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- PDB-8fb5: Crystal structure of Ky15.11-S100IK Fab in complex with circumspo... -

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Basic information

Entry
Database: PDB / ID: 8fb5
TitleCrystal structure of Ky15.11-S100IK Fab in complex with circumsporozoite protein KQPA peptide
Components
  • Circumsporozoite protein KQPA peptide
  • Ky15.11-SK Antibody, heavy chain
  • Ky15.11-SK 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
AuthorsKang, R.W. / 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ky15.11-SK Antibody, heavy chain
B: Ky15.11-SK Antibody, light chain
C: Ky15.11-SK Antibody, heavy chain
D: Ky15.11-SK Antibody, light chain
E: Ky15.11-SK Antibody, heavy chain
F: Ky15.11-SK Antibody, light chain
G: Ky15.11-SK Antibody, heavy chain
H: Ky15.11-SK Antibody, light chain
O: Circumsporozoite protein KQPA peptide
I: Circumsporozoite protein KQPA peptide
J: Circumsporozoite protein KQPA peptide
K: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)200,88812
Polymers200,88812
Non-polymers00
Water00
1
A: Ky15.11-SK Antibody, heavy chain
B: Ky15.11-SK Antibody, light chain
O: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)50,2223
Polymers50,2223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ky15.11-SK Antibody, heavy chain
D: Ky15.11-SK Antibody, light chain
I: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)50,2223
Polymers50,2223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ky15.11-SK Antibody, heavy chain
F: Ky15.11-SK Antibody, light chain
J: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)50,2223
Polymers50,2223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ky15.11-SK Antibody, heavy chain
H: Ky15.11-SK Antibody, light chain
K: Circumsporozoite protein KQPA peptide


Theoretical massNumber of molelcules
Total (without water)50,2223
Polymers50,2223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.392, 60.485, 184.907
Angle α, β, γ (deg.)90.000, 98.380, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 40 or resid 44...
d_2ens_1(chain "C" and (resid 1 through 12 or (resid 13...
d_3ens_1(chain "E" and (resid 1 through 12 or (resid 13...
d_4ens_1(chain "G" and (resid 1 through 12 or (resid 13...
d_1ens_2(chain "B" and (resid 1 through 40 or resid 44...
d_2ens_2(chain "D" and (resid 1 through 40 or resid 44...
d_3ens_2(chain "F" and (resid 1 through 40 or resid 44...
d_4ens_2(chain "H" and (resid 1 through 40 or resid 44...
d_1ens_3(chain "I" and resid 10 through 15)
d_2ens_3(chain "J" and resid 10 through 15)
d_3ens_3(chain "K" and resid 10 through 15)
d_4ens_3(chain "O" and resid 10 through 15)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNTHRA1 - 40
d_12ens_1GLYTRPA44 - 52
d_13ens_1TYRASNA60 - 74
d_14ens_1LEUALAA79 - 99
d_15ens_1SERGLUA136 - 164
d_16ens_1VALLYSA168 - 222
d_17ens_1VALLYSA227 - 230
d_21ens_1GLNTHRC1 - 40
d_22ens_1GLYTRPC44 - 52
d_23ens_1TYRASNC60 - 74
d_24ens_1LEUALAC79 - 99
d_25ens_1SERGLUC136 - 164
d_26ens_1VALLYSC168 - 222
d_27ens_1VALLYSC227 - 230
d_31ens_1GLNTHRE1 - 40
d_32ens_1GLYTRPE44 - 52
d_33ens_1TYRASNE60 - 74
d_34ens_1LEUALAE79 - 99
d_35ens_1SERGLUE136 - 164
d_36ens_1VALLYSE168 - 222
d_37ens_1VALLYSE227 - 230
d_41ens_1GLNTHRG1 - 40
d_42ens_1GLYTRPG44 - 52
d_43ens_1TYRASNG60 - 74
d_44ens_1LEUALAG79 - 99
d_45ens_1SERGLUG136 - 164
d_46ens_1VALLYSG168 - 222
d_47ens_1VALLYSG227 - 230
d_11ens_2ASPPROB1 - 40
d_12ens_2PROSERB44 - 52
d_13ens_2PROSERB59 - 65
d_14ens_2THRTHRB74
d_15ens_2LEUPROB78 - 140
d_16ens_2ALALYSB143 - 148
d_17ens_2SERTYRB158 - 185
d_18ens_2LYSVALB189 - 195
d_19ens_2THRARGB205 - 210
d_21ens_2ASPPROD1 - 40
d_22ens_2PROSERD44 - 52
d_23ens_2PROSERD59 - 65
d_24ens_2THRTHRD69
d_25ens_2LEULEUD73
d_26ens_2GLNPROD79 - 140
d_27ens_2ALALYSD143 - 148
d_28ens_2SERTYRD158 - 185
d_29ens_2LYSTHRD189 - 196
d_210ens_2LYSARGD206 - 210
d_31ens_2ASPPROF1 - 40
d_32ens_2PROSERF44 - 52
d_33ens_2PROSERF59 - 65
d_34ens_2THRTHRF69
d_35ens_2LEULEUF73
d_36ens_2GLNPROF79 - 140
d_37ens_2ALALYSF143 - 148
d_38ens_2SERTYRF158 - 185
d_39ens_2LYSTHRF189 - 196
d_310ens_2LYSARGF206 - 210
d_41ens_2ASPPROH1 - 40
d_42ens_2PROSERH44 - 52
d_43ens_2PROSERH59 - 65
d_44ens_2THRTHRH69
d_45ens_2LEULEUH73
d_46ens_2GLNPROH79 - 140
d_47ens_2ALALYSH143 - 148
d_48ens_2SERTYRH158 - 185
d_49ens_2LYSTHRH189 - 196
d_410ens_2LYSARGH206 - 210
d_11ens_3PROASNJ3 - 8
d_21ens_3PROASNK4 - 9
d_31ens_3PROASNL4 - 9
d_41ens_3PROASNI2 - 7

