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- PDB-7rm0: Antibody 2E10.E9 in complex with P. vivax CSP peptide ANGAGNQPGAN... -

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Basic information

Entry
Database: PDB / ID: 7rm0
TitleAntibody 2E10.E9 in complex with P. vivax CSP peptide ANGAGNQPGANGAGNQPG
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
Biological speciesMus musculus (house mouse)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2E10.E9 Fab heavy chain
B: 2E10.E9 Fab light chain
P: peptide from Circumsporozoite protein variant VK247
C: 2E10.E9 Fab heavy chain
D: 2E10.E9 Fab light chain
Q: peptide from Circumsporozoite protein variant VK247
E: 2E10.E9 Fab heavy chain
F: 2E10.E9 Fab light chain
R: peptide from Circumsporozoite protein variant VK247
G: 2E10.E9 Fab heavy chain
H: 2E10.E9 Fab light chain
S: peptide from Circumsporozoite protein variant VK247


Theoretical massNumber of molelcules
Total (without water)198,24012
Polymers198,24012
Non-polymers00
Water1,56787
1
A: 2E10.E9 Fab heavy chain
B: 2E10.E9 Fab light chain
P: peptide from Circumsporozoite protein variant VK247


Theoretical massNumber of molelcules
Total (without water)49,5603
Polymers49,5603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-31 kcal/mol
Surface area20170 Å2
MethodPISA
2
C: 2E10.E9 Fab heavy chain
D: 2E10.E9 Fab light chain
Q: peptide from Circumsporozoite protein variant VK247


Theoretical massNumber of molelcules
Total (without water)49,5603
Polymers49,5603
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-30 kcal/mol
Surface area20170 Å2
MethodPISA
3
E: 2E10.E9 Fab heavy chain
F: 2E10.E9 Fab light chain
R: peptide from Circumsporozoite protein variant VK247


Theoretical massNumber of molelcules
Total (without water)49,5603
Polymers49,5603
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-31 kcal/mol
Surface area19910 Å2
MethodPISA
4
G: 2E10.E9 Fab heavy chain
H: 2E10.E9 Fab light chain
S: peptide from Circumsporozoite protein variant VK247


Theoretical massNumber of molelcules
Total (without water)49,5603
Polymers49,5603
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-26 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.520, 66.310, 142.320
Angle α, β, γ (deg.)100.453, 92.305, 91.718
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43

