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- PDB-6b5s: Structure of PfCSP peptide 25 with human antibody CIS42 -

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Basic information

Entry
Database: PDB / ID: 6b5s
TitleStructure of PfCSP peptide 25 with human antibody CIS42
Components
  • CIS42 Fab Heavy chain
  • CIS42 Fab Light chain
  • pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-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
ISOPROPYL ALCOHOL / AMMONIUM ION / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium Falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.983 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 1.3Jan 9, 2019Group: Data collection / Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CIS42 Fab Heavy chain
L: CIS42 Fab Light chain
A: pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,24651
Polymers47,9373
Non-polymers1,30948
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-117 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.960, 70.817, 164.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN


Mass: 1564.569 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium Falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS

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Antibody , 2 types, 2 molecules HL

#1: 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)
#2: 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)

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Non-polymers , 4 types, 347 molecules

#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical...
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: H4N
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
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: 1.98→43.422 Å / Num. obs: 34887 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.983→43.422 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3
RfactorNum. reflection% reflection
Rfree0.2039 1745 5 %
Rwork0.1675 --
obs0.1694 34887 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.983→43.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 75 299 3661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053403
X-RAY DIFFRACTIONf_angle_d0.7674645
X-RAY DIFFRACTIONf_dihedral_angle_d11.051998
X-RAY DIFFRACTIONf_chiral_restr0.05526
X-RAY DIFFRACTIONf_plane_restr0.005587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9831-2.04150.24611440.21942586X-RAY DIFFRACTION95
2.0415-2.10740.21521420.19922754X-RAY DIFFRACTION100
2.1074-2.18270.23371090.1972735X-RAY DIFFRACTION100
2.1827-2.27010.22881380.18142717X-RAY DIFFRACTION100
2.2701-2.37340.23781660.1812724X-RAY DIFFRACTION100
2.3734-2.49850.23771560.18852753X-RAY DIFFRACTION100
2.4985-2.6550.22091480.18242730X-RAY DIFFRACTION100
2.655-2.860.23651490.18132752X-RAY DIFFRACTION100
2.86-3.14770.21611390.1722796X-RAY DIFFRACTION100
3.1477-3.6030.2251600.16912777X-RAY DIFFRACTION100
3.603-4.53860.15681310.13472839X-RAY DIFFRACTION100
4.5386-43.43220.18131630.16072979X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.20420.07610.2310.02820.08710.25650.2018-0.0225-0.32380.0265-0.06840.19050.1122-0.0699-0.00010.2953-0.0201-0.00270.3208-0.0160.333387.1993198.9691343.0955
20.1504-0.07430.25380.9563-0.0850.434-0.02940.059-0.0223-0.0219-0.05260.0314-0.00440.031400.2317-0.0014-0.00860.2924-0.0440.26987.1122203.2499332.4061
30.10150.10540.17980.58910.20450.3117-0.05680.09550.10010.0925-0.0708-0.0695-0.04390.0802-0.00010.24410.0104-0.01090.2877-0.01190.272786.8846208.4652337.0102
41.658-0.4641-0.48280.4606-0.33010.79170.0445-0.08780.09910.20630.0841-0.1056-0.04960.42730.00170.3872-0.0127-0.04230.23250.00170.3147103.3504207.4131366.7148
50.50310.51130.26630.9917-0.17240.54610.1327-0.01020.02140.031-0.09110.155-0.1211-0.012400.36580.0222-0.02550.3198-0.00050.315598.4456210.5597369.8601
60.01220.0515-0.04470.2184-0.19020.16420.24150.0333-0.09590.2269-0.2122-0.0380.1008-0.0690.00020.4654-0.0374-0.02820.3232-0.00220.303898.0556205.405377.4203
70.1442-0.0504-0.1270.1013-0.00910.1726-0.06380.1267-0.17590.12260.2595-0.1138-0.2234-0.074800.562-0.0692-0.06520.30880.00820.3516102.9416203.6768378.3596
81.2978-0.13420.38020.6427-0.40031.10220.01410.02110.12010.06060.023-0.0893-0.0383-0.1191-00.2693-0.0033-0.01920.27740.00870.289584.9885226.4663336.4014
90.42750.1870.4120.220.25620.84810.0166-0.00070.02210.0131-0.0009-0.12-0.0367-0.04480.00010.28390.0189-0.04380.2566-0.01050.290198.1944221.3031354.7928
100.34880.5613-0.08581.3909-0.04930.57190.156-0.09440.1958-0.2032-0.0616-0.2440.11440.090900.40420.0242-0.05760.3564-0.02370.3602109.1043218.204362.9625
110.27290.1784-0.06660.22740.00310.0985-0.24470.2423-0.01090.2990.0095-0.2312-0.50470.153900.45310.0061-0.0810.33980.03450.3796112.9958226.1895366.7255
120.1597-0.0495-0.12080.2386-0.0990.1774-0.24150.263-0.0823-0.6969-0.00840.36890.31990.3676-0.00390.46490.0165-0.0850.39930.01340.287778.522211.1064319.3601
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 82 )
3X-RAY DIFFRACTION3chain 'H' and (resid 83 through 106 )
4X-RAY DIFFRACTION4chain 'H' and (resid 107 through 145 )
5X-RAY DIFFRACTION5chain 'H' and (resid 146 through 188 )
6X-RAY DIFFRACTION6chain 'H' and (resid 189 through 203 )
7X-RAY DIFFRACTION7chain 'H' and (resid 204 through 214 )
8X-RAY DIFFRACTION8chain 'L' and (resid 2 through 75 )
9X-RAY DIFFRACTION9chain 'L' and (resid 76 through 151 )
10X-RAY DIFFRACTION10chain 'L' and (resid 152 through 188 )
11X-RAY DIFFRACTION11chain 'L' and (resid 189 through 210 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 13 )

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