[English] 日本語
Yorodumi
- EMDB-75113: Chloroplast Glutamyl Peptidase S781R in closed-closed conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75113
TitleChloroplast Glutamyl Peptidase S781R in closed-closed conformation
Map data
Sample
  • Complex: Chloroplast glutamyl endopeptidase dimeric protein
    • Protein or peptide: Isoform 2 of Probable glutamyl endopeptidase, chloroplastic
KeywordsS9 protease / enzyme / serine protease / alpha-beta-alpha sandwich fold / beta-propeller / PLANT PROTEIN
Function / homology
Function and homology information


chloroplast stroma / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Probable glutamyl endopeptidase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsEhrlich JJ / Routray P / van Wijk KJ / Kawate T
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2222495 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD030470 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R24GM154185 United States
CitationJournal: Protein Sci / Year: 2026
Title: Structural basis for dimerization, catalytic regulation, and substrate selectivity of the chloroplast S9D CGEP protease in Arabidopsis thaliana.
Authors: Jacqueline J Ehrlich / Pratyush Routray / Louis Enns / Klaas J van Wijk / Toshimitsu Kawate /
Abstract: S9 proteases are widely distributed across the tree-of-life and play essential roles in protein processing. However, the structural and mechanistic basis for protease activity in the S9D subfamily, ...S9 proteases are widely distributed across the tree-of-life and play essential roles in protein processing. However, the structural and mechanistic basis for protease activity in the S9D subfamily, restricted to photosynthetic eukaryotes (e.g., plants), cyanobacteria, proteobacteria and flavobacteria, is unknown. Here, we report the first high-resolution cryo-EM structures of an S9D protease, chloroplast glutamyl endopeptidase (CGEP) from the model plant Arabidopsis thaliana. CGEP adopts a dimeric architecture stabilized by two distinct interfaces: hydrophobic interactions between catalytic domains and an interdomain β-sheet linking the cap and catalytic domains. These interactions create a scaffold that supports a hinge loop, which acts as a steric gate to restrict substrate access and confine catalytic activity to the closed conformation. Unlike S9A-B-C proteases, CGEP maintains an intact catalytic triad in both open and closed states, relying on hinge-loop gating rather than catalytic disruption for regulation. Structural analysis and mutagenesis reveal that the hinge loop forms a conserved pocket favoring glutamate side chains, explaining CGEP's strong glutamate preference at cleavage sites. Together, these findings uncover a unique regulatory paradigm for S9D proteases and provide a structural framework for understanding substrate selectivity and dimerization.
History
DepositionJan 15, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75113.png

Downloads & links

-
Map

FileDownload / File: emd_75113.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 208 pix.
= 284.96 Å		1.37 Å/pix.
x 208 pix.
= 284.96 Å		1.37 Å/pix.
x 208 pix.
= 284.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.36454514 - 0.7206998
Average (Standard dev.)0.00006964568 (±0.01698616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 284.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_75113_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unmasked, unfiltered, unsharpened full map

Fileemd_75113_additional_1.map
Annotationunmasked, unfiltered, unsharpened full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75113_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_75113_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Chloroplast glutamyl endopeptidase dimeric protein

EntireName: Chloroplast glutamyl endopeptidase dimeric protein
Components
  • Complex: Chloroplast glutamyl endopeptidase dimeric protein
    • Protein or peptide: Isoform 2 of Probable glutamyl endopeptidase, chloroplastic

-
Supramolecule #1: Chloroplast glutamyl endopeptidase dimeric protein

SupramoleculeName: Chloroplast glutamyl endopeptidase dimeric protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 104.912 KDa

-
Macromolecule #1: Isoform 2 of Probable glutamyl endopeptidase, chloroplastic

MacromoleculeName: Isoform 2 of Probable glutamyl endopeptidase, chloroplastic
type: protein_or_peptide / ID: 1
Details: AtCGEP produced in plant tissues with S781R mutation and c-terminal strepII tag
Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 100.527898 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: ASRSASRLRS LASACSGGAE DGGGTSNGSL SASATATEDD ELAIGTGYRL PPPEIRDIVD APPVPALSFS PHRDKILFLK RRALPPLAD LARPEEKLAG VRIDGYCNTR SRMSFYTGLG IHQLLPDGTL SPEKEITGIP DGGKINFVTW SNDGKHLAFS I RVDENGNS ...String:
ASRSASRLRS LASACSGGAE DGGGTSNGSL SASATATEDD ELAIGTGYRL PPPEIRDIVD APPVPALSFS PHRDKILFLK RRALPPLAD LARPEEKLAG VRIDGYCNTR SRMSFYTGLG IHQLLPDGTL SPEKEITGIP DGGKINFVTW SNDGKHLAFS I RVDENGNS SKPVVWVADV ETGVARPLFN SQDIFLNAIF ESFVWIDNST LLVSTIPSSR GEPPKKPLVP SGPKTLSNET KT VVQVRTF QDLLKDEYDA DLFDYYASSQ LVLASLDGTV KEVGVPAVYT SLDPSTDHKY LLVSSLHRPY SFIVPCGRFP KKV EVWTTD GRFVRQLCDL PLAEDIPIAS NSVRKGMRSI NWRADKPSTL YWAETQDGGD AKMEVSPRDI VYMQSAEPLA GEEP EVLHK LDLRYGGISW CDDTLALVYE SWYKTRRTRT WVISPGSNDV SPRILFDRSS EDVYSDPGST MLRRTDAGTY VIAKI KKEN DEGTYVLLNG SGATPQGNVP FLDLFDINTG NKERIWESDK EKYFETVVAL MSDQKEGDLK MEELKILTSK ESKTEN TQY SLQLWPDRKV QQITNFPHPY PQLASLQKEM IRYQRKDGVQ LTATLYLPPG YDPSKDGPLP CLFWSYPGEF KSKDAAG QV RGSPNEFAGI GSTSALLWLA RRFAILSGPT IPIIGEGDEE ANDRYVEQLV ASAEAAVEEV VRRGVADRSK IAVGGHRY G AFMTANLLAH APHLFACGIA RSGAYNRTLT PFGFQNEDRT LWEATNVYVE MSPFMSANKI KKPILLIHGE EDNNPGTLT MQSDRFFNAL KGHGALCRLV VLPHESHGYS ARESIMHVLW ETDRWLQKYC VPNTSDADTS PDQSKEGSDS ADKVSTGTGG GNPEFGEHE VHSKLRRSLL WSHPQFEK

UniProtKB: Probable glutamyl endopeptidase, chloroplastic

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H19KN2O5SHEPES-KOH
10.0 mMMgCl2magnesium chloride
75.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 10.1325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 7 force, 4 seconds, no wait time or drain time.
DetailsStrepII affinity purified CGEP recombinantly expressed from plant tissues

-
Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1853 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 63000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 1851355
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Generated from Ab initio reconstruction of high resolution particle stack separated with 2D classification
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Local refinement / Number images used: 258593
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Local refinement

-
Atomic model buiding 1

Initial modelPDB ID:

8-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-10eo:
Chloroplast Glutamyl Peptidase S781R in closed-closed conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more