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- PDB-6uc5: Fab397 in complex with NPNA peptide -

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Basic information

Entry
Database: PDB / ID: 6uc5
TitleFab397 in complex with NPNA peptide
Components
  • Fab397 heavy chain
  • Fab397 light chain
  • NPNA peptide
KeywordsIMMUNE SYSTEM / Antibody / Malaria / Circumsporozoite protein / CSP / NANP / NANP repeats / Plasmodium / Plasmodium falciparum
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / side of membrane / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / cell surface ...entry into host cell by a symbiont-containing vacuole / side of membrane / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / cell surface / extracellular space / extracellular exosome / metal ion binding / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Circumsporozoite protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPholcharee, T. / Oyen, D. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: J Mol Biol / Year: 2020
Title: Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein.
Authors: Tossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / ...Authors: Tossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / Fidel Zavala / Andrew B Ward / Ian A Wilson /
Abstract: Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 ...Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This "conserved" Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding.
History
DepositionSep 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab397 heavy chain
L: Fab397 light chain
P: NPNA peptide


Theoretical massNumber of molelcules
Total (without water)48,5653
Polymers48,5653
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-26 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.268, 77.492, 87.701
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 Fab397 heavy chain


Mass: 23489.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A8K008
#2: Antibody Fab397 light chain


Mass: 23939.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8TCD0
#3: Protein/peptide NPNA peptide


Mass: 1136.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P02893*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 6.62, 22% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 41579 / % possible obs: 95.3 % / Redundancy: 10.6 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.969 / Rpim(I) all: 0.031 / Rsym value: 0.104 / Net I/σ(I): 24.5
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1315 / CC1/2: 0.823 / Rpim(I) all: 0.339 / Rsym value: 0.76

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.75→35.66 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.225 2105 10 %
Rwork0.19 --
obs0.193 41411 94.31 %
Refinement stepCycle: LAST / Resolution: 1.75→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 0 253 3575

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