[English] 日本語
Yorodumi
- EMDB-15966: Structure of Synechococcus elongatus PCC 7942 Rubisco recombinant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15966
TitleStructure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli
Map datamain map
Sample
  • Complex: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli
    • Protein or peptide: Ribulose 1,5-bisphosphate carboxylase small subunit
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
KeywordsRubisco / Synechococcus / carbon dioxide fixation / recombinant expression / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain ...Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsNi T / Sun Y / Liu LN / Zhang P
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Structure of Rubisco
Authors: Sun Y / Ni T
History
DepositionOct 17, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15966.png

Downloads & links

-
Map

FileDownload / File: emd_15966.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 296 pix.
= 245.68 Å		0.83 Å/pix.
x 296 pix.
= 245.68 Å		0.83 Å/pix.
x 296 pix.
= 245.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.498
Minimum - Maximum-2.0277624 - 3.9308655
Average (Standard dev.)0.002533119 (±0.16889034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 245.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map 1

Fileemd_15966_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_15966_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Synechococcus elongatus PCC 7942 Rubisco recombinantly co-express...

EntireName: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli
Components
  • Complex: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli
    • Protein or peptide: Ribulose 1,5-bisphosphate carboxylase small subunit
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain

-
Supramolecule #1: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-express...

SupramoleculeName: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)

-
Macromolecule #1: Ribulose 1,5-bisphosphate carboxylase small subunit

MacromoleculeName: Ribulose 1,5-bisphosphate carboxylase small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 13.349196 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSMKTLPKER RFETFSYLPP LSDRQIAAQI EYMIEQGFHP LIEFNEHSNP EEFYWTMWKL PLFDCKSPQQ VLDEVRECRS EYGDCYIRV AGFDNIKQCQ TVSFIVHRPG RY

UniProtKB: Ribulose bisphosphate carboxylase small subunit

-
Macromolecule #2: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942
Molecular weightTheoretical: 52.516605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQG EENSYFAFIA YPLDLFEEGS VTNILTSIVG NVFGFKAIRS LRLEDIRFPV ALVKTFQGPP HGIQVERDLL N KYGRPMLG ...String:
MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQG EENSYFAFIA YPLDLFEEGS VTNILTSIVG NVFGFKAIRS LRLEDIRFPV ALVKTFQGPP HGIQVERDLL N KYGRPMLG CTIKPKLGLS AKNYGRAVYE CLRGGLDFTK DDENINSQPF QRWRDRFLFV ADAIHKSQAE TGEIKGHYLN VT APTCEEM MKRAEFAKEL GMPIIMHDFL TAGFTANTTL AKWCRDNGVL LHIHRAMHAV IDRQRNHGIH FRVLAKCLRL SGG DHLHSG TVVGKLEGDK ASTLGFVDLM REDHIEADRS RGVFFTQDWA SMPGVLPVAS GGIHVWHMPA LVEIFGDDSV LQFG GGTLG HPWGNAPGAT ANRVALEACV QARNEGRDLY REGGDILREA GKWSPELAAA LDLWKEIKFE FETMDKL

UniProtKB: Ribulose bisphosphate carboxylase large chain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219865
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8bcm:
Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli

+
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