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- PDB-8fg0: Crystal structure of the 3764 Fab in complex with the C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 8fg0
TitleCrystal structure of the 3764 Fab in complex with the C-terminal PfCSP linker, PfCSP281-294.
Components
  • 3764 Fab Heavy chain
  • 3764 Fab Light chain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / 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 speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsBurn Aschner, C. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906 United States
CitationJournal: Embo Mol Med / Year: 2023
Title: Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies.
Authors: Oludada, O.E. / Costa, G. / Burn Aschner, C. / Obraztsova, A.S. / Prieto, K. / Canetta, C. / Hoffman, S.L. / Kremsner, P.G. / Mordmuller, B. / Murugan, R. / Julien, J.P. / Levashina, E.A. / Wardemann, H.
History
DepositionDec 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 3764 Fab Heavy chain
D: 3764 Fab Light chain
A: 3764 Fab Heavy chain
B: 3764 Fab Light chain
P: Circumsporozoite protein
Q: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)99,2156
Polymers99,2156
Non-polymers00
Water5,206289
1
C: 3764 Fab Heavy chain
D: 3764 Fab Light chain
P: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-31 kcal/mol
Surface area18920 Å2
MethodPISA
2
A: 3764 Fab Heavy chain
B: 3764 Fab Light chain
Q: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-30 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.236, 66.701, 95.540
Angle α, β, γ (deg.)90.000, 113.405, 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

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Components

#1: Antibody 3764 Fab Heavy chain


Mass: 23712.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 3764 Fab Light chain


Mass: 24284.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein / CS / PfCSP


