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- PDB-9uaq: CryoEM structure of GFP-like protein from Aequorea coerulescens w... -

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Basic information

Entry
Database: PDB / ID: 9uaq
TitleCryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
Components
  • GFP-nanobody-TAIL
  • Green fluorescent protein
  • H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
KDPG/KHG aldolase / KDPG and KHG aldolase / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Aldolase-type TIM barrel
Similarity search - Domain/homology
Green fluorescent protein / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciessynthetic construct (others)
Thermotoga maritima MSB8 (bacteria)
Aequorea coerulescens (belt jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsSong, J.Y. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
Authors: Wang, W. / Song, J.Y.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
B: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
C: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
D: GFP-nanobody-TAIL
E: GFP-nanobody-TAIL
F: GFP-nanobody-TAIL
G: Green fluorescent protein
H: Green fluorescent protein
I: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)257,2089
Polymers257,2089
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Mass: 34712.359 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: TM_0066 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXS1
#2: Antibody GFP-nanobody-TAIL


Mass: 25559.111 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein Green fluorescent protein


Mass: 25464.537 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea coerulescens (belt jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6YGZ0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1CryoEM structure of GFP-like protein from Aequorea coerulescens with TrimbodyCOMPLEXall0RECOMBINANT
2H3-PrAC-5350ACOMPLEX#11RECOMBINANT
3GFP-nanobody-TAILCOMPLEX#21RECOMBINANT
4Green fluorescent proteinCOMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)243274
71Aequorea coerulescens (belt jellyfish)210840
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1209700 / Symmetry type: POINT
RefinementHighest resolution: 2.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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