heavy chain
B: Ky15.2 Antibody, light chain
C: Circumsporozoite protein NDN peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1139
Polymers48,7403
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.479, 77.853, 123.649
Angle α, β, γ (deg.)90.000, 91.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Ky15.2 Antibody, heavy chain


Mass: 24137.158 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 Ky15.2 Antibody, light chain


Mass: 23366.986 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 NDN peptide / CS


Mass: 1236.248 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.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033192 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033192 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 50174 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 40.01 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.13 Å / Num. unique obs: 2056 / CC1/2: 0.85

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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: 2.1→39.26 Å / SU ML: 0.3038 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.6747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 1994 3.98 %
Rwork0.2053 48122 -
obs0.2063 50116 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6798 0 48 319 7165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277178
X-RAY DIFFRACTIONf_angle_d0.61359803
X-RAY DIFFRACTIONf_chiral_restr0.04491112
X-RAY DIFFRACTIONf_plane_restr0.00461254
X-RAY DIFFRACTIONf_dihedral_angle_d11.96652597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.34781370.29453437X-RAY DIFFRACTION99.69
2.15-2.210.34131480.28923409X-RAY DIFFRACTION99.75
2.21-2.280.31671360.283431X-RAY DIFFRACTION99.36
2.28-2.350.33811440.28293399X-RAY DIFFRACTION99.44
2.35-2.430.33141420.27683453X-RAY DIFFRACTION99.15
2.43-2.530.29151440.25443427X-RAY DIFFRACTION99.17
2.53-2.650.2571400.25133372X-RAY DIFFRACTION98.68
2.65-2.790.30381370.24593440X-RAY DIFFRACTION99.36
2.79-2.960.29291460.24593437X-RAY DIFFRACTION99.83
2.96-3.190.2891410.2293463X-RAY DIFFRACTION99.81
3.19-3.510.20681440.19723441X-RAY DIFFRACTION99.06
3.51-4.020.19621410.1833388X-RAY DIFFRACTION98.19
4.02-5.060.15351460.14913524X-RAY DIFFRACTION99.97
5.06-39.260.18441480.17323501X-RAY DIFFRACTION98.97
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)
12.59196861203-0.594850156818-0.3844503129011.975189915960.4689306060152.465608013240.1239944760570.2494067593330.169451875956-0.289128515155-0.0574883471040.074948128358-0.3240858497380.012219045721-0.05611677569920.3642607072180.0331145747063-0.01141583853930.1828342661010.0212506135910.244629348115-13.6074.97350.136
22.20283547445-0.719029471143-1.714475222223.791466145920.5862325851612.55902607642-0.0131593862250.5960706418220.00556613433028-0.6401024033650.1634585471860.201016624991-0.428428632845-0.243168169114-0.1402799246140.597373592447-0.0400125265072-0.04883543024720.6294317918830.00174358090120.2937726323896.957-14.24327.567
34.16797807357-2.16017478908-0.8024201220432.199229812120.71475160812.450532381230.0484219213141-0.0855425772599-0.0354628966391-0.130614250667-0.0448315507521-0.0900039255836-0.04012928340450.1462193130910.004279942204240.346571012157-0.0338415322135-0.02313308260870.2002429156850.01194684401960.2393995984572.222-1.91363.939
43.51690422052-0.470094679-1.583608774473.679262900020.7277271819475.728134993810.243836499980.6194930051030.367107690187-0.8658539329430.229163574433-0.400353394815-1.128623411260.207363082895-0.4900304121090.627300035849-0.0994508010760.1125250258550.427500103296-0.02162283270590.3610147503519.733-6.65832.899
50.711384486526-1.81410911701-1.708699556063.513970724642.436526228312.745248133470.02837588539420.581823894039-0.103759751653-0.210893138746-0.30764378030.5302222890750.0948154203176-0.8516941831510.2633770984110.306168691790.0211120869238-0.02942071639560.74567931017-0.02359320272350.4035177095225.88216.088-0.023
61.343323129531.710399184560.4820414170732.549266145262.450200559053.77649070646-0.086082283959-0.1200423871230.002026051460140.1266832719460.01983329149930.1265553608960.06233036705050.04855455557690.08844188948720.4922969436110.1848323692410.05446503598880.4179034555710.0969050519290.3760105638755.50234.05130.654
72.026494610412.18491843419-0.1059132499525.069738249282.917156086963.891130418920.0830270094238-0.211505270503-0.0624446157034-0.200551180810.0357667071444-0.379818506253-0.1858528929010.130609063206-0.1436785493150.3681386156040.1351036453310.08752734853450.5414665966470.1047487021810.40424966801826.98222.31.501
80.1801660688690.101688925501-0.09733662790112.400910797820.7752412874063.35734686524-0.296761052788-0.469140134386-0.01890837321130.6998982330570.38283802075-0.228796249881.069451919681.41854895272-0.06684903692380.8397895644350.4795560535520.03595637279220.9635094802360.03655288106060.43487331834817.76425.93535.787
92.031030341732.02424508601-0.8892704735466.675692449484.3869006353.32833341895-0.09892719366140.60772055012-0.202443740214-0.830988435906-0.5301361252010.0282343044040.98942153002-0.7771325879380.8148271544250.5858408783130.06969133562140.097551481970.8462524235590.06770209610240.43107787263514.15311.273-15.28
102.023621995723.00127597332.228754473588.018611073432.845665015346.731345534490.76028993038-0.09815490806281.49463138660.489672710506-0.2943070298261.00992582801-1.1434954542-0.499875325713-0.3016679414380.5039456930020.09382371798080.06692302525930.313199012067-0.003594914244140.381229653641-18.5939.64866.852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:123 )H1 - 123
2X-RAY DIFFRACTION2( CHAIN H AND RESID 124:216 )H124 - 216
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:106 )L1 - 106
4X-RAY DIFFRACTION4( CHAIN L AND RESID 107:213 )L107 - 213
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1:123 )A1 - 123
6X-RAY DIFFRACTION6( CHAIN A AND RESID 124:216 )A124 - 216
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:106 )B1 - 106
8X-RAY DIFFRACTION8( CHAIN B AND RESID 107:213 )B107 - 213
9X-RAY DIFFRACTION9( CHAIN C AND RESID 2:11 )C2 - 11
10X-RAY DIFFRACTION10( CHAIN P AND RESID 2:11 )P2 - 11

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