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
111ILEILETHRTHR(chain 'A' and (resid 2 through 55 or resid 57...AA2 - 544 - 57
121PROPROGLUGLU(chain 'A' and (resid 2 through 55 or resid 57...AA57 - 6160 - 64
131PHEPHEPHEPHE(chain 'A' and (resid 2 through 55 or resid 57...AA6366
141GLYGLYSERSER(chain 'A' and (resid 2 through 55 or resid 57...AA65 - 11368 - 121
151THRTHRPROPRO(chain 'A' and (resid 2 through 55 or resid 57...AA116 - 126124 - 134
161SERSERGLUGLU(chain 'A' and (resid 2 through 55 or resid 57...AA134 - 191142 - 199
171VALVALTHRTHR(chain 'A' and (resid 2 through 55 or resid 57...AA193 - 204201 - 212
181VALVALLYSLYS(chain 'A' and (resid 2 through 55 or resid 57...AA206 - 208214 - 216
191ILEILEILEILE(chain 'A' and (resid 2 through 55 or resid 57...AA210218
211ILEILETHRTHR(chain 'C' and (resid 2 through 55 or resid 57...CD2 - 544 - 57
221PROPROGLUGLU(chain 'C' and (resid 2 through 55 or resid 57...CD57 - 6160 - 64
231PHEPHEPHEPHE(chain 'C' and (resid 2 through 55 or resid 57...CD6366
241GLYGLYSERSER(chain 'C' and (resid 2 through 55 or resid 57...CD65 - 11368 - 121
251THRTHRPROPRO(chain 'C' and (resid 2 through 55 or resid 57...CD116 - 126124 - 134
261SERSERGLUGLU(chain 'C' and (resid 2 through 55 or resid 57...CD134 - 191142 - 199
271VALVALTHRTHR(chain 'C' and (resid 2 through 55 or resid 57...CD193 - 204201 - 212
281VALVALLYSLYS(chain 'C' and (resid 2 through 55 or resid 57...CD206 - 208214 - 216
291ILEILEILEILE(chain 'C' and (resid 2 through 55 or resid 57...CD210218
311ILEILETHRTHR(chain 'E' and (resid 2 through 55 or resid 57...EG2 - 544 - 57
321PROPROGLUGLU(chain 'E' and (resid 2 through 55 or resid 57...EG57 - 6160 - 64
331PHEPHEPHEPHE(chain 'E' and (resid 2 through 55 or resid 57...EG6366
341GLYGLYSERSER(chain 'E' and (resid 2 through 55 or resid 57...EG65 - 11368 - 121
351THRTHRPROPRO(chain 'E' and (resid 2 through 55 or resid 57...EG116 - 126124 - 134
361SERSERGLUGLU(chain 'E' and (resid 2 through 55 or resid 57...EG134 - 191142 - 199
371VALVALTHRTHR(chain 'E' and (resid 2 through 55 or resid 57...EG193 - 204201 - 212
381VALVALLYSLYS(chain 'E' and (resid 2 through 55 or resid 57...EG206 - 208214 - 216
391ILEILEILEILE(chain 'E' and (resid 2 through 55 or resid 57...EG210218
411ILEILETHRTHR(chain 'G' and (resid 2 through 55 or resid 57...GJ2 - 544 - 57
421PROPROGLUGLU(chain 'G' and (resid 2 through 55 or resid 57...GJ57 - 6160 - 64
431PHEPHEPHEPHE(chain 'G' and (resid 2 through 55 or resid 57...GJ6366
441GLYGLYSERSER(chain 'G' and (resid 2 through 55 or resid 57...GJ65 - 11368 - 121
451THRTHRPROPRO(chain 'G' and (resid 2 through 55 or resid 57...GJ116 - 126124 - 134
461SERSERGLUGLU(chain 'G' and (resid 2 through 55 or resid 57...GJ134 - 191142 - 199
471VALVALTHRTHR(chain 'G' and (resid 2 through 55 or resid 57...GJ193 - 204201 - 212
481VALVALLYSLYS(chain 'G' and (resid 2 through 55 or resid 57...GJ206 - 208214 - 216
491ILEILEILEILE(chain 'G' and (resid 2 through 55 or resid 57...GJ210218
112ASPASPGLUGLU(chain 'B' and (resid 1 through 17 or resid 19...BB1 - 171 - 17
122VALVALGLNGLN(chain 'B' and (resid 1 through 17 or resid 19...BB19 - 2719 - 27
132GLNGLNPROPRO(chain 'B' and (resid 1 through 17 or resid 19...BB29 - 4035 - 46
142PROPROGLNGLN(chain 'B' and (resid 1 through 17 or resid 19...BB43 - 7949 - 85
152ASPASPSERSER(chain 'B' and (resid 1 through 17 or resid 19...BB82 - 12288 - 128
162GLNGLNLYSLYS(chain 'B' and (resid 1 through 17 or resid 19...BB124 - 142130 - 148
172ILEILEVALVAL(chain 'B' and (resid 1 through 17 or resid 19...BB144 - 146150 - 152
182TRPTRPSERSER(chain 'B' and (resid 1 through 17 or resid 19...BB148 - 153154 - 159
192GLNGLNSERSER(chain 'B' and (resid 1 through 17 or resid 19...BB156 - 168162 - 174
1102ASPASPGLUGLU(chain 'B' and (resid 1 through 17 or resid 19...BB170 - 187176 - 193
1112HISHISCYSCYS(chain 'B' and (resid 1 through 17 or resid 19...BB189 - 194195 - 200
1122ALAALAPHEPHE(chain 'B' and (resid 1 through 17 or resid 19...BB196 - 209202 - 215
