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- EMDB-63989: CryoEM structure of GFP-like protein from Aequorea coerulescens w... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63989
TitleCryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
Map data
Sample
  • Complex: CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
    • Complex: H3-PrAC-5350A
      • Protein or peptide: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Complex: GFP-nanobody-TAIL
      • Protein or peptide: GFP-nanobody-TAIL
    • Complex: Green fluorescent protein
      • Protein or peptide: Green fluorescent protein
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 speciesThermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria) / Thermotoga maritima MSB8 (bacteria) / synthetic construct (others) / Aequorea coerulescens (belt jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsSong JY / Wang W
Funding support China, 1 items
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 JY
History
DepositionApr 1, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63989.png

Downloads & links

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Map

FileDownload / File: emd_63989.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 264.96 Å		0.92 Å/pix.
x 288 pix.
= 264.96 Å		0.92 Å/pix.
x 288 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017954588 - 2.57511
Average (Standard dev.)0.0001759487 (±0.033816114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CryoEM structure of GFP-like protein from Aequorea coerulescens w...

EntireName: CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
Components
  • Complex: CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
    • Complex: H3-PrAC-5350A
      • Protein or peptide: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
    • Complex: GFP-nanobody-TAIL
      • Protein or peptide: GFP-nanobody-TAIL
    • Complex: Green fluorescent protein
      • Protein or peptide: Green fluorescent protein

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Supramolecule #1: CryoEM structure of GFP-like protein from Aequorea coerulescens w...

SupramoleculeName: CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)

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Supramolecule #2: H3-PrAC-5350A

SupramoleculeName: H3-PrAC-5350A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: GFP-nanobody-TAIL

SupramoleculeName: GFP-nanobody-TAIL / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Supramolecule #4: Green fluorescent protein

SupramoleculeName: Green fluorescent protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydrox...

MacromoleculeName: H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 34.712359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KEIAKIVAEL LRGIARIIDD IKGRDREEEV EILAKAVEKT GKPEDVRLAL EAAERGVTLD QAKAIAQILS MPNLTDEQKR GFVQSLLDD PSVSKEILAE AKKLNEHQAA KAEEAARKME ELFKKHKIVA VLRANSVEEA IEKAVAVFAG GVHLIEITFT V PDADTVIK ...String:
KEIAKIVAEL LRGIARIIDD IKGRDREEEV EILAKAVEKT GKPEDVRLAL EAAERGVTLD QAKAIAQILS MPNLTDEQKR GFVQSLLDD PSVSKEILAE AKKLNEHQAA KAEEAARKME ELFKKHKIVA VLRANSVEEA IEKAVAVFAG GVHLIEITFT V PDADTVIK ALSVLKEKGA IIGAGTVTSV EQCRKAVESG AEFIVSPHLD EEISQFCKEK GVFYMPGVMT PTELVKAMKL GH TILKLFP GEVVGPQFVK AMKGPFPNVK FVPTGGVNLD NVCEWFKAGV LAVGVGSALV KGTPDEVREK AKAFVEKIRG CTE

UniProtKB: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

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Macromolecule #2: GFP-nanobody-TAIL

MacromoleculeName: GFP-nanobody-TAIL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.559111 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLVESGGA LVQPGGSLRL SCAASGFPVN RYSMRWYRQA PGKEREWVAG MSSAGDRSSY EDSVKGRFTI SRDDARNTVY LQMNSLKPE DTAVYYCNVN VGFEYWGQGT LVAVVKTVED AFLALLALEQ HLGVQPADLA ALAEKLNLSQ LLELGELLKA A GHPLAPQV ...String:
QVQLVESGGA LVQPGGSLRL SCAASGFPVN RYSMRWYRQA PGKEREWVAG MSSAGDRSSY EDSVKGRFTI SRDDARNTVY LQMNSLKPE DTAVYYCNVN VGFEYWGQGT LVAVVKTVED AFLALLALEQ HLGVQPADLA ALAEKLNLSQ LLELGELLKA A GHPLAPQV EALLKEKLKA ASAAEAAGVI FQALVKDEEL GKKILEWAKE FGTEEAKKAI EIAEKAYELY KKYLE

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Macromolecule #3: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aequorea coerulescens (belt jellyfish)
Molecular weightTheoretical: 25.464537 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAELFTGIVP ILIELNGDVN GHKFSVSGEG EGDATYGKLT LKFICTTGKL PVPWPTLVTT L(GYS)VQCFSRYP DHMKQH DFF KSAMPEGYIQ ERTIFFEDDG NYKSRAEVKF EGDTLVNRIE LTGTDFKEDG NILGNKMEYN YNAHNVYIMT DKAKNGI KV NFKIRHNIED ...String:
GAELFTGIVP ILIELNGDVN GHKFSVSGEG EGDATYGKLT LKFICTTGKL PVPWPTLVTT L(GYS)VQCFSRYP DHMKQH DFF KSAMPEGYIQ ERTIFFEDDG NYKSRAEVKF EGDTLVNRIE LTGTDFKEDG NILGNKMEYN YNAHNVYIMT DKAKNGI KV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDNHYLST QSALSKDPNE KRDHMIYFGF VTAAAIT

UniProtKB: Green fluorescent protein

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1209700
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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