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- PDB-6wfx: Crystal structure of Fab395 in complex with NPNA2 peptide from ci... -

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Basic information

Entry
Database: PDB / ID: 6wfx
TitleCrystal structure of Fab395 in complex with NPNA2 peptide from circumsporozoite protein
Components
  • Fab395 heavy chain
  • Fab395 light chain
  • NPNA2 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 / 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: 2.59 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: 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
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
H: Fab395 heavy chain
L: Fab395 light chain
P: NPNA2 peptide


Theoretical massNumber of molelcules
Total (without water)48,5933
Polymers48,5933
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-33 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 78.662, 90.666
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 Fab395 heavy chain


Mass: 24283.381 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 Fab395 light chain


Mass: 23475.084 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 NPNA2 peptide


Mass: 834.857 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.: 60 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG4000, 0.2 M ammonium acetate, 0.1 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 16577 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.787 / Rpim(I) all: 0.114 / Rsym value: 0.276 / Net I/σ(I): 10.2
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 749 / CC1/2: 0.338 / Rpim(I) all: 0.77 / Rsym value: 1.762 / % possible all: 99.5

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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: 2.59→47.917 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 699 5.03 %
Rwork0.198 --
obs0.2003 13902 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→47.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 0 60 3305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023330
X-RAY DIFFRACTIONf_angle_d0.5984557
X-RAY DIFFRACTIONf_dihedral_angle_d11.2111945
X-RAY DIFFRACTIONf_chiral_restr0.042522
X-RAY DIFFRACTIONf_plane_restr0.004583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.790.3881450.28162537X-RAY DIFFRACTION98
2.79-3.07070.30511330.25872604X-RAY DIFFRACTION100
3.0707-3.51490.30061200.2082658X-RAY DIFFRACTION100
3.5149-4.42790.21471540.16862628X-RAY DIFFRACTION100
4.4279-47.9170.1771470.16812776X-RAY DIFFRACTION100
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)
10.20750.03240.05570.0698-0.05090.14220.0978-0.1275-0.11950.0648-0.0605-0.143-0.03960.04680.0660.0545-0.02350.0330.08810.01430.10227.24215.33525.3124
20.0234-0.01690.0020.0135-0.00150.0029-0.0074-0.01340.0024-0.0025-0.00670.0015-0.0207-0.019500.40080.13610.1850.36070.07120.294425.538665.0926-9.7886
3-0.0276-0.0099-0.08950.05180.01770.33310.00960.110.1356-0.0304-0.0476-0.18260.1215-0.6003-0.03580.1445-0.0110.07970.07690.08080.118528.403649.1362-14.4004
40.03150.00990.03380.0740.04160.0864-0.15680.0629-0.0530.01980.1412-0.1355-0.0814-0.05930.0359-0.0791-0.0930.12910.07980.01780.086220.243217.3765-7.5305
50.0207-0.03530.02480.0422-0.04420.0816-0.034-0.14440.07170.51940.0234-0.124-0.1192-0.07630.00730.4913-0.1257-0.0050.197-0.01580.082328.382348.49998.701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 91 through 213 )
2X-RAY DIFFRACTION2chain 'P' and (resid 2 through 7 )
3X-RAY DIFFRACTION3chain 'H' and (resid 2 through 109 )
4X-RAY DIFFRACTION4chain 'H' and (resid 110 through 215 )
5X-RAY DIFFRACTION5chain 'L' and (resid 2 through 90 )

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