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- PDB-8fba: Crystal structure of Ky315 Fab in complex with circumsporozoite p... -

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Basic information

Entry
Database: PDB / ID: 8fba
TitleCrystal structure of Ky315 Fab in complex with circumsporozoite protein DND peptide
Components
  • Circumsporozoite protein DND peptide
  • Ky315 Antibody, heavy chain
  • Ky315 Antibody, light chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody
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 falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBurn Aschner, C. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906 United States
CitationJournal: Cell Rep / Year: 2023
Title: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.
Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / ...Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / Huntwork, R.H.C. / Bolscher, J.M. / de Bruijni, M.H.C. / Sauerwein, R. / Dennison, S.M. / Tomaras, G.D. / Zavala, F. / Kellam, P. / Wardemann, H. / Julien, J.P.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ky315 Antibody, heavy chain
B: Ky315 Antibody, light chain
C: Ky315 Antibody, heavy chain
D: Ky315 Antibody, light chain
P: Circumsporozoite protein DND peptide
Q: Circumsporozoite protein DND peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,09516
Polymers97,4756
Non-polymers62110
Water11,998666
1
A: Ky315 Antibody, heavy chain
B: Ky315 Antibody, light chain
P: Circumsporozoite protein DND peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,17210
Polymers48,7373
Non-polymers4347
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-18 kcal/mol
Surface area20330 Å2
MethodPISA
2
C: Ky315 Antibody, heavy chain
D: Ky315 Antibody, light chain
Q: Circumsporozoite protein DND peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9246
Polymers48,7373
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-24 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.348, 65.245, 128.690
Angle α, β, γ (deg.)90.000, 97.250, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Antibody Ky315 Antibody, heavy chain


Mass: 24060.014 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 Ky315 Antibody, light chain


Mass: 23412.059 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: Protein/peptide Circumsporozoite protein DND peptide / CS


Mass: 1265.286 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (isolate NF54) (eukaryote)
References: UniProt: P08307
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate pH 5.9, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920088 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920088 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / Num. obs: 79772 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 27.19 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.6
Reflection shellResolution: 1.96→1.99 Å / Num. unique obs: 3529 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 6ULF

