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- PDB-6b5t: Structure of PfCSP peptide 29 with human antibody CIS42 -

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Basic information

Entry
Database: PDB / ID: 6b5t
TitleStructure of PfCSP peptide 29 with human antibody CIS42
Components
  • CIS42 Fab Heavy chain
  • CIS42 Fab Light chain
  • pfCSP peptide 29: ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA
KeywordsIMMUNE SYSTEM / Malaria / pfCSP / vaccine / antibodies
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / 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
AMMONIUM ION / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium Falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.222 Å
AuthorsPancera, M. / Weidle, C.
CitationJournal: Nat. Med. / Year: 2018
Title: A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite.
Authors: Kisalu, N.K. / Idris, A.H. / Weidle, C. / Flores-Garcia, Y. / Flynn, B.J. / Sack, B.K. / Murphy, S. / Schon, A. / Freire, E. / Francica, J.R. / Miller, A.B. / Gregory, J. / March, S. / Liao, ...Authors: Kisalu, N.K. / Idris, A.H. / Weidle, C. / Flores-Garcia, Y. / Flynn, B.J. / Sack, B.K. / Murphy, S. / Schon, A. / Freire, E. / Francica, J.R. / Miller, A.B. / Gregory, J. / March, S. / Liao, H.X. / Haynes, B.F. / Wiehe, K. / Trama, A.M. / Saunders, K.O. / Gladden, M.A. / Monroe, A. / Bonsignori, M. / Kanekiyo, M. / Wheatley, A.K. / McDermott, A.B. / Farney, S.K. / Chuang, G.Y. / Zhang, B. / Kc, N. / Chakravarty, S. / Kwong, P.D. / Sinnis, P. / Bhatia, S.N. / Kappe, S.H.I. / Sim, B.K.L. / Hoffman, S.L. / Zavala, F. / Pancera, M. / Seder, R.A.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pfCSP peptide 29: ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA
H: CIS42 Fab Heavy chain
L: CIS42 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8974
Polymers47,8793
Non-polymers181
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-31 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.580, 70.664, 163.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide pfCSP peptide 29: ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA


Mass: 1506.493 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium Falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#2: Antibody CIS42 Fab Heavy chain


Mass: 23617.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CIS42 Fab Light chain


Mass: 22755.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG3350, 9% Isopropanol, 0.12M Ammonium Citrate pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→37.055 Å / Num. obs: 24551 / % possible obs: 99.6 % / Redundancy: 6.6 % / Net I/σ(I): 31.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.222→37.055 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1251 5.11 %
Rwork0.1832 --
obs0.1845 24491 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.222→37.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 1 267 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053350
X-RAY DIFFRACTIONf_angle_d0.7994586
X-RAY DIFFRACTIONf_dihedral_angle_d9.5071982
X-RAY DIFFRACTIONf_chiral_restr0.048522
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2222-2.31110.24471300.20552505X-RAY DIFFRACTION98
2.3111-2.41630.2281320.20352532X-RAY DIFFRACTION100
2.4163-2.54360.26931140.20882558X-RAY DIFFRACTION100
2.5436-2.7030.23451330.20272550X-RAY DIFFRACTION100
2.703-2.91160.20541470.20132548X-RAY DIFFRACTION100
2.9116-3.20450.20711310.19622608X-RAY DIFFRACTION100
3.2045-3.66780.20971600.18322559X-RAY DIFFRACTION100
3.6678-4.61960.1861550.1522623X-RAY DIFFRACTION100
4.6196-37.06030.1971490.17352757X-RAY DIFFRACTION100
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)
11.15170.90732.11480.831.82254.2140.0184-0.3350.11330.4107-0.02660.1037-0.26660.24750.21910.3941-0.05140.04930.359-0.01780.1916-4.5464-2.22699.3003
21.99210.5222-1.30611.4042-0.02423.00650.0499-0.07470.1213-0.0051-0.05330.136-0.25490.0377-0.00020.16910.003-0.00030.1408-0.02120.19643.91278.9945-7.6291
33.6146-0.5122-0.5294.5782-0.22782.70760.21580.15-0.2279-0.2097-0.07190.1565-0.2079-0.0428-0.08040.2593-0.0140.04430.1767-0.00450.230816.37042.8932-39.6374
44.29411.32112.24532.79151.33735.62880.50030.4713-0.6054-0.84490.2065-0.2787-0.44880.0585-0.73050.45120.0630.00870.2923-0.04240.304515.9546-2.4053-45.1776
54.11252.16751.62873.95733.27777.64070.31160.2913-0.0442-0.952-0.41110.3372-0.3902-0.60290.14490.530.1531-0.0310.2864-0.02110.274213.73746.8785-47.27
66.1709-4.4336-3.89393.25582.78352.46720.3340.59420.2832-1.1393-0.2840.0059-0.2512-0.0827-0.18190.68760.09690.0890.31520.05440.298817.58749.5451-47.4362
74.9165-0.85252.67830.8407-0.16117.32690.02540.4091-0.26480.13680.0563-0.27230.69190.5694-0.13670.17870.02460.04660.1672-0.0110.2685.6596-18.3166-11.1242
81.99040.09620.01222.50551.01295.4827-0.00030.06990.0069-0.0326-0.02790.03680.0045-0.30050.03060.15260.00420.01820.16320.020.2045-0.2002-11.7465-6.9508
95.37342.1452-2.51494.195-0.71173.80390.1855-0.01950.23460.0666-0.08390.0595-0.1440.0026-0.11890.17030.02160.0180.1737-0.01080.166222.4023-7.8355-36.4672
104.4508-0.1855-0.62594.60761.06213.52520.0387-0.1230.04830.3666-0.0189-0.20660.01230.27240.00860.2659-0.01880.00980.17730.01310.184924.9371-5.949-32.8694
118.5834-0.7452-1.31371.50450.8321.8584-0.3095-0.3557-0.1767-0.41340.0288-0.53340.6150.37880.08820.31160.0255-0.01920.21120.05660.3329.1339-13.981-36.6777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 14 )
2X-RAY DIFFRACTION2chain 'H' and (resid 2 through 119 )
3X-RAY DIFFRACTION3chain 'H' and (resid 120 through 175 )
4X-RAY DIFFRACTION4chain 'H' and (resid 176 through 188 )
5X-RAY DIFFRACTION5chain 'H' and (resid 189 through 203 )
6X-RAY DIFFRACTION6chain 'H' and (resid 204 through 213 )
7X-RAY DIFFRACTION7chain 'L' and (resid 2 through 24 )
8X-RAY DIFFRACTION8chain 'L' and (resid 25 through 107 )
9X-RAY DIFFRACTION9chain 'L' and (resid 108 through 151 )
10X-RAY DIFFRACTION10chain 'L' and (resid 152 through 188 )
11X-RAY DIFFRACTION11chain 'L' and (resid 189 through 210 )

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