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- EMDB-9114: Cryo-EM structure of the circumsporozoite protein of Plasmodium f... -

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Basic information

Entry
Database: EMDB / ID: EMD-9114
TitleCryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts
Map dataVaccine-elicited Fab311 in complex with Plasmodium falciparum recombinant shortened circumsporozoite protein
Sample
  • Complex: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP
    • Complex: Plasmodium falciparum recombinant shortened CSP
      • Protein or peptide: circumsporozoite protein
    • Complex: Fab311
      • Protein or peptide: Fab311 heavy chain
      • Protein or peptide: Fab311 light chain
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / side of membrane / cell surface / membrane / 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 subtype ...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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Circumsporozoite protein / Epididymis luminal protein 214
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsTorres JL / Cottrell CA / Ward AB
CitationJournal: Sci Adv / Year: 2018
Title: Cryo-EM structure of circumsporozoite protein with a vaccine-elicited antibody is stabilized by somatically mutated inter-Fab contacts.
Authors: David Oyen / Jonathan L Torres / Christopher A Cottrell / C Richter King / Ian A Wilson / Andrew B Ward /
Abstract: The circumsporozoite protein (CSP) on the surface of sporozoites is important for parasite development, motility, and host hepatocyte invasion. However, intrinsic disorder of the NANP repeat ...The circumsporozoite protein (CSP) on the surface of sporozoites is important for parasite development, motility, and host hepatocyte invasion. However, intrinsic disorder of the NANP repeat sequence in the central region of CSP has hindered its structural and functional characterization. Here, the cryo-electron microscopy structure at ~3.4-Å resolution of a recombinant shortened CSP construct with the variable domains (Fabs) of a highly protective monoclonal antibody reveals an extended spiral conformation of the central NANP repeat region surrounded by antibodies. This unusual structure appears to be stabilized and/or induced by interaction with an antibody where contacts between adjacent Fabs are somatically mutated and enhance the interaction. This maturation in non-antigen contact residues may be an effective mechanism for antibodies to target tandem repeat sequences and provide novel insights into malaria vaccine design.
History
DepositionSep 17, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseOct 31, 2018-
UpdateOct 31, 2018-
Current statusOct 31, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.81
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.81
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6mhg
  • Surface level: 0.81
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9114.png

Downloads & links

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Map

FileDownload / File: emd_9114.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVaccine-elicited Fab311 in complex with Plasmodium falciparum recombinant shortened circumsporozoite protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.81 / Movie #1: 0.81
Minimum - Maximum-2.8438306 - 5.6057243
Average (Standard dev.)0.0023496626 (±0.22099224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 296.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-2.8445.6060.002

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Supplemental data

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Sample components

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Entire : Fab311 in complex with Plasmodium falciparum recombinant shortened CSP

EntireName: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP
Components
  • Complex: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP
    • Complex: Plasmodium falciparum recombinant shortened CSP
      • Protein or peptide: circumsporozoite protein
    • Complex: Fab311
      • Protein or peptide: Fab311 heavy chain
      • Protein or peptide: Fab311 light chain

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Supramolecule #1: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP

SupramoleculeName: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Plasmodium falciparum recombinant shortened CSP

SupramoleculeName: Plasmodium falciparum recombinant shortened CSP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Fab311

SupramoleculeName: Fab311 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: circumsporozoite protein

MacromoleculeName: circumsporozoite protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 30.232156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YGSSSNTRVL NELNYDNAGT NLYNELEMNY YGKQENWYSL KKNSRSLGEN DDGNNEDNEK LRKPKHKKLK QPADGNPDPN ANPNVDPNA NPNVDPNANP NVDPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP N ANPNANPN ...String:
YGSSSNTRVL NELNYDNAGT NLYNELEMNY YGKQENWYSL KKNSRSLGEN DDGNNEDNEK LRKPKHKKLK QPADGNPDPN ANPNVDPNA NPNVDPNANP NVDPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP N ANPNANPN KNNQGNGQGH NMPNDPNRNV DENANANSAV KNNNNEEPSD KHIKEYLNKI QNSLSTEWSP CSVTCGNGIQ VR IKPGSAN KPKDELDYAN DIEKKICKME KCSSVFNVVN S

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Macromolecule #2: Fab311 heavy chain

MacromoleculeName: Fab311 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.098877 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG VVPPGRSLRL SCATSGFTFS NYGMHWVRQA PGKGLEWVAI IWYDGSRNFY AASVEGRFTI SRDNSKNTLY LQMNSLRVE DTAVYYCARA AYYDTSGYGD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLVESGGG VVPPGRSLRL SCATSGFTFS NYGMHWVRQA PGKGLEWVAI IWYDGSRNFY AASVEGRFTI SRDNSKNTLY LQMNSLRVE DTAVYYCARA AYYDTSGYGD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCD

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Macromolecule #3: Fab311 light chain

MacromoleculeName: Fab311 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.980484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ESVLTQPPSV SGAPGQTVTI SCTGGSSNIG AGYDVHWYQQ LPGTAPKLLI YGNINRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRRLSG SWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLVSDFYPGA VTVAWKADGS P VKVGVETT ...String:
ESVLTQPPSV SGAPGQTVTI SCTGGSSNIG AGYDVHWYQQ LPGTAPKLLI YGNINRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRRLSG SWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLVSDFYPGA VTVAWKADGS P VKVGVETT KPSKQSNNKY AASSYLSLTP EQWKSHRSYS CRVTHEGSTV EKTVAPAECS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 0-47 / Number grids imaged: 1 / Number real images: 1497 / Average exposure time: 12.0 sec. / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 312806
CTF correctionSoftware - Name: Gctf
Startup modelType of model: NONE / Details: cryoSPARC ab initio
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 206990
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6axk

chain_id: A

6axk

chain_id: B

6axk

chain_id: E
RefinementSpace: REAL / Protocol: OTHER / Target criteria: EMRinger
Output model

PDB-6mhg:
Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts

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