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- PDB-7rlx: Antibody 2F2 in complex with P. vivax CSP peptide GDRADGQPAGDRAAGQPA -

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Basic information

Entry
Database: PDB / ID: 7rlx
TitleAntibody 2F2 in complex with P. vivax CSP peptide GDRADGQPAGDRAAGQPA
Components
  • 2F2 Fab heavy chain
  • 2F2 Fab light chain
  • peptide from Circumsporozoite protein variant VK210
KeywordsANTIMICROBIAL PROTEIN / antibody / malaria / Plasmodium vivax / circumsporozoite protein
Function / homology
Function and homology information


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
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKucharska, I. / 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain
P: peptide from Circumsporozoite protein variant VK210


Theoretical massNumber of molelcules
Total (without water)50,0433
Polymers50,0433
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-26 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.615, 60.810, 81.352
Angle α, β, γ (deg.)90.000, 101.573, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

21A-320-

HOH

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Components

#1: Antibody 2F2 Fab light chain


Mass: 24284.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 2F2 Fab heavy chain


Mass: 24046.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide peptide from Circumsporozoite protein variant VK210 / CS


Mass: 1711.750 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
References: UniProt: P08677
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium acetate 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-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 1.97→29.71 Å / Num. obs: 31038 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 35.5 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.3
Reflection shellResolution: 1.97→2.02 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1962 / CC1/2: 0.603

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xiw

1xiw


Resolution: 1.97→29.71 Å / SU ML: 0.256 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 1552 5 %
Rwork0.186 29479 -
obs0.1884 31031 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.68 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 177 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513503
X-RAY DIFFRACTIONf_angle_d1.32394771
X-RAY DIFFRACTIONf_chiral_restr0.0819537
X-RAY DIFFRACTIONf_plane_restr0.0083609
X-RAY DIFFRACTIONf_dihedral_angle_d13.67551250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.33271290.27472449X-RAY DIFFRACTION90.65
2.03-2.110.2841400.24332661X-RAY DIFFRACTION99.19
2.11-2.190.30021420.21172685X-RAY DIFFRACTION99.54
2.19-2.290.26631420.21362694X-RAY DIFFRACTION99.58
2.29-2.410.28131410.2032714X-RAY DIFFRACTION99.48
2.41-2.560.26891410.19872680X-RAY DIFFRACTION99.75
2.56-2.760.25821430.20622717X-RAY DIFFRACTION99.31
2.76-3.040.2691420.2152692X-RAY DIFFRACTION99.65
3.04-3.480.28631430.19662710X-RAY DIFFRACTION99.17
3.48-4.380.19631420.1682699X-RAY DIFFRACTION99.06
4.38-29.710.16821470.14842778X-RAY DIFFRACTION99.09
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)
11.66392697486-0.602528211842-0.7683020290030.558356209989-0.4009228254894.637115802260.2069734397090.589488214656-0.0425622183886-0.766235583716-0.128698137017-0.05484179523580.373797156896-0.153349700419-0.07436520315150.6796946407180.03348970830150.03849244730690.502790770624-0.01346495964460.3043184350586.57776136186-3.325648942529.89908017173
22.487376426131.49383432648-1.722578233071.08341440628-0.3252445502173.993675174910.1000268046390.7744131090230.434975936761-0.837967159632-0.0243499910934-0.250815924732-0.1324564923380.114970226779-0.07829364386840.5770418049870.06151241987080.1724091984540.5401150001070.1092268444070.34202979487414.84039045533.244938488488.68504839342
31.441945285490.676544298388-0.3702300062661.73750214678-0.05806406990332.839211321320.169415063787-0.0849634994103-0.247202767650.2526667560780.0888322673165-0.2146501676940.1343546050850.0269698202444-0.2556273100090.2223551486240.0254736322487-0.02670601734950.170118124651-0.02398866410520.31389787753410.2739888464-5.8883598904543.0096431033
42.784591241311.797220880172.687088705584.217604074592.92972030945.940897188230.109685058717-0.06607912514230.1051510685220.231851290668-0.0137329544477-0.07113326470420.138940624332-0.0179279456278-0.09289413476270.2090454352620.0198480768768-0.007820555032290.2003226171030.005754604733650.3056866834757.84368077487-1.3578817213643.8049912586
55.551281577341.259185581182.581076333012.516917856060.865712620214.69282150580.0218915383438-0.7789643668060.262636998410.850150089671-0.14709657896-0.08477241294420.0385707847304-0.175544242560.1296004858440.3921765850540.00767629688706-0.07062029993910.279427455351-0.04332566367280.2658917814949.40438393626-1.3829118223655.4515098893
62.037821191820.008292941790890.9837014522653.739175148670.9309831510734.968146358740.228670284840.403529547180.159233643168-0.602247858492-0.0758234726629-0.936195087290.3114954124590.253366859681-0.1285501790520.444875402670.08064149098950.2206066745050.407003214670.1094402782490.59028528277330.0710486928-2.9173768278916.7876636843
72.19927770338-0.627487175552-0.850170083190.2334952135090.6979394602134.424091096640.1129269049030.5907724743830.217911137629-0.747113630427-0.201380494519-0.747521192374-0.2464150131180.3713441484520.01032838668340.6155734446880.01997027146170.3041906899840.6116916046180.1149594726680.66402741814532.74418089882.7617726396911.1770510716
81.37202216590.1752911700750.07699367490711.86219291514-0.9185390107862.19492980619-0.09440721073480.297395403288-0.0780133726501-0.306224928948-0.167916273604-0.4266303096760.176835427990.05843619997830.2278959951250.2264017801030.04912512504980.05635781155960.238877572344-0.02083679060490.43664260173522.0590407022-6.4946695970229.1595876211
92.295665293841.76355510878-0.562247940116.41258773881-1.339030892051.00868740323-0.054574202872-0.0529265659170.0960163577565-0.103893741775-0.0687292215336-0.344646500890.05030489479040.1132674124260.1211953801910.1790496361810.0186105195286-0.06088660065030.20557147212-0.02622273722780.32581229273522.3763048327-10.589762322441.1899166143
101.30944888328-0.408082651919-0.8696923898310.3782135753650.3463644921131.35906749683-0.1198884245760.107122931238-0.317772597577-0.248029275296-0.12773455104-0.2367982850410.4853418432850.3989646950980.002830858537251.157499505670.284301949580.4728275278780.8767741051680.08675671931070.58011541277226.1498969998-4.82674018645-1.64711258284
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 83 )BA1 - 831 - 88
22chain 'B' and (resid 84 through 101 )BA84 - 10189 - 106
33chain 'B' and (resid 102 through 128 )BA102 - 128107 - 133
44chain 'B' and (resid 129 through 174 )BA129 - 174134 - 179
55chain 'B' and (resid 175 through 213 )BA175 - 213180 - 218
66chain 'A' and (resid 3 through 44 )AB3 - 441 - 42
77chain 'A' and (resid 45 through 87 )AB45 - 8743 - 89
88chain 'A' and (resid 88 through 145 )AB88 - 14590 - 151
99chain 'A' and (resid 146 through 215 )AB146 - 215152 - 221
1010chain 'P' and (resid 1 through 11 )PC1 - 111 - 11

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