6ulf


Resolution: 1.96→39.37 Å / SU ML: 0.2354 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 1999 2.51 %
Rwork0.1777 77750 -
obs0.1788 79749 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 1.96→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 40 666 7436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537119
X-RAY DIFFRACTIONf_angle_d0.75839711
X-RAY DIFFRACTIONf_chiral_restr0.05121079
X-RAY DIFFRACTIONf_plane_restr0.00541267
X-RAY DIFFRACTIONf_dihedral_angle_d12.84842541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.33931410.27515504X-RAY DIFFRACTION99.98
2.01-2.060.29761420.24675528X-RAY DIFFRACTION99.96
2.06-2.120.29251420.23785529X-RAY DIFFRACTION99.98
2.12-2.190.25831420.22255501X-RAY DIFFRACTION99.93
2.19-2.270.24331420.2075527X-RAY DIFFRACTION99.98
2.27-2.360.23971420.19565522X-RAY DIFFRACTION100
2.36-2.470.24571420.1915551X-RAY DIFFRACTION99.98
2.47-2.60.22961430.19435550X-RAY DIFFRACTION99.91
2.6-2.760.21031420.18835530X-RAY DIFFRACTION99.98
2.76-2.980.24381430.18475538X-RAY DIFFRACTION100
2.98-3.270.22841430.17935573X-RAY DIFFRACTION100
3.27-3.750.22151440.1645582X-RAY DIFFRACTION100
3.75-4.720.17871440.13615595X-RAY DIFFRACTION99.95
4.72-39.370.16931470.15125720X-RAY DIFFRACTION99.91
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)
12.73986026416-1.23869816339-0.2767396628472.067166117880.8697180704921.25248218280.1383304992320.2696898272220.202418029588-0.644593765003-0.2027640516820.129164444893-0.209184574155-0.1936781683230.04384062095260.3808625699010.0887400181555-0.05825201078370.2585063693250.01434038254870.21197178394213.15694664531.6280330312435.0436408768
22.42511973625-0.1985595807641.108898020443.363215223771.137248073992.946674376910.0422102138478-0.08471318640040.1245350913680.137912974479-0.1183878836850.0153150552079-0.065980361569-0.1020056291980.08066313015190.11490009816-0.00220966600595-0.008099435588840.2060741475250.008088214637120.214346875428-0.98479881372924.110773963361.4089094393
31.535231834590.006233780873040.4654115391922.516651734981.352510696172.3260365854-0.00177657422989-0.09935154262720.0402819811891-0.123017234565-0.00477888858002-0.13180638727-0.0884312182147-0.01206628598220.0004236911220210.1318299579250.0158022680734-0.01539617285220.1651013128370.008170567744760.16975008362825.7257050566-1.5955034717353.5927276072
43.372074091170.21892057546-0.1017007071211.14842772787-0.1432758838761.294485419940.05552892294290.0338238278909-0.04536359759310.0507105274854-0.01667884866430.176585075168-0.00949232396992-0.169709026939-0.03426310102410.133292736234-0.00182894089334-0.008304755787320.200895269604-0.01374889025460.185742394376-1.7030728138511.923795794471.344694864
52.09266853944-0.205666489504-0.2802851982722.251565856830.5035274154452.546411218690.01540497744180.13844333386-0.085507702767-0.261559448680.02890424711460.2040694383650.14726669277-0.115216723377-0.0218598849730.22751170340.00689224203119-0.06466435771560.202496925621-0.004993107067480.18154103244514.276686244829.276804670130.0493167724
61.830365980580.03600625510990.9757820176362.924714079091.118230936962.54441244832-0.210716305743-0.0666367437191-0.368051109430.4579722896650.0632480075177-0.02702492908390.8535311251850.01686151087110.09866149467170.9655306215090.04480626831160.1079577879780.342545272194-0.01169482952860.30683709560132.61380827717.071771765247.87498735857
72.84982819057-1.081704478260.3383579793212.81682263187-0.0004602267305622.476261519620.0644163627780.0880580349032-0.205770026415-0.06561305578720.0281267163892-0.129425196840.2634438928150.273221022887-0.09536200106530.2246377015330.0396532511959-0.03092138425090.237840617975-0.03713394701410.1789000342335.800412226930.516593673936.2215554643
81.93601660426-0.225221131019-0.4009162005231.326432281880.3313448017075.131094528580.008272973933730.1164455113990.0895042566773-0.4277278208310.244871191203-0.2829931064190.09022973737080.365647449433-0.2609545147210.7087977695430.0716924786890.1379870258820.371761782242-0.07427902156810.35223137690743.40437243819.23043589243.85906586398
95.798189018491.374705654173.117456776752.0818351058-1.006913260663.415334979490.1477369544620.366846618244-0.19253595623-0.5142249225230.205447462401-0.442245100995-0.52577668922-0.00579610622282-0.1822762411730.4806689808910.07928223497290.09702567672060.279741901056-0.003512596090030.18319329921424.144441684-10.281634870730.1650651466
105.49325407113-0.1065821821614.336481278659.44174007451-4.024382358235.27517422885-0.111759264856-0.4387007378390.05875493635540.8185129605190.08536960311630.415561818673-0.197303649902-0.0129461166757-0.04466564343260.2281389947020.03614808304860.03137406512140.244085571402-0.05208877316180.16965005566514.277857196540.584373028142.7325477045
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 113 )AA1 - 1131 - 124
22chain 'A' and (resid 114 through 216 )AA114 - 216125 - 227
33chain 'B' and (resid 1 through 107)BB1 - 1071 - 106
44chain 'B' and (resid 108 through 214 )BB108 - 214107 - 213
55chain 'C' and (resid 1 through 113 )CC1 - 1131 - 124
66chain 'C' and (resid 114 through 214 )CC114 - 214125 - 219
77chain 'D' and (resid 1 through 107 )DD1 - 1071 - 106
88chain 'D' and (resid 108 through 213 )DD108 - 213107 - 212
99chain 'P' and (resid 1 through 11 )PE1 - 111 - 11
1010chain 'Q' and (resid 1 through 11 )QF1 - 111 - 11

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