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- PDB-6b5r: Structure of PfCSP peptide 21 with human antibody CIS42 -

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Basic information

Entry
Database: PDB / ID: 6b5r
TitleStructure of PfCSP peptide 21 with human antibody CIS42
Components
  • CIS42 Fab Heavy chain
  • CIS42 Fab Light chain
  • PfCSP peptide 21: ASN-PRO-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
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.775 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 2.0Oct 16, 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: CIS42 Fab Heavy chain
L: CIS42 Fab Light chain
A: PfCSP peptide 21: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN


Theoretical massNumber of molelcules
Total (without water)47,9353
Polymers47,9353
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-33 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.131, 70.570, 165.379
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: 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)
#3: Protein/peptide PfCSP peptide 21: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN


Mass: 1562.553 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.: 408 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
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: 1.77→26.949 Å / Num. obs: 35657 / % possible obs: 74.1 % / Redundancy: 3.8 % / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.775→26.949 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 1810 5.08 %
Rwork0.1906 --
obs0.193 35651 75.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.775→26.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 0 408 3677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063378
X-RAY DIFFRACTIONf_angle_d0.784628
X-RAY DIFFRACTIONf_dihedral_angle_d9.4892012
X-RAY DIFFRACTIONf_chiral_restr0.049526
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7754-1.82340.3525240.3194401X-RAY DIFFRACTION12
1.8234-1.8770.2592690.28721214X-RAY DIFFRACTION36
1.877-1.93760.3027940.24541966X-RAY DIFFRACTION57
1.9376-2.00680.27781350.22152435X-RAY DIFFRACTION71
2.0068-2.08710.2691530.222821X-RAY DIFFRACTION82
2.0871-2.18210.28621670.20183179X-RAY DIFFRACTION92
2.1821-2.29710.2361560.19743304X-RAY DIFFRACTION95
2.2971-2.44090.26671540.2093197X-RAY DIFFRACTION93
2.4409-2.62920.25331650.20823117X-RAY DIFFRACTION90
2.6292-2.89350.27131700.20912982X-RAY DIFFRACTION86
2.8935-3.31160.26571730.19362871X-RAY DIFFRACTION83
3.3116-4.16980.20831530.17612828X-RAY DIFFRACTION79
4.1698-26.95240.19111970.15673526X-RAY DIFFRACTION95
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)
11.8566-0.12950.27981.0109-0.3211.7352-0.0058-0.03170.04150.145-0.01320.12140.07230.01370.01790.1572-0.0036-0.00190.1181-0.04150.151784.7242132.0474172.2122
20.9928-0.35460.68410.9972-0.08611.4718-0.0191-0.0747-0.03540.1465-0.00350.06770.05180.07370.02820.1475-0.00970.01180.117-0.0120.107688.1495132.1218174.5439
33.56830.5636-0.2395.91162.53324.05390.0684-0.10010.3339-0.0696-0.17660.7945-0.1313-0.15930.05920.22630.0035-0.0180.1982-0.01970.248398.9411136.914206.6354
43.47130.3911-0.72277.02473.18756.8050.1657-0.33230.43560.1917-0.30420.7217-0.16440.03670.13940.2308-0.0327-0.02770.2339-0.01850.280297.3791137.9245208.7854
52.0756-2.2547-1.44124.6263.48636.29260.0913-0.5320.68810.4544-0.11630.40180.07770.6093-0.51510.2815-0.10520.1030.2134-0.18050.452289.1538158.4181177.3145
66.47382.62292.70964.686-2.99916.69120.08940.21390.34230.0122-0.0028-0.5779-0.10320.3307-0.08210.1064-0.0048-0.01940.12170.02790.265288.8682156.4687166.4099
72.655-0.28551.44613.2205-0.49143.63760.1099-0.28270.28380.28560.11980.4535-0.2121-0.2394-0.15790.15480.00660.03750.1091-0.04540.236178.7876153.6133172.2483
81.59710.1440.80652.5321-0.75612.37620.0213-0.23160.35460.2101-0.06610.3342-0.149-0.24450.04210.0900.04040.1624-0.05470.246684.1821150.2432173.4033
93.9393-0.74983.76450.1448-0.75483.7504-0.4844-0.71120.2535-0.0155-0.49710.1715-0.3702-1.23180.74710.34530.0209-0.08430.3951-0.14830.368889.7022159.6456191.9729
107.6201-4.05152.82637.0073-1.1443.26410.06440.0113-0.1411-0.1070.0744-0.04640.11260.1928-0.18690.2086-0.0397-0.0380.1723-0.01250.133106.7953146.9985203.3827
117.3848-0.52451.23177.48910.36545.884-0.09110.26990.0061-0.3970.0626-0.2975-0.15380.04780.070.23750.00820.04940.15140.0210.195107.4448147.1553199.2431
123.2089-2.76241.76533.4521-0.89233.2673-0.18380.09620.41760.04750.364-1.1316-0.25930.442-0.11810.45480.0341-0.04010.31640.01980.4861110.9095155.4757202.5299
134.8251-0.2804-0.83312.10070.07753.4241-0.08040.40480.1488-0.8292-0.1193-0.0188-0.42680.18080.11410.2604-0.037-0.05770.23030.03570.144776.2384139.3471155.8865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:59 )H2 - 59
2X-RAY DIFFRACTION2( CHAIN H AND RESID 60:119 )H60 - 119
3X-RAY DIFFRACTION3( CHAIN H AND RESID 120:157 )H120 - 157
4X-RAY DIFFRACTION4( CHAIN H AND RESID 158:214 )H158 - 214
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:18 )L1 - 18
6X-RAY DIFFRACTION6( CHAIN L AND RESID 19:27 )L19 - 27
7X-RAY DIFFRACTION7( CHAIN L AND RESID 28:75 )L28 - 75
8X-RAY DIFFRACTION8( CHAIN L AND RESID 76:101 )L76 - 101
9X-RAY DIFFRACTION9( CHAIN L AND RESID 102:114 )L102 - 114
10X-RAY DIFFRACTION10( CHAIN L AND RESID 115:151 )L115 - 151
11X-RAY DIFFRACTION11( CHAIN L AND RESID 152:188 )L152 - 188
12X-RAY DIFFRACTION12( CHAIN L AND RESID 189:209 )L189 - 209
13X-RAY DIFFRACTION13( CHAIN A AND RESID 1:13 )A1 - 13

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