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- EMDB-67276: ATP-bound ADP-Glucose Pyrophosphorylase -

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Basic information

Entry
Database: EMDB / ID: EMD-67276
TitleATP-bound ADP-Glucose Pyrophosphorylase
Map data
Sample
  • Complex: ATP-bound ADP-Glucose Pyrophosphorylase
    • Protein or peptide: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
    • Protein or peptide: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
  • Ligand: 3-PHOSPHOGLYCERIC ACID
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsheterotetramer / ADPG / PLANT PROTEIN / amylosynthesis
Function / homology
Function and homology information


heterotetrameric ADPG pyrophosphorylase complex / glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / starch biosynthetic process / photoperiodism, flowering / apoplast / chloroplast envelope / glycogen biosynthetic process / chloroplast stroma ...heterotetrameric ADPG pyrophosphorylase complex / glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / starch biosynthetic process / photoperiodism, flowering / apoplast / chloroplast envelope / glycogen biosynthetic process / chloroplast stroma / plastid / chloroplast / ATP binding
Similarity search - Function
GLGC left-handed parallel beta-helix domain / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / Nucleotidyl transferase domain / Nucleotidyl transferase / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic / Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsWu YT / Lin HJ / Fan MR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: ATP-bound ADP-Glucose Pyrophosphorylase
Authors: Wu YT / Lin HJ / Fan MR
History
DepositionNov 24, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67276.png

Downloads & links

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Map

FileDownload / File: emd_67276.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.08 Å		1.06 Å/pix.
x 256 pix.
= 270.08 Å		1.06 Å/pix.
x 256 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.6516811 - 1.0104654
Average (Standard dev.)0.00030290085 (±0.031056913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67276_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67276_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67276_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ATP-bound ADP-Glucose Pyrophosphorylase

EntireName: ATP-bound ADP-Glucose Pyrophosphorylase
Components
  • Complex: ATP-bound ADP-Glucose Pyrophosphorylase
    • Protein or peptide: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
    • Protein or peptide: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
  • Ligand: 3-PHOSPHOGLYCERIC ACID
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ATP-bound ADP-Glucose Pyrophosphorylase

SupramoleculeName: ATP-bound ADP-Glucose Pyrophosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic

MacromoleculeName: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glucose-1-phosphate adenylyltransferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 51.517086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSHHHHHHH HGSGSGSGSG SVSDSQNSQT CLDPDASSSV LGIILGGGAG TRLYPLTKKR AKPAVPLGAN YRLIDIPVSN CLNSNISKI YVLTQFNSAS LNRHLSRAYA SNMGGYKNEG FVEVLAAQQS PENPNWFQGT ADAVRQYLWL FEEHNVLEYL I LAGDHLYR ...String:
MGSHHHHHHH HGSGSGSGSG SVSDSQNSQT CLDPDASSSV LGIILGGGAG TRLYPLTKKR AKPAVPLGAN YRLIDIPVSN CLNSNISKI YVLTQFNSAS LNRHLSRAYA SNMGGYKNEG FVEVLAAQQS PENPNWFQGT ADAVRQYLWL FEEHNVLEYL I LAGDHLYR MDYEKFIQAH RETDADITVA ALPMDEQRAT AFGLMKIDEE GRIIEFAEKP KGEHLKAMKV DTTILGLDDQ RA KEMPFIA SMGIYVVSRD VMLDLLRNQF PGANDFGSEV IPGATSLGLR VQAYLYDGYW EDIGTIEAFY NANLGITKKP VPD FSFYDR SAPIYTQPRY LPPSKMLDAD VTDSVIGEGC VIKNCKIHHS VVGLRSCISE GAIIEDSLLM GADYYETATE KSLL SAKGS VPIGIGKNSH IKRAIIDKNA RIGDNVKIIN SDNVQEAARE TDGYFIKSGI VTVIKDALIP TGTVI

UniProtKB: Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic

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Macromolecule #2: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic

MacromoleculeName: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: glucose-1-phosphate adenylyltransferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 52.535211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSWSHPQFE KGSGSGSGSG SSLNSVAGES KVQELETEKR DPRTVASIIL GGGAGTRLFP LTKRRAKPAV PIGGAYRLID VPMSNCINS GINKVYILTQ YNSASLNRHL ARAYNSNGLG FGDGYVEVLA ATQTPGESGK RWFQGTADAV RQFHWLFEDA R SKDIEDVL ...String:
MGSWSHPQFE KGSGSGSGSG SSLNSVAGES KVQELETEKR DPRTVASIIL GGGAGTRLFP LTKRRAKPAV PIGGAYRLID VPMSNCINS GINKVYILTQ YNSASLNRHL ARAYNSNGLG FGDGYVEVLA ATQTPGESGK RWFQGTADAV RQFHWLFEDA R SKDIEDVL ILSGDHLYRM DYMDFIQDHR QSGADISISC IPIDDRRASD FGLMKIDDKG RVISFSEKPK GDDLKAMAVD TT ILGLSKE EAEKKPYIAS MGVYVFKKEI LLNLLRWRFP TANDFGSEII PFSAKEFYVN AYLFNDYWED IGTIRSFFEA NLA LTEHPG AFSFYDAAKP IYTSRRNLPP SKIDNSKLID SIISHGSFLT NCLIEHSIVG IRSRVGSNVQ LKDTVMLGAD YYET EAEVA ALLAEGNVPI GIGENTKIQE CIIDKNARVG KNVIIANSEG IQEADRSSDG FYIRSGITVI LKNSVIKDGV VI

UniProtKB: Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic

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Macromolecule #3: 3-PHOSPHOGLYCERIC ACID

MacromoleculeName: 3-PHOSPHOGLYCERIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: 3PG
Molecular weightTheoretical: 186.057 Da
Chemical component information

ChemComp-3PG:
3-PHOSPHOGLYCERIC ACID

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 196233
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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