1132ARGARGARGARG(chain 'B' and (resid 1 through 17 or resid 19...BB211217
212ASPASPGLUGLU(chain 'D' and (resid 1 through 17 or resid 19...DE1 - 171 - 17
222VALVALGLNGLN(chain 'D' and (resid 1 through 17 or resid 19...DE19 - 2719 - 27
232GLNGLNPROPRO(chain 'D' and (resid 1 through 17 or resid 19...DE29 - 4035 - 46
242PROPROGLNGLN(chain 'D' and (resid 1 through 17 or resid 19...DE43 - 7949 - 85
252ASPASPSERSER(chain 'D' and (resid 1 through 17 or resid 19...DE82 - 12288 - 128
262GLNGLNLYSLYS(chain 'D' and (resid 1 through 17 or resid 19...DE124 - 142130 - 148
272ILEILEVALVAL(chain 'D' and (resid 1 through 17 or resid 19...DE144 - 146150 - 152
282TRPTRPSERSER(chain 'D' and (resid 1 through 17 or resid 19...DE148 - 153154 - 159
292GLNGLNSERSER(chain 'D' and (resid 1 through 17 or resid 19...DE156 - 168162 - 174
2102ASPASPGLUGLU(chain 'D' and (resid 1 through 17 or resid 19...DE170 - 187176 - 193
2112HISHISCYSCYS(chain 'D' and (resid 1 through 17 or resid 19...DE189 - 194195 - 200
2122ALAALAPHEPHE(chain 'D' and (resid 1 through 17 or resid 19...DE196 - 209202 - 215
2132ARGARGARGARG(chain 'D' and (resid 1 through 17 or resid 19...DE211217
312ASPASPGLUGLU(chain 'F' and (resid 1 through 17 or resid 19...FH1 - 171 - 17
322VALVALGLNGLN(chain 'F' and (resid 1 through 17 or resid 19...FH19 - 2719 - 27
332GLNGLNPROPRO(chain 'F' and (resid 1 through 17 or resid 19...FH29 - 4035 - 46
342PROPROGLNGLN(chain 'F' and (resid 1 through 17 or resid 19...FH43 - 7949 - 85
352ASPASPSERSER(chain 'F' and (resid 1 through 17 or resid 19...FH82 - 12288 - 128
362GLNGLNLYSLYS(chain 'F' and (resid 1 through 17 or resid 19...FH124 - 142130 - 148
372ILEILEVALVAL(chain 'F' and (resid 1 through 17 or resid 19...FH144 - 146150 - 152
382TRPTRPSERSER(chain 'F' and (resid 1 through 17 or resid 19...FH148 - 153154 - 159
392GLNGLNSERSER(chain 'F' and (resid 1 through 17 or resid 19...FH156 - 168162 - 174
3102ASPASPGLUGLU(chain 'F' and (resid 1 through 17 or resid 19...FH170 - 187176 - 193
3112HISHISCYSCYS(chain 'F' and (resid 1 through 17 or resid 19...FH189 - 194195 - 200
3122ALAALAPHEPHE(chain 'F' and (resid 1 through 17 or resid 19...FH196 - 209202 - 215
3132ARGARGARGARG(chain 'F' and (resid 1 through 17 or resid 19...FH211217
412ASPASPGLUGLU(chain 'H' and (resid 1 through 17 or resid 19...HK1 - 171 - 17
422VALVALGLNGLN(chain 'H' and (resid 1 through 17 or resid 19...HK19 - 2719 - 27
432GLNGLNPROPRO(chain 'H' and (resid 1 through 17 or resid 19...HK29 - 4035 - 46
442PROPROGLNGLN(chain 'H' and (resid 1 through 17 or resid 19...HK43 - 7949 - 85
452ASPASPSERSER(chain 'H' and (resid 1 through 17 or resid 19...HK82 - 12288 - 128
462GLNGLNLYSLYS(chain 'H' and (resid 1 through 17 or resid 19...HK124 - 142130 - 148
472ILEILEVALVAL(chain 'H' and (resid 1 through 17 or resid 19...HK144 - 146150 - 152
482TRPTRPSERSER(chain 'H' and (resid 1 through 17 or resid 19...HK148 - 153154 - 159
492GLNGLNSERSER(chain 'H' and (resid 1 through 17 or resid 19...HK156 - 168162 - 174
4102ASPASPGLUGLU(chain 'H' and (resid 1 through 17 or resid 19...HK170 - 187176 - 193
4112HISHISCYSCYS(chain 'H' and (resid 1 through 17 or resid 19...HK189 - 194195 - 200
4122ALAALAPHEPHE(chain 'H' and (resid 1 through 17 or resid 19...HK196 - 209202 - 215
4132ARGARGARGARG(chain 'H' and (resid 1 through 17 or resid 19...HK211217
113ALAALAASNASN(chain 'P' and (resid 4 through 6 or resid 8 through 11))PC4 - 64 - 6
123PROPROASNASN(chain 'P' and (resid 4 through 6 or resid 8 through 11))PC8 - 118 - 11
213ALAALAASNASN(chain 'Q' and (resid 4 through 6 or resid 8 through 11))QF4 - 64 - 6
223PROPROASNASN(chain 'Q' and (resid 4 through 6 or resid 8 through 11))QF8 - 118 - 11
313ALAALAASNASN(chain 'R' and (resid 4 through 6 or resid 8 through 11))RI4 - 64 - 6
323PROPROASNASN(chain 'R' and (resid 4 through 6 or resid 8 through 11))RI8 - 118 - 11
413ALAALAASNASN(chain 'S' and (resid 4 through 6 or resid 8 through 11))SL4 - 64 - 6
423PROPROASNASN(chain 'S' and (resid 4 through 6 or resid 8 through 11))SL8 - 118 - 11

