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- PDB-6w00: Crystal structure of Fab239 in complex with NPNA2 peptide from ci... -

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Basic information

Entry
Database: PDB / ID: 6w00
TitleCrystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein
Components
  • Fab239 heavy chain
  • Fab239 light chain
  • Immunoglobulin G-binding protein G
  • NPNA2 peptide
KeywordsIMMUNE SYSTEM / Malaria / Sporozoite / Circumsporozoite protein / Antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / IgG binding / side of membrane / cell surface / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / Plasmodium circumsporozoite protein / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Thrombospondin type 1 domain / Immunoglobulin/albumin-binding domain superfamily ...: / Plasmodium circumsporozoite protein / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Thrombospondin type 1 domain / Immunoglobulin/albumin-binding domain superfamily / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Circumsporozoite protein / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 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
DepositionFeb 28, 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 1.3Oct 30, 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

Downloads & links

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Assembly

Deposited unit
G: Immunoglobulin G-binding protein G
L: Fab239 light chain
H: Fab239 heavy chain
P: NPNA2 peptide


Theoretical massNumber of molelcules
Total (without water)54,9764
Polymers54,9764
Non-polymers00
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-33 kcal/mol
Surface area21300 Å2
Unit cell
Length a, b, c (Å)121.517, 121.517, 82.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6327.939 Da / Num. of mol.: 1 / Fragment: domain III (UNP residues 438-497)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
#2: Antibody Fab239 light chain


Mass: 23614.164 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: Antibody Fab239 heavy chain


Mass: 24197.186 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)
#4: Protein/peptide NPNA2 peptide


Mass: 836.849 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 52998 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.951 / Net I/σ(I): 18.6
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2623 / CC1/2: 0.725 / Rpim(I) all: 0.303 / Rsym value: 0.933

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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: 1.853→48.946 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 2577 4.87 %
Rwork0.1873 --
obs0.1882 52931 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.853→48.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 0 349 4153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093916
X-RAY DIFFRACTIONf_angle_d0.8715343
X-RAY DIFFRACTIONf_dihedral_angle_d12.1922760
X-RAY DIFFRACTIONf_chiral_restr0.054610
X-RAY DIFFRACTIONf_plane_restr0.006686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8532-1.88880.26741410.25252735X-RAY DIFFRACTION99
1.8888-1.92740.28791230.24862781X-RAY DIFFRACTION100
1.9274-1.96930.2351400.20542734X-RAY DIFFRACTION100
1.9693-2.01510.25161520.18962752X-RAY DIFFRACTION100
2.0151-2.06550.2331260.1882790X-RAY DIFFRACTION100
2.0655-2.12140.20981240.18012783X-RAY DIFFRACTION100
2.1214-2.18380.19581490.18332736X-RAY DIFFRACTION100
2.1838-2.25430.22661390.18412795X-RAY DIFFRACTION100
2.2543-2.33480.24351320.18882767X-RAY DIFFRACTION100
2.3348-2.42830.18051410.17292790X-RAY DIFFRACTION100
2.4283-2.53880.23231480.1852767X-RAY DIFFRACTION100
2.5388-2.67270.20151290.18652806X-RAY DIFFRACTION100
2.6727-2.84010.21941630.18062783X-RAY DIFFRACTION100
2.8401-3.05940.20341600.18282797X-RAY DIFFRACTION100
3.0594-3.36720.18691570.19022795X-RAY DIFFRACTION100
3.3672-3.85420.18741480.17952835X-RAY DIFFRACTION100
3.8542-4.85530.15671420.16152891X-RAY DIFFRACTION100
4.8553-48.9460.22011630.21083017X-RAY DIFFRACTION100

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