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- PDB-6b5o: Structure of PfCSP peptide 29 with human protective antibody CIS43 -

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Basic information

Entry
Database: PDB / ID: 6b5o
TitleStructure of PfCSP peptide 29 with human protective antibody CIS43
Components
  • CIS43 Fab Heavy chain
  • CIS43 Fab Light chain
  • PfCSP peptide 29: ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN
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
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium Falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.194 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
Revision 2.0Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CIS43 Fab Heavy chain
L: CIS43 Fab Light chain
A: PfCSP peptide 29: ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN


Theoretical massNumber of molelcules
Total (without water)49,8513
Polymers49,8513
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-30 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.244, 60.410, 84.841
Angle α, β, γ (deg.)90.00, 107.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody CIS43 Fab Heavy chain


Mass: 24206.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CIS43 Fab Light chain


Mass: 24138.707 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: Protein/peptide PfCSP peptide 29: ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN


Mass: 1506.493 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium Falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.6M Sodium Citrate Tribasic Dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 22790 / % possible obs: 98.7 % / Redundancy: 13.5 % / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.194→50 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.89
RfactorNum. reflection% reflection
Rfree0.2401 1169 5.13 %
Rwork0.1929 --
obs0.1953 22773 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.194→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 0 124 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023505
X-RAY DIFFRACTIONf_angle_d0.6074778
X-RAY DIFFRACTIONf_dihedral_angle_d11.4912105
X-RAY DIFFRACTIONf_chiral_restr0.046543
X-RAY DIFFRACTIONf_plane_restr0.003610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.29410.32941250.28372303X-RAY DIFFRACTION83
2.2941-2.41510.32041330.26062750X-RAY DIFFRACTION99
2.4151-2.56640.3041600.24412690X-RAY DIFFRACTION100
2.5664-2.76450.31031490.24122762X-RAY DIFFRACTION100
2.7645-3.04270.26121470.23022743X-RAY DIFFRACTION100
3.0427-3.48290.27491520.20762756X-RAY DIFFRACTION100
3.4829-4.38760.19191490.16422762X-RAY DIFFRACTION100
4.3876-50.02440.20431540.15632838X-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)
12.57451.1795-1.31995.8216-0.76683.2728-0.0142-0.1103-0.0375-0.52060.17890.50450.3521-0.3858-0.11630.3511-0.0444-0.07230.47520.03930.4831-43.4878-8.730317.6874
23.17370.0077-0.93023.7244-1.033.6883-0.0069-0.49120.16220.33430.03770.1951-0.2492-0.0855-0.15890.3739-0.03210.02840.5729-0.01240.4622-38.3486-7.316229.9732
34.00720.5911-1.48035.4229-3.38435.59580.3204-0.5880.1887-0.0972-0.18061.078-0.2789-0.5698-0.18730.36060.04060.04650.7-0.00290.6266-47.1141-6.799526.5633
47.5216-2.1956-1.02343.2039-1.10188.07530.34070.01360.42210.1232-0.0724-0.0589-0.65310.065-0.12120.3479-0.0115-0.02460.3718-0.07910.3431-37.86920.135419.2137
50.98740.04760.14050.74740.70332.48140.0316-0.147-0.0826-0.0808-0.05240.14860.0502-0.09280.12860.3386-0.0155-0.03440.33730.01210.44-31.7151-13.79817.0316
61.22780.0632-0.02352.33660.80130.7999-0.07470.0386-0.0475-0.1704-0.00220.2094-0.05960.00770.0650.38040.0039-0.05350.31190.03470.3651-28.8449-16.2466-1.1532
78.8215-4.8323-5.9715.30515.26477.4112-0.15080.44810.0062-0.15-0.04420.3610.2305-0.26690.13610.5019-0.12430.09240.4628-0.03150.5655-35.9555-20.1691-6.5471
82.45910.41370.03731.81340.15813.0973-0.0294-0.3854-0.12790.01160.06320.04710.20830.0637-0.04450.34570.0266-0.02570.53490.02180.32-18.0617-11.952630.1459
91.0376-0.5114-0.48290.68690.31691.5029-0.0636-0.16840.0738-0.07750.04340.11660.08570.0458-0.08830.3728-0.0539-0.01170.301-0.02960.4302-21.5437-10.10017.2518
102.6329-2.13152.33971.8863-1.23015.74440.0482-0.10120.1417-0.17560.05520.1715-0.1954-0.01780.1830.3655-0.055-0.02170.24860.01220.3721-16.0876-7.5555-3.9275
114.3553-1.49024.01262.1956-0.81655.1656-0.01110.65110.3389-0.4355-0.1741-0.01290.13080.2510.15090.5211-0.0403-0.0060.34130.05920.3603-17.5481-7.3969-15.4502
120.0209-0.02760.0240.0309-0.02420.0159-0.8124-0.89730.43470.58850.0579-0.2043-0.4989-0.2377-0.00120.65450.0114-0.01931.0351-0.09590.6158-33.5172-10.607440.7821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'H' and (resid 26 through 63 )
3X-RAY DIFFRACTION3chain 'H' and (resid 64 through 82 )
4X-RAY DIFFRACTION4chain 'H' and (resid 83 through 93 )
5X-RAY DIFFRACTION5chain 'H' and (resid 94 through 157 )
6X-RAY DIFFRACTION6chain 'H' and (resid 158 through 203 )
7X-RAY DIFFRACTION7chain 'H' and (resid 204 through 214 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 90 )
9X-RAY DIFFRACTION9chain 'L' and (resid 91 through 128 )
10X-RAY DIFFRACTION10chain 'L' and (resid 129 through 174 )
11X-RAY DIFFRACTION11chain 'L' and (resid 175 through 213 )
12X-RAY DIFFRACTION12chain 'A' and (resid 3 through 11 )

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