[English] 日本語
Yorodumi
- PDB-9lpw: Cryo-EM structure of rice PHS1-DPE1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lpw
TitleCryo-EM structure of rice PHS1-DPE1 complex
Components
  • 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
  • Alpha-1,4 glucan phosphorylase
KeywordsTRANSFERASE / Complex / Starch biosynthersis / Rice / Maltooligosaccharide elongation
Function / homology
Function and homology information


amyloplast / maltose catabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / starch catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / polysaccharide catabolic process / chloroplast / glucose metabolic process ...amyloplast / maltose catabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / starch catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / polysaccharide catabolic process / chloroplast / glucose metabolic process / pyridoxal phosphate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase / 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsJian, L. / Junjie, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400216 China
National Natural Science Foundation of China (NSFC)32270255 China
CitationJournal: To Be Published
Title: Cryo-EM structure of rice PHS1-DPE1 complex protomer I
Authors: Jian, L. / Junjie, Y.
History
DepositionJan 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Alpha-1,4 glucan phosphorylase
D: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic
A: Alpha-1,4 glucan phosphorylase
C: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic


Theoretical massNumber of molelcules
Total (without water)351,3194
Polymers351,3194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Alpha-1,4 glucan phosphorylase


Mass: 109299.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Rice
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: pho1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3IYE3, glycogen phosphorylase
#2: Protein 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic / Amylomaltase / Disproportionating enzyme / D-enzyme / Protein DISPROPORTIONATING ENZYME 1


Mass: 66360.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Rice
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: DPE1, Os07g0627000, LOC_Os07g43390, OJ1339_F05.134, P0506F02.102
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8LI30, 4-alpha-glucanotransferase
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: PHS1-DPE1 complex protomer I / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa subsp. japonica (Rice) (Japanese rice)
Cellular location: chloroplast
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HCl 8.0C4H11NO31
2150 mMNaClNaCl1
SpecimenConc.: 1.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 1.07 mg/ml complex
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1160

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6.0particle selection
4cryoSPARC4.6.0CTF correction
7cryoSPARC4.6.0model fitting
9PHENIX1.21.2model refinement5419
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1077846
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 281533 / Num. of class averages: 22 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 2.78 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422208
ELECTRON MICROSCOPYf_angle_d0.57130103
ELECTRON MICROSCOPYf_dihedral_angle_d5.0292961
ELECTRON MICROSCOPYf_chiral_restr0.0443249
ELECTRON MICROSCOPYf_plane_restr0.0043888

+
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