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- EMDB-66135: The cryo-EM structure of Zea mays GLN1 -

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Basic information

Entry
Database: EMDB / ID: EMD-66135
TitleThe cryo-EM structure of Zea mays GLN1
Map data
Sample
  • Complex: The cryo-EM structure of Zea mays GLN1
    • Protein or peptide: Glutamine synthetase
Keywordschloroplast-localized / Glutamine synthetase / a decameric complex / PLANT PROTEIN
Function / homology
Function and homology information


glutamine synthetase / : / glutamine synthetase activity / chloroplast / ATP binding
Similarity search - Function
: / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain ...: / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesZea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsCheng YQ / Wu XX / Zhang Y / Huang YC
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB1120102 China
CitationJournal: Nature / Year: 2026
Title: Plastoglobules compartmentalize nitrogen assimilation in maize.
Authors: Di Chen / Lulu Gao / Shujun Li / Yiqiu Cheng / Xiaoxian Wu / Wenhao Li / Jinman Zhang / Xueling Fu / Pan Xiang / Lu Sun / Zhiteng Chen / Hua Zhang / Youliang Li / Shiqi Luo / Chong You / ...Authors: Di Chen / Lulu Gao / Shujun Li / Yiqiu Cheng / Xiaoxian Wu / Wenhao Li / Jinman Zhang / Xueling Fu / Pan Xiang / Lu Sun / Zhiteng Chen / Hua Zhang / Youliang Li / Shiqi Luo / Chong You / Linhan Sun / Xing Huang / Yidong Zhu / Xing Zeng / Wenqin Wang / Yan He / Haihai Wang / Yu Zhang / Xuewei Chen / Yongrui Wu / Yongcai Huang /
Abstract: Efficient nitrogen assimilation is important for sustainable agriculture, yet its subcellular organization remains unknown. Here we show that plastoglobules (PGs) in the chloroplasts of mesophyll ...Efficient nitrogen assimilation is important for sustainable agriculture, yet its subcellular organization remains unknown. Here we show that plastoglobules (PGs) in the chloroplasts of mesophyll cells function as a metabolic hub that orchestrates nitrogen utilization in maize. Nitrogen-responsive dynamics of PGs represent a conserved feature across plant species. We identify two key enzymes, nitrite reductase 2 (ZmNIR2) and glutamine synthetase 1 (ZmGLN1), specifically targeted to PGs by a chloroplast transit peptide and hydrophobic region. Cryogenic electron microscopy analysis of recombinant ZmGLN1 shows a decameric complex, enabling a metabolon with ZmNIR2 for enhanced efficiency. Among two NIR and six GLN enzymes, ZmNIR2 and ZmGLN1 are the primary PG-localized components that orchestrate sub-organellar nitrogen assimilation and dictate nitrogen use efficiency. Genetic variation in ZmNIR2 splicing in cultivated germplasm generates a PG-targeted isoform (ZmNIR2) that boosts NUE. Our work establishes PGs as a central compartment for primary nitrogen assimilation, providing a promising strategy to develop high-NUE crops for global food security.
History
DepositionSep 8, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66135.png

Downloads & links

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Map

FileDownload / File: emd_66135.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 500 pix.
= 253. Å		0.51 Å/pix.
x 500 pix.
= 253. Å		0.51 Å/pix.
x 500 pix.
= 253. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.506 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.10424553 - 0.25904673
Average (Standard dev.)0.0001856859 (±0.0093230745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 252.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66135_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_66135_half_map_2.map
Projections & Slices
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Sample components

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Entire : The cryo-EM structure of Zea mays GLN1

EntireName: The cryo-EM structure of Zea mays GLN1
Components
  • Complex: The cryo-EM structure of Zea mays GLN1
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: The cryo-EM structure of Zea mays GLN1

SupramoleculeName: The cryo-EM structure of Zea mays GLN1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Zea mays (maize)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 46.082855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAQAVVPAMQ CRVGVKAAAG RVWSAGRTRT GRGGASPGFK VMAVSTGSTG VVPRLEQLLN MDTTPYTDKV IAEYIWVGGS GIDIRSKSR TISKPVEDPS ELPKWNYDGS STGQAPGEDS EVILYPQAIF KDPFRGGNNV LVICDTYTPQ GEPLPTNKRH R AAQIFSDP ...String:
MAQAVVPAMQ CRVGVKAAAG RVWSAGRTRT GRGGASPGFK VMAVSTGSTG VVPRLEQLLN MDTTPYTDKV IAEYIWVGGS GIDIRSKSR TISKPVEDPS ELPKWNYDGS STGQAPGEDS EVILYPQAIF KDPFRGGNNV LVICDTYTPQ GEPLPTNKRH R AAQIFSDP KVAEQVPWFG IEQEYTLLQK DVNWPLGWPV GGFPGPQGPY YCAVGADKSF GRDISDAHYK ACLYAGINIS GT NGEVMPG QWEYQVGPSV GIEAGDHIWI SRYILERITE QAGVVLTLDP KPIQGDWNGA GCHTNYSTKT MREDGGFEEI KRA ILNLSL RHDLHISAYG EGNERRLTGK HETASIGTFS WGVANRGCSI RVGRDTEAKG KGYLEDRRPA SNMDPYIVTG LLAE TTILW QPSLEAEALA AKKLALKV

UniProtKB: Glutamine synthetase

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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: 7.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 302580
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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