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- PDB-6o23: Crystal structure of 2243 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6o23
TitleCrystal structure of 2243 Fab in complex with circumsporozoite protein NANP5
Components
  • 2243 Fab heavy chain
  • 2243 kappa light chain
  • 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScally, S.W. / Bosch, A. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation
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 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: 2243 Fab heavy chain
B: 2243 kappa light chain
C: 2243 Fab heavy chain
D: 2243 kappa light chain
E: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,88629
Polymers96,9965
Non-polymers1,89024
Water14,682815
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.148, 67.900, 100.357
Angle α, β, γ (deg.)90.00, 106.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide Circumsporozoite protein / CS


Mass: 2000.006 Da / Num. of mol.: 1 / Fragment: residues 148-167 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody 2243 Fab heavy chain


Mass: 24164.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 2243 kappa light chain


Mass: 23333.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 839 molecules

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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG 3350, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 68815 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.089 / Net I/σ(I): 6.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2909 / CC1/2: 0.542 / Rpim(I) all: 0.385 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.292 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1999 2.91 %
Rwork0.1859 --
obs0.187 68790 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 110 815 7615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036955
X-RAY DIFFRACTIONf_angle_d0.6459461
X-RAY DIFFRACTIONf_dihedral_angle_d13.974133
X-RAY DIFFRACTIONf_chiral_restr0.0451054
X-RAY DIFFRACTIONf_plane_restr0.0041199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31081400.25474684X-RAY DIFFRACTION98
2.05-2.10550.30461400.24124667X-RAY DIFFRACTION98
2.1055-2.16740.26841410.2324743X-RAY DIFFRACTION99
2.1674-2.23740.26561400.21954695X-RAY DIFFRACTION99
2.2374-2.31730.2671440.22034778X-RAY DIFFRACTION99
2.3173-2.41010.25481420.21714745X-RAY DIFFRACTION99
2.4101-2.51970.28181430.21394781X-RAY DIFFRACTION99
2.5197-2.65260.25681420.20614756X-RAY DIFFRACTION100
2.6526-2.81870.26681440.20074797X-RAY DIFFRACTION100
2.8187-3.03630.2441430.19424780X-RAY DIFFRACTION100
3.0363-3.34170.22871430.18014798X-RAY DIFFRACTION100
3.3417-3.82490.18471450.1544800X-RAY DIFFRACTION100
3.8249-4.81760.16751440.13744849X-RAY DIFFRACTION100
4.8176-39.29930.17241480.17324918X-RAY DIFFRACTION99
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)
12.33551.1552-0.94782.2508-0.34572.0899-0.04170.07120.0001-0.02740.0062-0.0383-0.08880.03770.02630.1479-0.01230.0040.1586-0.00610.1477-23.56850.459425.4157
21.1681-0.3225-0.67772.10991.61373.3056-0.0529-0.0314-0.10080.06190.03410.01060.1855-0.01980.03980.1580.0012-0.00420.12920.01280.1873-47.1896-5.966852.7602
31.75040.1145-0.95721.74320.72262.86620.1059-0.2723-0.00050.181-0.0865-0.1485-0.16030.3439-0.01250.1849-0.0845-0.01570.2493-0.00950.2134-12.25124.639643.5483
42.40841.83240.25193.87280.09742.3352-0.054-0.0341-0.1632-0.04840.0839-0.10780.20130.2169-0.03180.18720.05110.00330.1690.00610.1718-37.1203-14.493361.3781
52.8662-0.5460.02892.78921.11452.27850.06750.3185-0.0056-0.4156-0.25940.3363-0.2077-0.36120.16540.21960.0461-0.040.2516-0.04870.17527.0037-13.68027.6043
62.6696-0.44290.96842.35050.07614.46360.04870.1548-0.1273-0.1213-0.0767-0.0326-0.03910.00290.02390.16810.00040.01890.1064-0.02160.142933.8394-39.50234.4991
71.2185-0.97370.59791.7089-0.35251.21490.01310.05670.1181-0.0502-0.0872-0.0332-0.0681-0.01360.06410.1462-0.00960.01480.1253-0.01380.167119.4092-11.96325.6125
81.82010.2332-1.25461.6989-0.15442.6583-0.01620.1850.0484-0.22320.0201-0.11580.01540.0539-0.00980.17220.00860.00990.14340.00670.187143.5783-26.92199.0405
94.76-1.666-2.16640.5790.76851.11510.2553-0.106-0.0012-0.1466-0.0948-0.089-0.23540.3184-0.1380.24060.0026-0.01730.3316-0.05370.2325-3.88513.232618.4202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 214 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 212 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 113 )
6X-RAY DIFFRACTION6chain 'C' and (resid 114 through 214 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 107 )
8X-RAY DIFFRACTION8chain 'D' and (resid 108 through 213 )
9X-RAY DIFFRACTION9chain 'E' and (resid 3 through 20 )

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