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- PDB-6wfw: Crystal structure of Fab364 in complex with NPNA2 peptide from ci... -

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Basic information

Entry
Database: PDB / ID: 6wfw
TitleCrystal structure of Fab364 in complex with NPNA2 peptide from circumsporozoite protein
Components
  • Fab364 heavy chain
  • Fab364 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 / 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. ...Plasmodium circumsporozoite protein / IgG-binding B / B domain / 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
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: 2.093 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

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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
H: Fab364 heavy chain
L: Fab364 light chain
P: NPNA2 peptide


Theoretical massNumber of molelcules
Total (without water)54,1714
Polymers54,1714
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-29 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.440, 117.045, 116.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 6563.201 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 Fab364 heavy chain


Mass: 23598.660 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 Fab364 light chain


Mass: 23197.848 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: 810.812 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 / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG8000, 0.05 M potassium phosphate dibasic

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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: 2.093→50 Å / Num. obs: 28464 / % possible obs: 86.3 % / Redundancy: 5.3 % / CC1/2: 0.934 / Rpim(I) all: 0.048 / Rsym value: 0.108 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 556 / CC1/2: 0.738 / Rpim(I) all: 0.313 / Rsym value: 0.4 / % possible all: 34.8

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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: 2.093→43.845 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 1431 5.04 %
Rwork0.2132 --
obs0.2154 28419 86.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→43.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 0 123 3767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043730
X-RAY DIFFRACTIONf_angle_d0.6645096
X-RAY DIFFRACTIONf_dihedral_angle_d10.5962179
X-RAY DIFFRACTIONf_chiral_restr0.047589
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.093-2.16760.3416680.27591206X-RAY DIFFRACTION40
2.1676-2.25430.33041140.27171754X-RAY DIFFRACTION58
2.2543-2.35690.3121240.26272358X-RAY DIFFRACTION76
2.3569-2.48120.32731350.26012822X-RAY DIFFRACTION91
2.4812-2.63660.33321550.25233074X-RAY DIFFRACTION99
2.6366-2.84020.28571660.24733113X-RAY DIFFRACTION100
2.8402-3.12590.27551750.24363084X-RAY DIFFRACTION100
3.1259-3.57810.2781590.21913141X-RAY DIFFRACTION100
3.5781-4.50730.23411600.18533177X-RAY DIFFRACTION100
4.5073-43.8450.20521750.18143259X-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)
11.0399-0.00330.28023.6413-0.44591.90780.07030.1603-0.2716-0.2613-0.32040.1520.57160.13240.20610.47420.0660.09430.4604-0.02720.3626-5.501-36.75120.513
22.5080.6354-0.08233.42660.33611.8323-0.16230.1679-0.37960.19630.1374-0.74590.44870.1924-0.01140.35990.0070.0220.3578-0.00850.3138-6.781-30.58821.304
33.2219-1.19250.27845.0077-0.30592.17230.24730.7512-0.1791-0.4104-0.50140.37030.1815-0.11460.18030.3507-0.0008-0.01110.5407-0.03220.3075-9.941-31.82414.002
41.19270.3414-0.81930.6090.46571.544-0.0311-0.0380.0863-0.1582-0.0145-0.0739-0.11380.17930.00370.33480.0508-0.03610.623-0.0270.2816-2.966-27.65614.086
52.9187-0.381-0.11343.0349-0.32993.5198-0.0715-0.0371-0.2508-0.46860.4532-0.38040.54080.1808-0.19080.36340.077-0.02020.4919-0.02220.35610.394-31.19517.285
62.50060.4011-0.52471.48110.59051.3213-0.1402-0.2111-0.4409-0.72560.0129-0.33320.85940.48210.18111.0350.13270.28340.44610.07110.6106-32.513-46.01446.584
70.91240.7268-2.00980.5867-1.62454.4527-0.238-0.2165-0.23681.39660.01771.03251.1022-0.40150.33740.8480.02010.30370.58540.00460.6332-21.346-36.70530.465
81.5518-0.2851-0.54181.1642-0.10761.75850.0570.0130.1127-0.00340.0058-0.1363-0.02190.0981-0.08520.19730.01710.00540.360.0170.3074-14.726-16.94130.505
91.26710.768-0.80873.1371-1.74673.5637-0.1451-0.03530.0546-0.41040.20260.25880.2925-0.5893-0.06580.3446-0.0169-0.01050.490.04630.2697-42.643-27.9653.253
101.3614-0.1634-0.05961.2034-0.57972.40490.05820.02820.2302-0.0595-0.0728-0.03630.03150.15040.02440.2431-0.00140.03860.32330.0350.3382-28.569-8.63828.56
110.25990.2469-0.1480.8195-0.09730.08820.2884-0.0095-0.087-0.1718-0.26920.2292-0.36450.1064-0.06551.296-0.1830.01960.78390.06610.6773-45.474-50.03852.624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND RESID 3:13 )G3 - 13
2X-RAY DIFFRACTION2( CHAIN G AND RESID 14:27 )G14 - 27
3X-RAY DIFFRACTION3( CHAIN G AND RESID 28:41 )G28 - 41
4X-RAY DIFFRACTION4( CHAIN G AND RESID 42:51 )G42 - 51
5X-RAY DIFFRACTION5( CHAIN G AND RESID 52:62 )G52 - 62
6X-RAY DIFFRACTION6( CHAIN H AND RESID 1:106 )H1 - 106
7X-RAY DIFFRACTION7( CHAIN H AND RESID 107:118 )H107 - 118
8X-RAY DIFFRACTION8( CHAIN H AND RESID 119:213 )H119 - 213
9X-RAY DIFFRACTION9( CHAIN L AND RESID 2:102 )L2 - 102
10X-RAY DIFFRACTION10( CHAIN L AND RESID 103:213 )L103 - 213
11X-RAY DIFFRACTION11( CHAIN P AND RESID 1:8 )P1 - 8

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