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- PDB-7rlw: Antibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGDRAAGQPA -

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Basic information

Entry
Database: PDB / ID: 7rlw
TitleAntibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGDRAAGQPA
Components
  • 2F2 Fab heavy chain
  • 2F2 Fab light chain
  • PvCSPvk210 peptide from Circumsporozoite protein
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.54 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: PvCSPvk210 peptide from Circumsporozoite protein
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain
D: 2F2 Fab light chain
C: 2F2 Fab heavy chain
R: PvCSPvk210 peptide from Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)99,9976
Polymers99,9976
Non-polymers00
Water1448
1
P: PvCSPvk210 peptide from Circumsporozoite protein
B: 2F2 Fab light chain
A: 2F2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,9993
Polymers49,9993
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 2F2 Fab light chain
C: 2F2 Fab heavy chain
R: PvCSPvk210 peptide from Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)49,9993
Polymers49,9993
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.911, 60.396, 158.300
Angle α, β, γ (deg.)90.000, 101.457, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 27 or (resid 28...
d_2ens_1(chain "C" and (resid 3 through 119 or resid 121 through 178 or resid 180 through 214))
d_1ens_2(chain "B" and resid 1 through 213)
d_2ens_2(chain "D" and ((resid 1 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNPROC1 - 125
d_12ens_1VALLEUC127 - 184
d_13ens_1SERLYSC186 - 220
d_21ens_1GLNPROE1 - 125
d_22ens_1VALLEUE127 - 184
d_23ens_1SERLYSE186 - 220
d_11ens_2ASPGLUB1 - 218
d_21ens_2ASPGLUD1 - 218

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.997550059504, -0.0327514616431, 0.0618160217455), (-0.0354418781686, 0.998448804808, -0.0429401612689), (-0.0603137799851, -0.0450258363404, -0.997163437961)30.2094165553, -27.0407376172, 78.7987800261
2given(-0.998896134203, -0.00461296672705, 0.0467464823498), (-0.00703957826732, 0.998628559273, -0.0518791378333), (-0.0464430555834, -0.0521509457487, -0.997558680703)30.5895957798, -27.7616287398, 78.5898798715

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Components

#1: Protein/peptide PvCSPvk210 peptide from Circumsporozoite protein / CS


Mass: 1667.740 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
References: UniProt: P08677
#2: Antibody 2F2 Fab light chain


Mass: 24284.227 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)
#3: Antibody 2F2 Fab heavy chain


Mass: 24046.723 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.6 and 20% (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: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.54→29.21 Å / Num. obs: 28642 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 64.73 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.7
Reflection shellResolution: 2.54→2.65 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3484 / CC1/2: 0.529 / % possible all: 100

