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- EMDB-45440: Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthas... -

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Basic information

Entry
Database: EMDB / ID: EMD-45440
TitleCryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)
Map data
Sample
  • Complex: Complex of CSP-P1-CSP and CSP-P2-CSP
    • Complex: CSP-P1-CSP
      • Protein or peptide: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1
    • Complex: CSP-P2-CSP
      • Protein or peptide: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2
Keywordssynthase / complex / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


vitamin B6 biosynthetic process / amine-lyase activity / pyridoxine metabolic process / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / response to singlet oxygen / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / host cell surface binding ...vitamin B6 biosynthetic process / amine-lyase activity / pyridoxine metabolic process / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / response to singlet oxygen / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / host cell surface binding / glutaminase / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / glutaminase activity / heparan sulfate proteoglycan binding / amino acid metabolic process / catalytic activity / side of membrane / cell surface / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. ...Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / : / 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 / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit Pdx1 / Circumsporozoite protein / Pyridoxal 5'-phosphate synthase subunit PDX2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsShi D / Ma R / Tang WK / Tolia NH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001253 United States
CitationJournal: Nat Microbiol / Year: 2025
Title: A Plasmodium-derived nanoparticle vaccine elicits sterile protection against malaria in mice.
Authors: Dashuang Shi / Rui Ma / Richi Gupta / Thayne H Dickey / Palak N Patel / Nichole D Salinas / Wai Kwan Tang / Alaysies Queen / Myesha Singleton / Nida Delbe / Solomon Conteh / Lynn E Lambert / ...Authors: Dashuang Shi / Rui Ma / Richi Gupta / Thayne H Dickey / Palak N Patel / Nichole D Salinas / Wai Kwan Tang / Alaysies Queen / Myesha Singleton / Nida Delbe / Solomon Conteh / Lynn E Lambert / Patrick E Duffy / Niraj H Tolia /
Abstract: Protein nanoparticles in infectious disease vaccines enable protection through the periodic arrangement of antigens on their surface. These nanoparticles arise from organisms unrelated to the target ...Protein nanoparticles in infectious disease vaccines enable protection through the periodic arrangement of antigens on their surface. These nanoparticles arise from organisms unrelated to the target disease, limiting their role as presentation platforms. Nanoparticles may also be compromised by pre-existing immunity to the nanoparticle carrier and may induce autoimmunity if conserved epitopes exist. Here we developed a potent multivalent malaria vaccine using an engineered Plasmodium falciparum pyridoxal 5'-phosphate (PLP) synthase as a nanoparticle that presents a designed P. falciparum circumsporozoite protein (CSP) and the Plasmodium vivax cell-transversal protein for ookinetes and sporozoites (CelTOS). These engineered vaccines elicited high titres of anti-CSP and anti-CelTOS antibodies, and three doses provided complete sterile protection against malaria in a mouse model. Cryogenic electron microscopy resolved a 2.95-Å resolution structure of the PLP nanoparticle including amino acid changes engineered to stabilize the nanoparticle. PLP synthase has no identifiable human ortholog limiting its propensity for autoimmunity or pre-existing immunity, and the engineered nanoparticles possess desirable manufacturing characteristics. These studies established an effective nanoparticle platform for malaria and infectious disease vaccines.
History
DepositionJun 21, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45440.png

Downloads & links

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Map

FileDownload / File: emd_45440.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.76
Minimum - Maximum-18.289476000000001 - 29.140779999999999
Average (Standard dev.)0.000000000003271 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45440_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45440_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of CSP-P1-CSP and CSP-P2-CSP

EntireName: Complex of CSP-P1-CSP and CSP-P2-CSP
Components
  • Complex: Complex of CSP-P1-CSP and CSP-P2-CSP
    • Complex: CSP-P1-CSP
      • Protein or peptide: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1
    • Complex: CSP-P2-CSP
      • Protein or peptide: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2

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Supramolecule #1: Complex of CSP-P1-CSP and CSP-P2-CSP

SupramoleculeName: Complex of CSP-P1-CSP and CSP-P2-CSP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: CSP-P1-CSP

SupramoleculeName: CSP-P1-CSP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Supramolecule #3: CSP-P2-CSP

SupramoleculeName: CSP-P2-CSP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1

