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- PDB-6b5l: Structure of PfCSP peptide 20 with human protective antibody CIS43 -

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Basic information

Entry
Database: PDB / ID: 6b5l
TitleStructure of PfCSP peptide 20 with human protective antibody CIS43
Components
  • CIS43 Fab Heavy chain
  • CIS43 Fab Light Chain
  • PfCSP peptide 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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
H: CIS43 Fab Heavy chain
L: CIS43 Fab Light Chain
A: PfCSP peptide 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL


Theoretical massNumber of molelcules
Total (without water)49,5283
Polymers49,5283
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-29 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.942, 61.668, 75.371
Angle α, β, γ (deg.)90.00, 106.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody CIS43 Fab Heavy chain


Mass: 24223.258 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 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL


Mass: 1166.155 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 / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Sulfate, 0.1M Sodium 659 Acetate Trihydrate pH 4.6, 30% PEG MME 2000

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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: 2.4→45.142 Å / Num. obs: 15363 / % possible obs: 93.3 % / Redundancy: 2.9 % / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.14 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 817 5.32 %
Rwork0.199 --
obs0.201 15352 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 65 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063491
X-RAY DIFFRACTIONf_angle_d0.8264761
X-RAY DIFFRACTIONf_dihedral_angle_d14.0091258
X-RAY DIFFRACTIONf_chiral_restr0.051542
X-RAY DIFFRACTIONf_plane_restr0.005608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3959-2.5460.30241190.25791970X-RAY DIFFRACTION76
2.546-2.74260.33721340.25962244X-RAY DIFFRACTION88
2.7426-3.01860.28511180.24722518X-RAY DIFFRACTION97
3.0186-3.45520.24611450.21942596X-RAY DIFFRACTION100
3.4552-4.35260.21421540.17852574X-RAY DIFFRACTION100
4.3526-45.14990.20811470.16552633X-RAY DIFFRACTION99
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)
12.7334-0.8319-0.91040.8516-0.50846.44550.2029-0.0814-0.1945-0.2071-0.03720.35450.8225-0.9775-0.23010.4337-0.1601-0.03710.4990.06340.329677.955-10.675994.2297
27.5367-1.95832.71265.96322.40516.2819-0.78810.46840.627-0.96110.6122-0.29970.2244-0.01040.30550.50890.00450.03470.3125-0.04940.289685.0949-2.682799.0538
36.2677-0.0507-2.04951.16570.65781.0264-0.1033-0.72980.61840.31180.06970.04250.0757-0.5009-0.54390.59060.00560.22880.76010.01360.420576.7609-2.0023104.7424
45.1541-0.47460.69683.97471.63225.16190.5588-0.42890.0097-0.2768-0.29080.1858-0.1175-1.2516-0.06050.7805-0.15360.20421.0877-0.06060.487971.9712-6.998297.781
55.6264-2.3253-1.39242.11240.03346.15780.4411-0.144-0.17-0.044-0.28140.47970.42560.1601-0.16850.4395-0.1541-0.05350.3202-0.05680.316683.6973-8.378695.7828
62.7327-1.8918-0.64915.54581.72632.86050.1638-0.00040.1813-0.3805-0.1108-0.1318-0.13110.0138-0.05290.2242-0.01230.00690.2890.04760.257190.3646-13.799169.9009
74.2704-3.7671-0.18047.54041.59910.7171-0.0468-0.0094-0.3614-0.0197-0.05980.37530.22350.05960.13480.3224-0.0507-0.00930.2876-0.00880.289588.5046-21.446269.1784
83.4284-2.958-5.7296.11625.08369.79570.3418-0.18590.0892-0.16270.0105-0.4033-0.42410.053-0.43640.4178-0.0847-0.07720.4120.04310.3768106.5246-5.195799.0158
93.2492-1.0187-1.95073.5283-0.86955.8193-0.156-0.1916-0.26240.18410.0496-0.10931.1545-0.06920.05850.4965-0.1003-0.04670.27020.04950.294497.3347-12.7297105.944
100.7101-0.2861-0.7553-0.07030.08483.23250.0465-0.1348-0.01850.08740.1141-0.00650.12110.3367-0.17460.3529-0.0632-0.01540.16670.02250.3388100.7377-10.697188.5983
112.1828-1.18951.59260.6157-0.93114.64060.07880.0117-0.0472-0.03850.09650.21390.09430.2308-0.13440.3389-0.04010.0330.2504-0.01810.3499103.7092-8.426468.5019
124.1545-0.60142.63910.2988-1.17825.36320.00940.4290.0551-0.03750.1239-0.0505-0.0801-0.009-0.06270.4038-0.04080.07340.22910.00060.3111102.6456-8.216857.1926
130.32940.8550.98317.15338.02469.031-0.2689-0.07520.07421.0575-0.56631.2060.3392-0.58410.54840.4752-0.1052-0.02080.4747-0.01450.44785.3166-6.6199113.4493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 40 )
2X-RAY DIFFRACTION2chain 'H' and (resid 41 through 52 )
3X-RAY DIFFRACTION3chain 'H' and (resid 53 through 63 )
4X-RAY DIFFRACTION4chain 'H' and (resid 64 through 82 )
5X-RAY DIFFRACTION5chain 'H' and (resid 83 through 111 )
6X-RAY DIFFRACTION6chain 'H' and (resid 112 through 175 )
7X-RAY DIFFRACTION7chain 'H' and (resid 176 through 213 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 25 )
9X-RAY DIFFRACTION9chain 'L' and (resid 26 through 61 )
10X-RAY DIFFRACTION10chain 'L' and (resid 62 through 128 )
11X-RAY DIFFRACTION11chain 'L' and (resid 129 through 174 )
12X-RAY DIFFRACTION12chain 'L' and (resid 175 through 212 )
13X-RAY DIFFRACTION13chain 'A' and (resid 1 through 10 )

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