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- PDB-7rm3: Antibody 2E10.E9 in complex with P. vivax CSP peptide ANGAGNQPGAN... -

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Basic information

Entry
Database: PDB / ID: 7rm3
TitleAntibody 2E10.E9 in complex with P. vivax CSP peptide ANGAGNQPGANGAGNQPGANGAGGQAA
Components
  • 2E10.E9 Fab heavy chain
  • 2E10.E9 Fab light chain
  • peptide from Circumsporozoite protein variant VK247
KeywordsANTIMICROBIAL PROTEIN / antibody / malaria / Plasmodium vivax / circumsporozoite protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / Circumsporozoite protein variant VK247
Function and homology information
Biological speciesMus musculus (house mouse)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKucharska, I. / Ivanochko, D. / Julien, J.P.
Funding support Canada, 4items
OrganizationGrant numberCountry
Other governmentOntario Early Researcher Awards program Canada
Other governmentCanada Foundation for Innovation Canada
Other governmentOntario Research Fund Canada
Other governmentCanada Research Chairs Canada
CitationJournal: Elife / Year: 2022
Title: Structural basis of Plasmodium vivax inhibition by antibodies binding to the circumsporozoite protein repeats.
Authors: Kucharska, I. / Hossain, L. / Ivanochko, D. / Yang, Q. / Rubinstein, J.L. / Pomes, R. / Julien, J.P.
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 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

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Assembly

Deposited unit
A: 2E10.E9 Fab heavy chain
B: 2E10.E9 Fab light chain
C: 2E10.E9 Fab heavy chain
D: 2E10.E9 Fab light chain
P: peptide from Circumsporozoite protein variant VK247
Q: peptide from Circumsporozoite protein variant VK247
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9159
Polymers100,8106
Non-polymers1053
Water61334
1
A: 2E10.E9 Fab heavy chain
B: 2E10.E9 Fab light chain
Q: peptide from Circumsporozoite protein variant VK247
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4284
Polymers50,4053
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-43 kcal/mol
Surface area19950 Å2
MethodPISA
2
C: 2E10.E9 Fab heavy chain
D: 2E10.E9 Fab light chain
P: peptide from Circumsporozoite protein variant VK247
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4875
Polymers50,4053
Non-polymers822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-43 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.404, 144.436, 60.471
Angle α, β, γ (deg.)90.000, 102.831, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILECYSCYS(chain 'A' and (resid 2 through 22 or resid 24 through 61 or resid 63 through 215))AA2 - 224 - 24
121ALAALAGLUGLU(chain 'A' and (resid 2 through 22 or resid 24 through 61 or resid 63 through 215))AA24 - 6126 - 64
131PHEPHESERSER(chain 'A' and (resid 2 through 22 or resid 24 through 61 or resid 63 through 215))AA63 - 21566 - 223
211ILEILECYSCYS(chain 'C' and (resid 2 through 22 or resid 24 through 61 or resid 63 through 215))CC2 - 224 - 24
221ALAALAGLUGLU(chain 'C' and (resid 2 through 22 or resid 24 through 61 or resid 63 through 215))CC24 - 6126 - 64
231PHEPHESERSER(chain 'C' and (resid 2 through 22 or resid 24 through 61 or resid 63 through 215))CC63 - 21566 - 223
112ASPASPASPASP(chain 'B' and (resid 1 through 122 or resid 124 through 168 or resid 170 through 212))BB1 - 1221 - 128
122GLNGLNSERSER(chain 'B' and (resid 1 through 122 or resid 124 through 168 or resid 170 through 212))BB124 - 168130 - 174
132ASPASPARGARG(chain 'B' and (resid 1 through 122 or resid 124 through 168 or resid 170 through 212))BB170 - 211176 - 217
212ASPASPASPASP(chain 'D' and (resid 1 through 122 or resid 124 through 168 or resid 170 through 212))DD1 - 1221 - 128
222GLNGLNSERSER(chain 'D' and (resid 1 through 122 or resid 124 through 168 or resid 170 through 212))DD124 - 168130 - 174
232ASPASPARGARG(chain 'D' and (resid 1 through 122 or resid 124 through 168 or resid 170 through 212))DD170 - 211176 - 217

NCS ensembles :
ID
1
2

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Components

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Protein/peptide , 1 types, 2 molecules PQ

#3: Protein/peptide peptide from Circumsporozoite protein variant VK247


Mass: 2249.234 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
References: UniProt: B7SA67

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody 2E10.E9 Fab heavy chain


Mass: 23939.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 2E10.E9 Fab light chain


Mass: 24215.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 37 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate and 30% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.68→29.48 Å / Num. obs: 26439 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 47.39 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.2
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2627 / CC1/2: 0.578 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uyw

1uyw


Resolution: 2.68→29.48 Å / SU ML: 0.4171 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 1314 4.97 %
Rwork0.2065 25125 -
obs0.2081 26439 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.29 Å2
Refinement stepCycle: LAST / Resolution: 2.68→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 2 34 6885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00927010
X-RAY DIFFRACTIONf_angle_d1.24079525
X-RAY DIFFRACTIONf_chiral_restr0.06561059
X-RAY DIFFRACTIONf_plane_restr0.0081219
X-RAY DIFFRACTIONf_dihedral_angle_d16.82362504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.790.33761410.32192779X-RAY DIFFRACTION100
2.79-2.910.38211500.28572766X-RAY DIFFRACTION99.93
2.91-3.070.29631320.28722790X-RAY DIFFRACTION99.9
3.07-3.260.32491490.26412779X-RAY DIFFRACTION99.97
3.26-3.510.28451470.23862812X-RAY DIFFRACTION99.87
3.51-3.860.27031490.20952782X-RAY DIFFRACTION99.97
3.86-4.420.2021520.1652768X-RAY DIFFRACTION99.86
4.42-5.560.16481620.14562821X-RAY DIFFRACTION99.93
5.56-29.480.18811320.17952828X-RAY DIFFRACTION99.66

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