Mass: 1609.679 Da / Num. of mol.: 2 / Fragment: residues 281-294 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q7K740
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 19% (v/v) isopropanol, 19% (w/v) PEG 4000, 5% (v/v) glycerol, 0.095 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.36→40 Å / Num. obs: 43719 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 43.7 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 2.36→2.46 Å / Num. unique obs: 5067 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→39.21 Å / SU ML: 0.3238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2372 1995 4.57 %
Rwork0.1755 41701 -
obs0.1782 43696 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.54 Å2
Refinement stepCycle: LAST / Resolution: 2.36→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6663 0 0 289 6952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726885
X-RAY DIFFRACTIONf_angle_d0.92889404
X-RAY DIFFRACTIONf_chiral_restr0.05511061
X-RAY DIFFRACTIONf_plane_restr0.00691216
X-RAY DIFFRACTIONf_dihedral_angle_d6.4661972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.420.33131400.26882949X-RAY DIFFRACTION98.5
2.42-2.480.29291460.25642967X-RAY DIFFRACTION99.36
2.48-2.560.33271440.24912956X-RAY DIFFRACTION99.52
2.56-2.640.27011440.22892980X-RAY DIFFRACTION99.71
2.64-2.730.33121350.20932970X-RAY DIFFRACTION99.36
2.73-2.840.27461460.2012980X-RAY DIFFRACTION99.21
2.84-2.970.26581420.20812938X-RAY DIFFRACTION98.81
2.97-3.130.26671390.21592920X-RAY DIFFRACTION97.61
3.13-3.330.25951450.18573009X-RAY DIFFRACTION99.34
3.33-3.580.24361500.17052945X-RAY DIFFRACTION99.52
3.58-3.940.23161370.16663024X-RAY DIFFRACTION99.47
3.94-4.510.19791400.13642955X-RAY DIFFRACTION97.91
4.51-5.680.18791400.13033035X-RAY DIFFRACTION99.65
5.68-39.210.20181470.16293073X-RAY DIFFRACTION98.71
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)
17.83148850439-0.966456687531-0.05551648873062.66293989976-0.06118187355693.12354358969-0.0783987965808-0.2158873053580.4647788619920.3021993070460.015499848086-0.3509303470.1293102167150.5088562128930.05962146016960.363576894410.0580003235291-0.03896473262320.526185332728-0.02387733745060.332938089577-56.5643294872.1931053034157.5968591099
23.15907080178-0.503790926066-0.934796421240.8290789336530.1131350236911.594498358990.0887995395536-0.2571396052690.299465744513-0.01021093554170.0355932360542-0.0449771702928-0.1676902099430.319647056548-0.1256368158070.353169650395-0.0238471073325-0.01771100169610.349584920246-0.05424282442810.390618807565-42.84156444147.7835903993230.9581504586
35.276026957720.288544849795-1.299554466961.26915310897-0.2320317259416.39698300258-0.07758977035150.7886780975330.24577187092-0.1457571944270.04385163717010.0235253217349-0.1483491320110.2401231369640.01739276021050.28418908830.00871847833231-0.01174464382950.482361440080.0522890019730.361268797175-74.6138627792.6591487444842.5286920436
4-0.0244559181838-0.0520271322684-0.6646528062950.504251871919-0.3863483841293.48225338332-0.0393642292133-0.00712925191429-0.00727851704365-0.01281935196770.0600742591074-0.09262878554970.0767903191211-0.245699985968-0.04441370688640.330846427160.00738512006949-0.0002475492535230.296173134420.004891340854610.326051726311-56.29213976670.83250532559630.3985673791
55.5975649522-2.248852879210.5878221246372.451637185890.3678415830562.870538886230.138443669625-0.0112979621376-0.112383522536-0.297048388337-0.0449288797312-0.004978740967030.3366929060160.0966488105988-0.04860033349210.4355098341970.0215672255514-0.01567431571710.2598203427320.04054522814670.339319228032-47.4262208007-2.0116764066815.5669717686
64.89842475257-0.116125341043-1.920674559741.652278245480.2480813394152.76791046726-0.0332790608868-0.4219005894980.1829644875210.2855708958180.00318459594930.0281743778750.05416020510680.08820648267790.03537814885130.3011176823780.0015002752625-0.03341828489270.279831205313-0.02689463652110.29915101312-17.4439503743-20.152076745933.2083400843
73.59379322836-0.8411393861542.325829099882.60420372873-2.403217817158.880766606670.04900391767470.1301490182570.154884499751-0.037153644505-0.1121617582280.109562770817-0.5005142394820.3148703954520.09897761680980.236827305029-0.04670970965230.008680181895020.201515652974-0.03335899692130.309217008348-7.37860754692-12.67196179453.67431304375
84.91991687536-1.411440114943.545662490513.86072455715-4.710316614648.93764982805-0.06611993434850.297967453974-0.354693823130.1453833305910.0126406093190.0204840372813-0.2248135676960.482819149743-0.004734982814290.330751535277-0.06212930032950.02489655547580.275573274154-0.0558976977790.304834137823-32.4078705427-35.569426232216.8378015603
99.093785071481.41308106059-4.256221974225.860289177791.889358788949.20514329008-0.238024936589-0.607156070222-0.1504313524890.6882625704030.0180896192315-0.2459359666670.2669114472250.04921838140420.3516579181110.374271859421-0.06831755941840.03350998268910.2990951003340.007670679310130.239483190979-38.8876149124-32.87810191635.9138834969
102.976455764212.17598015396-3.901334241375.272527716990.1872832673048.438905355270.0025334329240.6441150539270.519676827139-0.4230850044240.256334031444-0.346094669457-0.5250242025930.1855432532-0.3298586125460.28072064779-0.02340089503380.02130857150220.3007780384850.05485950996110.374182361922-30.2094952414-22.919932363620.3829776917
114.953551138054.10737850018-3.2191050249.796334119250.8121343902178.46045029746-0.0398051311673-0.08321673672090.262105601599-0.0118693441086-0.1415485999980.244138244491-0.0134416783518-0.5366077772450.0577392378530.2176655097150.00418476819246-0.03886941368190.373277647965-0.01966475788160.314828741204-40.7015400813-27.589921463520.8108351707
121.09562156096-0.115164618636-1.275915598870.06306917957460.2402142851452.92188365723-0.0833368814941-0.0610560550163-0.02149347713230.0102409090499-0.0480576305793-0.08745297934880.128618241675-0.03610217438860.1938774081260.321782479886-0.005117377438540.01512170119940.2007180844480.0484960093480.306874494321-22.0683268835-25.775519451410.3411717484
138.79903331287-2.12172061278-1.406504991170.9959575910160.1659427054641.37542216530.1106916554260.147444011123-0.285501668461-0.0103223573454-0.1892542340090.07321358395480.1553172634380.03061685524320.07137437704050.326288945602-0.00283585563407-0.0335411926260.2553448943590.02017839714670.267938386168-11.7226358957-27.8207817538-2.56517013007
147.229332720380.2456069054690.2137442951360.2871201956040.2752399913482.61871388852-0.04409670609340.275879582424-0.201124224395-0.205217044975-0.0122645569611-0.179676106816-0.02712627745970.3678069090670.05288063716860.3854059081640.05371739717190.04293348434480.2636761307320.04414983039150.384288226935-2.62919808684-26.5626103467-9.8800385769
156.921054927013.598465866712.538040554764.20136435368-2.405843758327.26156427487-0.116227512898-0.5946970532310.557565311372-0.0512055363204-0.315157029681-0.215270139199-0.09081550358150.03331271826810.3642106076520.4162803780020.06036254660990.03272813858790.770722779939-0.1003713097350.382403609448-70.47042363345.3404346563365.4205067902
165.685066677573.406205772081.24388731084.13967758477-1.81072905573.37534654784-0.378043209696-1.497814347520.2486915869540.5382455792860.5476729598490.412061670953-0.222313558616-1.008873143020.06322280824360.4385104234630.0150382289110.05454186634760.7493441664830.000662141048220.46089740579-33.1481628851-21.30977337342.7439951462
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 1 through 100C)CA1 - 1001 - 107
22chain 'C' and (resid 101 through 213 )CA101 - 213108 - 214
33chain 'D' and (resid 1 through 90 )DB1 - 901 - 95
44chain 'D' and (resid 91 through 128 )DB91 - 12896 - 133
55chain 'D' and (resid 129 through 213 )DB129 - 213134 - 218
66chain 'A' and (resid 1 through 119 )AC1 - 1191 - 126
77chain 'A' and (resid 120 through 214 )AC120 - 214127 - 217
88chain 'B' and (resid 1 through 25 )BD1 - 251 - 25
99chain 'B' and (resid 26 through 32 )BD26 - 3226 - 37
1010chain 'B' and (resid 33 through 48 )BD33 - 4838 - 53
1111chain 'B' and (resid 49 through 75 )BD49 - 7554 - 80
1212chain 'B' and (resid 76 through 128 )BD76 - 12881 - 133
1313chain 'B' and (resid 129 through 174 )BD129 - 174134 - 179
1414chain 'B' and (resid 175 through 213 )BD175 - 213180 - 218
1515chain 'P' and (resid 5 through 12 )PE5 - 121 - 8
1616chain 'Q' and (resid 4 through 13 )QF4 - 131 - 10

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