[English] 日本語
Yorodumi
- EMDB-61188: Cryo-EM structure of the rice isoamylase ISA1-ISA2 heterocomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61188
TitleCryo-EM structure of the rice isoamylase ISA1-ISA2 heterocomplex
Map data
Sample
  • Complex: SA1-ISA2 heterocomplex
    • Protein or peptide: Isoamylase 1, chloroplastic
    • Protein or peptide: Isoamylase 2, chloroplastic
Keywordsisoamylase ISA1-ISA2 / HYDROLASE
Function / homology
Function and homology information


chloroplast isoamylase complex / isoamylase / isoamylase complex / isoamylase activity / amylopectin biosynthetic process / starch biosynthetic process / starch catabolic process / chloroplast
Similarity search - Function
Isoamylase 2, catalytic domain / : / Isoamylase 1-3, C-terminal / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta ...Isoamylase 2, catalytic domain / : / Isoamylase 1-3, C-terminal / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Isoamylase 1, chloroplastic / Isoamylase 2, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGuan ZY / Yan JJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The tree-like architecture of the rice isoamylase ISA1-ISA2 heterocomplex facilitates branch trimming and amylopectin synthesis
Authors: Guan ZY / Yan JJ
History
DepositionAug 17, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61188.png

Downloads & links

-
Map

FileDownload / File: emd_61188.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 460 pix.
= 386.4 Å		0.84 Å/pix.
x 460 pix.
= 386.4 Å		0.84 Å/pix.
x 460 pix.
= 386.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.0796921 - 3.996145
Average (Standard dev.)-0.0005177941 (±0.07640761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61188_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61188_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SA1-ISA2 heterocomplex

EntireName: SA1-ISA2 heterocomplex
Components
  • Complex: SA1-ISA2 heterocomplex
    • Protein or peptide: Isoamylase 1, chloroplastic
    • Protein or peptide: Isoamylase 2, chloroplastic

-
Supramolecule #1: SA1-ISA2 heterocomplex

SupramoleculeName: SA1-ISA2 heterocomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

-
Macromolecule #1: Isoamylase 1, chloroplastic

MacromoleculeName: Isoamylase 1, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: isoamylase
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 87.281594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH SDEVDAHMSV ASAVEVGVGE DEEEGVEEEE EEVEAVVMPE RYALGGACRV LAGMPAPLGA TALDGGVNF AVYSAGASAA SLCLFTPDDL EADEVTEEVP LDPLFNRTGN VWHVFIEGEL HNMLYGYRFD GMFAPHCGQY F DVSNVVVD ...String:
MGSSHHHHHH SSGLVPRGSH SDEVDAHMSV ASAVEVGVGE DEEEGVEEEE EEVEAVVMPE RYALGGACRV LAGMPAPLGA TALDGGVNF AVYSAGASAA SLCLFTPDDL EADEVTEEVP LDPLFNRTGN VWHVFIEGEL HNMLYGYRFD GMFAPHCGQY F DVSNVVVD PYAKAVISRG EYGVPGPGGD CWPQMAGMIP LPYSTFDWQG DLPLRYPQKD LVIYEMHLRG FTKHSSSNVE HP GTYIGAI SKLDYLKELG VNCVELMPCH EFNELEYFSC SSKMNFWGYS TINFFSPMIR YSSGGIRNCG RDAINEFKTF VRE AHKRGI EVIMDVVFNH TAEGNEKGPI LSFRGIDNST YYMLAPKGEF YNYSGCGNTF NCNHPVVREF IVDCLRYWVT EMHV DGFRF DLASIMTRGC SLWDPVNVYG SPVEGDMTTT GTPLATPPLI DMISNDPILG DVKLIAEAWD AGGLYQVGQF PHWKI WSEW NGKYRDIVRQ FIKGTDGFAG GFAECLCGSP HLYQAGGRKP WHSINFVCAH DGFTLADLVT YNKKYNSSNG EDNRDG ENH NLSWNCGEEG EFAGLSVKRL RKRQMRNFFV SLMVSQGVPM FYMGDEYGHT KGGNNNTYCH DHYVNYFRWD KKEESSD LQ RFCSLMTKFR KQCESLGLAD FPTAQRLHWH GHQPGKPDWS ETSRFVAFST KDETKGEIYV AFNASHLPAV VGLPERPG Y RWEPLVDTGK PAPYDFLTDD LPDRAHAVHL FSHFLNSNLY PMLSYSSIIL ELQPDD

UniProtKB: Isoamylase 1, chloroplastic

-
Macromolecule #2: Isoamylase 2, chloroplastic

MacromoleculeName: Isoamylase 2, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: isoamylase
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 86.622008 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASLPAPPTP LGSCPRGRGG GRVVARPRRA GLACAARSCY RFRTDDDGVV DVAVSGEDGD GGGGGYAVSV EVPGTRGREG GLVLRASGS GEGVPLAPAA GGASLAAELS FDPTRAPFYL SFLLTDASGA EIRTHRKTSF RVPVGVGPGS PAPLGMSISG D GAVNFAVY ...String:
MASLPAPPTP LGSCPRGRGG GRVVARPRRA GLACAARSCY RFRTDDDGVV DVAVSGEDGD GGGGGYAVSV EVPGTRGREG GLVLRASGS GEGVPLAPAA GGASLAAELS FDPTRAPFYL SFLLTDASGA EIRTHRKTSF RVPVGVGPGS PAPLGMSISG D GAVNFAVY SKNANAVSLY LYAAAVGGGG GDEPALEIDL DPYIHRTGNV WHVSLASVDG YVSYAFCCGG IRRPLLDPYA KV IGDFVSS NSVYDEGVTA PSMRCFASLA IAPSYNWGRD RHPRLPLEKL VVYRANVALF TKDRSSGLPD DAAGTFTGLS AKV EHFRSL GVNAILLEPV FPFHQVKGPY FPYHFFSPMN LYSSKGLSVS AIKSMKDMVR VMHRNGIEVL LEVVFTHTAE GESE CQTIS MRGIDNSSYY IANGIAGCKA SILNCNHPVT QKLILDSLRH WVLDFHVDGF CFINAPFLVR GPGGEYLSRP PLLEA ITFD PVLSMTKIIA DPWSPLDISN VQFPFPHWKR WAEVNTRFSI DVRKFLKREA LISDLATRLC GSGDLFSTRG PAFSFN HVS RNSGLSLVDL VSFSNDDLLS ESSWNCGEEG PSENSAVLQT RLRQIRNFLF ILFVSLGVPV LNMGDECGHS AAGSVSY KD RGPLNWRGMK TTFVKEVTGF ISFLTALRSR RGDIFQRREF LKLENIHWYG SDLCEPGWDD PTSNFLCMHI NAEVDEMA A DSVRGDLYIC FNANEESVSA ALPALAEGSV WLRLVDTSLA FPGFFATESN PKVQQVPGLS SYHVEAHTCV LFESKSALA

UniProtKB: Isoamylase 2, chloroplastic

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148552
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

+
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