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- PDB-6wg0: Crystal structure of Fab366 in complex with NPNA3 peptide from ci... -

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Basic information

Entry
Database: PDB / ID: 6wg0
TitleCrystal structure of Fab366 in complex with NPNA3 peptide from circumsporozoite protein
Components
  • Fab366 heavy chain
  • Fab366 light chain
  • NPNA3 peptide
KeywordsIMMUNE SYSTEM / Malaria / Sporozoite / Circumsporozoite protein / 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
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsPholcharee, T. / Oyen, D. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Citation
Journal: Nat Commun / Year: 2021
Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum.
Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / Richter King, C. / Zavala, F. / Wilson, I.A.
#1: Journal: Biorxiv / Year: 2020
Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum
Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / King, C.R. / Zavala, F. / Wilson, I.A.
History
DepositionApr 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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
H: Fab366 heavy chain
L: Fab366 light chain
P: NPNA3 peptide


Theoretical massNumber of molelcules
Total (without water)48,4083
Polymers48,4083
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-33 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.662, 68.713, 108.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab366 heavy chain


Mass: 24034.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab366 light chain


Mass: 23237.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide NPNA3 peptide


Mass: 1136.132 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9.6 / Details: 40% PEG600, 0.1 M CHES, pH 9.5

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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: Oct 15, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 56859 / % possible obs: 95.1 % / Redundancy: 11.7 % / CC1/2: 0.954 / Rpim(I) all: 0.022 / Rsym value: 0.076 / Net I/σ(I): 28.9
Reflection shellResolution: 1.599→1.63 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1420 / CC1/2: 0.719 / Rpim(I) all: 0.326 / Rsym value: 0.559 / % possible all: 48.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 1.599→45.05 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 2793 4.92 %
Rwork0.1885 --
obs0.1896 56784 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 265 3614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073497
X-RAY DIFFRACTIONf_angle_d0.894788
X-RAY DIFFRACTIONf_dihedral_angle_d6.5812785
X-RAY DIFFRACTIONf_chiral_restr0.056546
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5994-1.6270.3671560.33631342X-RAY DIFFRACTION48
1.627-1.65660.2959990.30531943X-RAY DIFFRACTION69
1.6566-1.68840.3581410.27662479X-RAY DIFFRACTION90
1.6884-1.72290.30371340.23742748X-RAY DIFFRACTION97
1.7229-1.76040.24871360.2032763X-RAY DIFFRACTION98
1.7604-1.80130.20661810.19972749X-RAY DIFFRACTION100
1.8013-1.84640.23391360.17762813X-RAY DIFFRACTION99
1.8464-1.89630.22581300.18722825X-RAY DIFFRACTION99
1.8963-1.95210.22481240.18352799X-RAY DIFFRACTION99
1.9521-2.01510.20231520.18022820X-RAY DIFFRACTION100
2.0151-2.08710.20761420.18472823X-RAY DIFFRACTION100
2.0871-2.17070.2131470.18332807X-RAY DIFFRACTION100
2.1707-2.26950.21741420.18732834X-RAY DIFFRACTION100
2.2695-2.38910.22811430.1932851X-RAY DIFFRACTION100
2.3891-2.53880.26061570.18782840X-RAY DIFFRACTION100
2.5388-2.73480.19441500.18372846X-RAY DIFFRACTION100
2.7348-3.00990.21981490.19122863X-RAY DIFFRACTION100
3.0099-3.44530.21431740.18822868X-RAY DIFFRACTION100
3.4453-4.34020.18911470.17262918X-RAY DIFFRACTION100
4.3402-45.050.17981530.18553060X-RAY DIFFRACTION100

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