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
2E10.E9 Fab heavy chain


Mass: 23784.713 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody
2E10.E9 Fab light chain


Mass: 24223.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide
peptide from Circumsporozoite protein variant VK247


Mass: 1551.536 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.71→29.34 Å / Num. obs: 53126 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 59.2 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.4
Reflection shellResolution: 2.71→2.81 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1111 / CC1/2: 0.729 / % 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: 2.71→29.34 Å / SU ML: 0.3969 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 27.2793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 2067 3.89 %
Rwork0.2089 51059 -
obs0.2104 53126 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.67 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13620 0 0 87 13707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009613964
X-RAY DIFFRACTIONf_angle_d1.211919024
X-RAY DIFFRACTIONf_chiral_restr0.06432121
X-RAY DIFFRACTIONf_plane_restr0.00932427
X-RAY DIFFRACTIONf_dihedral_angle_d16.95374968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.31981440.26113414X-RAY DIFFRACTION100
2.77-2.840.32541330.27383400X-RAY DIFFRACTION100
2.84-2.920.34251430.27653408X-RAY DIFFRACTION99.97
2.92-30.33891350.27823445X-RAY DIFFRACTION99.94
3-3.10.34241360.26893339X-RAY DIFFRACTION100
3.1-3.210.31131440.25333426X-RAY DIFFRACTION100
3.21-3.340.29771390.24423372X-RAY DIFFRACTION100
3.34-3.490.31231330.25123445X-RAY DIFFRACTION99.94
3.49-3.680.30071490.22343399X-RAY DIFFRACTION100
3.68-3.910.26061320.21893408X-RAY DIFFRACTION99.97
3.91-4.210.23171310.20813410X-RAY DIFFRACTION100
4.21-4.630.21521280.17223396X-RAY DIFFRACTION100
4.63-5.30.1981310.16953404X-RAY DIFFRACTION100
5.3-6.660.21261820.18513382X-RAY DIFFRACTION100
6.66-29.340.15431070.16763411X-RAY DIFFRACTION99.63

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