MacromoleculeName: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1
type: protein_or_peptide / ID: 1
Details: Pdx1 between duplicated portions of CSP (residues 101 to 114, 131 to 150, 310 to 383), so that it is CSP-Pdx1-CSP
Number of copies: 12 / Enantiomer: LEVO
EC number: pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 58.417055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTGNPDPNAN PNVDPNANPN ANPNANPNAN PNANPNAEPS DKHIKEYLNK IQNSLSTEWS PCSVTCGNGI QVRIKPGSAN KPKDELDYA NDIEKKICKM EKCSSVFNVV NSGGSGTENH KDDAVLLKHG WCEMLKGGVI MDVKSVEQAK IAEEAGAIGV M VLENIPSE ...String:
MTGNPDPNAN PNVDPNANPN ANPNANPNAN PNANPNAEPS DKHIKEYLNK IQNSLSTEWS PCSVTCGNGI QVRIKPGSAN KPKDELDYA NDIEKKICKM EKCSSVFNVV NSGGSGTENH KDDAVLLKHG WCEMLKGGVI MDVKSVEQAK IAEEAGAIGV M VLENIPSE LRNKEGVARS VDPSKVEEIK KCVSINVLAR VRIGHFVEAQ ILEELKIDMI DESEVLTIAD EMHHIDKHKF KT PFVCGCT NLGEALRRIS EGASMIRTKG EAGTGNIIEA IKHIRTVNNE ICYLCCLSDS EVYHFAKKIN APIDLVLLTK KLK RLPVVN FAAGGVATPA DAAMCMQLGM DGVFVGSGIF ESENPRKMAA SIVSAVSNFN NPKILLDVSM NLGKAMCGST RVSD KWKNK NEEHTKFLTP QTGNPDPNAN PNVDPNANPN ANPNANPNAN PNANPNAEPS DKHIKEYLNK IQNSLSTEWS PCSVT CGNG IQVRIKPGSA NKPKDELDYA NDIEKKICKM EKCSSVFNVV NSGGSLEHHH HHH

UniProtKB: Circumsporozoite protein, Circumsporozoite protein, Circumsporozoite protein, Pyridoxal 5'-phosphate synthase subunit Pdx1

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Macromolecule #2: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2

MacromoleculeName: Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2
type: protein_or_peptide / ID: 2
Details: Pdx2 between duplicated portions of CSP (residues 101 to 114, 131 to 150, 310 to 383), so that it is CSP-Pdx2-CSP
Number of copies: 12 / Enantiomer: LEVO
EC number: pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 49.843617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTGNPDPNAN PNVDPNANPN ANPNANPNAN PNANPNAEPS DKHIKEYLNK IQNSLSTEWS PCSVTCGNGI QVRIKPGSAN KPKDELDYA NDIEKKICKM EKCSSVFNVV NSGGSGTEIT IGVLSLQGDF EPHINHFIKL QIPSLNIIQV RNVHDLGLCD G LVIPGGES ...String:
MTGNPDPNAN PNVDPNANPN ANPNANPNAN PNANPNAEPS DKHIKEYLNK IQNSLSTEWS PCSVTCGNGI QVRIKPGSAN KPKDELDYA NDIEKKICKM EKCSSVFNVV NSGGSGTEIT IGVLSLQGDF EPHINHFIKL QIPSLNIIQV RNVHDLGLCD G LVIPGGES TTVRRCCAYE QDTLYNALVH FIHVLKKPIW GTCAGCILLS KNVENIKLYS NFGNKFSFGG LDITICRNFY GS QQDSFIC SLNIISDSSA FKKDLTAACI RAPYIREILS DEVKVLATFS HESYGPNIIA AVEQNNCLGT VFNPELLPHT AFQ QYFYEK VKNYKYSTGN PDPNANPNVD PNANPNANPN ANPNANPNAN PNAEPSDKHI KEYLNKIQNS LSTEWSPCSV TCGN GIQVR IKPGSANKPK DELDYANDIE KKICKMEKCS SVFNVVNSGG SLEHHHHHH

UniProtKB: Circumsporozoite protein, Circumsporozoite protein, Circumsporozoite protein, Pyridoxal 5'-phosphate synthase subunit PDX2

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251050
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4adt

source_name: PDB, initial_model_type: experimental model

2abw

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coeffcient
Output model

PDB-9cca:
Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)

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