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.99957960692, 0.0106655555673, -0.0269602550849), (0.0105926950418, 0.999939851731, 0.00284389395527), (0.0269889651812, 0.00255711664156, -0.999632460914)46.8181304029, 30.053399754, -4.83035638508
2given(-0.999948973348, -0.00945012093769, 0.00357014213937), (0.00938422779592, -0.999793165252, -0.0180433639897), (0.00373991568174, -0.0180089402702, 0.999830831241)33.7207774881, -71.6699341733, 90.5628064664
3given(0.99979366295, -0.00438077687146, 0.0198353300561), (-0.0040494767383, -0.999852144523, -0.0167119965968), (0.019905608822, 0.0166282255851, -0.999663577836)-12.283794844, -41.1751460595, 87.5745425134
4given(-0.999508997201, 0.0015905381165, -0.0312927260446), (0.00148231865137, 0.999992842001, 0.00348118928705), (0.0312980390156, 0.0034330942219, -0.9995042004)46.3614097235, 30.2454710871, -4.77240733574
5given(-0.999922409062, -0.010504677329, -0.00669534233005), (0.0106652767637, -0.999644887428, -0.0244202970955), (-0.00643643738855, -0.0244898099808, 0.999679359335)33.5641757288, -71.5698703117, 90.1924625943
6given(0.999626841821, 0.00353442604415, 0.0270866192866), (0.00408869596919, -0.999782825565, -0.0204348787798), (0.0270085111976, 0.0205380022887, -0.999424199619)-11.8862220618, -41.2964969057, 87.8438832608
7given(0.998504186997, -0.0326562298701, -0.0438515586985), (-0.0310195130917, -0.998815078447, 0.0374997183144), (-0.0450241974628, -0.036083371749, -0.998334018215)-12.4235270644, -40.7394614506, 87.303380481
8given(-0.999867669249, 0.0156334357285, -0.0044988528493), (-0.0158375095602, -0.998643048383, 0.0496108376072), (-0.00371716028248, 0.0496755231929, 0.998758491886)34.9015533328, -11.4117332304, 93.3031746273
9given(-0.998124782225, 0.0177345728391, 0.058586722342), (0.017994256795, 0.999830453374, 0.00390784180338), (-0.0585074852558, 0.00495473827557, -0.998274673994)45.600084565, -30.8867157415, -2.6285758315

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Components

#1: Antibody
Ky15.11-SK Antibody, heavy chain


Mass: 25210.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
Ky15.11-SK Antibody, light chain


Mass: 23462.064 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P19597
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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 46810 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 49.67 Å2 / CC1/2: 0.968 / Net I/σ(I): 5.2
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 2271 / CC1/2: 0.433

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.65 Å / SU ML: 0.4522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2743 1995 4.27 %
Rwork0.2483 44766 -
obs0.2495 46761 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.72 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13766 0 0 0 13766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002214100
X-RAY DIFFRACTIONf_angle_d0.531419173
X-RAY DIFFRACTIONf_chiral_restr0.04262130
X-RAY DIFFRACTIONf_plane_restr0.00492449
X-RAY DIFFRACTIONf_dihedral_angle_d10.61645013
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.438665013622
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.478936957043
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.442492564388
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.80085850267
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.79749605057
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS1.82874249621
ens_3d_2JX-RAY DIFFRACTIONTorsion NCS0.303132027066
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS0.274629335222
ens_3d_4JX-RAY DIFFRACTIONTorsion NCS0.247192728116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.42791400.35163149X-RAY DIFFRACTION99.64
2.97-3.050.36721410.3393168X-RAY DIFFRACTION99.67
3.05-3.140.37591420.3193176X-RAY DIFFRACTION99.82
3.14-3.240.37941420.2933158X-RAY DIFFRACTION99.85
3.24-3.360.31821410.30093185X-RAY DIFFRACTION99.82
3.36-3.490.32221400.26363150X-RAY DIFFRACTION99.76
3.49-3.650.28791440.2623196X-RAY DIFFRACTION99.32
3.65-3.850.29361400.25613182X-RAY DIFFRACTION99.82
3.85-4.090.2521420.23023190X-RAY DIFFRACTION99.85
4.09-4.40.2571430.19893201X-RAY DIFFRACTION99.94
4.4-4.840.17851420.19033203X-RAY DIFFRACTION99.85
4.84-5.540.23211460.20623237X-RAY DIFFRACTION99.47
5.54-6.980.26641430.25583225X-RAY DIFFRACTION99.56
6.98-39.650.22021490.2393346X-RAY DIFFRACTION99.32

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