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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: 2.54→29.21 Å / SU ML: 0.4178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 1432 5.01 %
Rwork0.2012 27173 -
obs0.2038 28605 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.92 Å2
Refinement stepCycle: LAST / Resolution: 2.54→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 0 8 6866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167036
X-RAY DIFFRACTIONf_angle_d0.47989568
X-RAY DIFFRACTIONf_chiral_restr0.04051071
X-RAY DIFFRACTIONf_plane_restr0.00411218
X-RAY DIFFRACTIONf_dihedral_angle_d9.16872522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.602108450139
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.532432436279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.630.36411440.32822722X-RAY DIFFRACTION99.86
2.63-2.740.35741420.31262695X-RAY DIFFRACTION99.75
2.74-2.860.36561400.28562650X-RAY DIFFRACTION99.93
2.86-3.010.34731430.27242717X-RAY DIFFRACTION99.86
3.01-3.20.28751430.25362714X-RAY DIFFRACTION99.97
3.2-3.450.31271430.22962717X-RAY DIFFRACTION99.72
3.45-3.790.26651410.22552695X-RAY DIFFRACTION99.68
3.79-4.340.24961450.18322730X-RAY DIFFRACTION99.48
4.34-5.460.1871430.14932746X-RAY DIFFRACTION99.9
5.46-29.210.20271480.16442787X-RAY DIFFRACTION99.26
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)
16.05287709841-2.55114001917-0.5473894033714.779434783331.339364795126.170399736131.11015259936-0.705900414405-0.8294066837740.23099165844-0.18064197598-0.01441969445650.127804271881-2.92880127643-1.007743663481.22697971407-0.349563860713-0.2641275334351.228250906470.415464924240.70168249906513.0646980781-7.4737317040843.1609603928
26.422542774125.721964053721.86871598785.854835191252.754003642923.850121283590.267749206173-0.8638159366680.9017687599421.022969054771.486219649610.60401713668-0.070770625425-1.38356145108-1.734642422090.853563782678-0.2752723753410.116063355731.08063007636-0.01029425233630.77025501465515.45733430785.3451799701140.9657812787
38.45726104173-0.995880550088-2.600423752861.374219476330.3594959409664.866211151830.0789405935692-0.6386220494090.1690787447380.567150281747-0.100675155669-0.4054074853730.0530614094090.3087878130540.006715249764520.708214775701-0.141262325222-0.1182978398670.4936963317740.02821812643880.52025351092431.2108209114-2.0088102562329.5160679251
41.39544515437-0.009017653269961.509791966992.870260193950.4517637817134.342411283940.4287225440180.0730597062217-0.445959476473-0.333231259017-0.00355144137109-0.4745998704490.4951993456510.129034046456-0.4196784408160.500452444772-0.003289631648210.1432644311560.46023727389-0.009310836306330.60078436419327.3862193707-8.0739485735-3.57705115793
52.08497456585-1.267672398972.053398281083.96068785015-1.766895946956.221126131430.1287689719390.3903968982570.222268690396-0.793752270636-0.380824776475-0.5700366185380.07797246376550.3128804729010.2993082498910.6629484053210.08122987114560.1930484620440.558265531460.01550193917070.79392068332929.1611805361-3.91617971224-9.61920726425
63.19285836233-0.7961773481741.72130532834.22325621406-2.502187906756.113749204820.339512995253-0.553657194585-0.1301478423780.367509104772-0.2872327965290.6119677123980.252269376148-0.389157326431-0.04125748244910.665922675086-0.07666314136760.1523372889530.556333577233-0.0423443332670.5512829124219.27289342439-3.6674460044224.0676814505
73.74462701877-0.7533500572720.7921867856434.74725664798-2.210100052885.238430302190.137413625678-0.3447128635270.1133607137850.588619234629-0.2358227233180.226938119365-0.175472093417-0.4786812803520.07234782008440.577616119512-0.1615921139740.1050492992780.624435475195-0.1065511813760.49088599374710.2275801903-1.0157885793629.151914361
84.5534285665-1.67305618781-0.5646367923397.838180999080.7315534516432.807455486220.00284999538040.178106675627-0.0835109321506-0.264362374971-0.1658371904880.00333296826769-0.03957132165-0.2294244276870.1354863100030.427186282335-0.01385972158370.02565619293340.490720670690.01085739398720.49947334435615.9717961527-11.7735679264-2.43349117591
96.20533957103-0.389877520817-3.096336951181.47965378637-0.9868728464539.55477403608-0.3191822071580.5968025354080.0280420373067-0.583604791720.244150011231-0.02109129288990.583130989314-0.4366568279110.07693341308360.620520615444-0.1396291649070.00494181644190.50096919029-0.003646722375380.3708766325950.469068889732-31.873390036946.9503427911
102.646358749581.22229925761-3.304356825041.61230831817-2.562545819857.49717191184-0.2036822936240.33765195446-0.0626300255686-0.486713813610.1441741832670.09054896584180.561280079388-0.4523990003940.07037852733020.489390622717-0.0331209735157-0.04676567880090.394334875873-0.0189325529340.39517854393-0.730631870116-31.851406479454.2174107923
114.753173835620.8443532003352.557152224153.049182872772.303692069085.54126903753-0.0286689482649-0.357507368749-0.04532683833660.5424341538520.120063566348-0.2528083718-0.0782466777930.128611985835-0.1065903683090.563454444251-0.00759154027873-0.01813109796820.3396098619240.01056577261560.4933913777922.49943456686-31.972028578987.7181769515
124.442718337570.8411951434420.2985892085784.033337997311.164581710858.89472510363-0.1234654831490.354538229296-0.357445176209-0.374037466592-0.0239789126148-0.7453924881030.2103639690150.6289709671760.1468876061520.4611731393880.00267339741460.1218072277850.5156812827760.04685703970760.6864680644422.0182844763-30.541148636951.2212005605
133.250279299361.45741664282-1.04937448113.90048730289-2.122201295483.05627778508-0.077181302649-0.07786850062650.03246090530330.2376454646540.00309750528320.0210048657367-0.01821186311680.09484295336480.1052388819050.5650285746910.0148517532395-0.1688168263910.405490592027-0.03615643917220.70093581986514.7007842923-39.103676845880.3960609239
145.45782244246-0.9411296377333.238796456161.7071892059-1.139693280752.21375542288-0.312627239311.25950625952-0.565210585235-0.3523226675590.101477246616-1.046418091510.917627242542.248474100030.09946655749281.17784964305-0.03918452021050.4603721150561.11178336864-0.26379192030.85720575061618.9868796432-35.120080049736.3850273077
152.56164574841-2.23700110771-0.8650893332033.6517291828-2.01065451467.23416684218-0.3852260655560.4533144747561.08646574722-1.019669032420.986869410173-2.499660784330.862482742011.31794614403-0.5548184313510.853930860757-0.1692270251520.2876201026670.715636333875-0.2231014540421.0010845166817.1929280541-24.184819198936.9463097195
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'P' and (resid 1 through 7 )PA1 - 71 - 7
22chain 'P' and (resid 8 through 12 )PA8 - 128 - 12
33chain 'B' and (resid 1 through 101 )BB1 - 1011 - 106
44chain 'B' and (resid 102 through 128 )BB102 - 128107 - 133
55chain 'B' and (resid 129 through 214 )BB129 - 214134 - 219
66chain 'A' and (resid 3 through 44 )AC3 - 441 - 42
77chain 'A' and (resid 45 through 111 )AC45 - 11143 - 117
88chain 'A' and (resid 112 through 215 )AC112 - 215118 - 221
99chain 'D' and (resid 1 through 69 )DD1 - 691 - 74
1010chain 'D' and (resid 70 through 113 )DD70 - 11375 - 118
1111chain 'D' and (resid 114 through 213 )DD114 - 213119 - 218
1212chain 'C' and (resid 3 through 111 )CE3 - 1111 - 117
1313chain 'C' and (resid 112 through 214 )CE112 - 214118 - 220
1414chain 'R' and (resid 3 through 7 )RF3 - 71 - 5
1515chain 'R' and (resid 8 through 12 )RF8 - 126 - 10

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