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- PDB-6o2c: Crystal structure of 4493 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6o2c
TitleCrystal structure of 4493 Fab in complex with circumsporozoite protein NANP3 and anti-kappa VHH domain
Components
  • 4493 Fab heavy chain
  • 4493 Kappa light chain
  • Anti-kappa VHH domain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.017 Å
AuthorsScally, S.W. / Bosch, A. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Nat. Med. / Year: 2020
Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.
Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
K: Anti-kappa VHH domain
C: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,41612
Polymers59,7874
Non-polymers6298
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.978, 68.111, 84.635
Angle α, β, γ (deg.)90.000, 102.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules C

#4: Protein/peptide Circumsporozoite protein / CS


Mass: 1207.210 Da / Num. of mol.: 1 / Fragment: residues 148-159 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893

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Antibody , 3 types, 3 molecules ABK

#1: Antibody 4493 Fab heavy chain


Mass: 23792.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 4493 Kappa light chain


Mass: 23460.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Anti-kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 449 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 40 % (w/v) PEG600, 0.1 M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979329 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979329 Å / Relative weight: 1
ReflectionResolution: 2.017→30 Å / Num. obs: 46495 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.741 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Net I/σ(I): 9.7
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1934 / CC1/2: 0.741 / Rpim(I) all: 0.242 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house model

Resolution: 2.017→29.093 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 1998 4.3 %
Rwork0.1615 44494 -
obs0.1629 46492 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.17 Å2 / Biso mean: 34.0224 Å2 / Biso min: 17.07 Å2
Refinement stepCycle: final / Resolution: 2.017→29.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 41 441 4598
Biso mean--56.75 44.51 -
Num. residues----572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.017-2.06720.25141300.2267290291
2.0672-2.12310.25491430.1978316999
2.1231-2.18560.23711410.19313599
2.1856-2.25610.2451420.1835316599
2.2561-2.33670.24211430.1785318699
2.3367-2.43020.18491440.1796318399
2.4302-2.54070.23071430.16953189100
2.5407-2.67460.21471440.17483200100
2.6746-2.8420.22771440.16683203100
2.842-3.06130.19791420.16983182100
3.0613-3.36890.20571450.16063225100
3.3689-3.85540.18681440.14933214100
3.8554-4.85380.13731450.13063241100
4.8538-29.0930.18671480.16053300100
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)
11.87850.80140.10331.87291.00671.9113-0.00180.0584-0.0357-0.0430.0036-0.0486-0.11060.0351-0.00220.2937-0.01170.01470.2076-0.02290.262725.30091.4055-2.713
21.8445-0.027-1.44511.714-0.28694.8198-0.0251-0.1571-0.06130.09920.00580.0318-0.03790.17910.0130.1773-0.0015-0.01210.19090.01810.252530.604112.90632.9351
31.5815-0.384-1.60161.33541.08616.35990.06670.2284-0.0098-0.1464-0.17240.13910.0613-0.63880.06960.22470.0035-0.00310.2842-0.04930.31834.9751.9336.1885
43.21912.1440.25623.32390.76420.84540.0256-0.0568-0.0518-0.06590.002-0.2513-0.08920.0157-0.02160.23130.0181-0.00110.23070.00130.230319.016223.065631.1636
53.94050.4341-0.99312.412-0.67443.07140.0091-0.27960.16110.01970.01950.0776-0.07190.0629-0.04150.19270.0103-0.01570.2426-0.00380.2435-9.279718.415431.1824
67.5023.5618-2.57612.6625-0.062.27720.14811.52260.9817-0.3299-0.0730.9474-0.6842-0.3154-0.09780.4020.01140.00480.4980.04670.414113.87212.0527-16.2665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )A1 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 216 )A114 - 216
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )B1 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 214 )B108 - 214
5X-RAY DIFFRACTION5chain 'K' and (resid 1 through 113 )K1 - 113
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 12 )C2 - 12

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