[English] 日本語
Yorodumi
- EMDB-11028: CryoEM structure of Rubisco Activase with its substrate Rubisco f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11028
TitleCryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120)
Map data
Sample
  • Complex: NosRca-deltaC:Rubisco complex
    • Complex: AAA-core of the Rca hexamer from Nostoc sp. PCC7120 in complex with ATP/ATPgammaS
      • Protein or peptide: Ribulose bisphosphate carboxylase/oxygenase activase
    • Complex: Rubisco complex from Nostoc sp. PCC7120 in complex with inhibitor CABP
      • Protein or peptide: Ribulose bisphosphate carboxylase large chain
      • Protein or peptide: Ribulose bisphosphate carboxylase small chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
KeywordsAAA+ / beta barrel / CHAPERONE
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Ribulose bisphosphate carboxylase/oxygenase activase-like / : / Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical / 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/oxygenase activase-like / : / Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical / 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 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase/oxygenase activase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsWang H / Bracher A
CitationJournal: Cell / Year: 2020
Title: Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes.
Authors: Mirkko Flecken / Huping Wang / Leonhard Popilka / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone ...Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.
History
DepositionMay 13, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6z1f
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11028.png

Downloads & links

-
Map

FileDownload / File: emd_11028.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306.432 Å		0.85 Å/pix.
x 360 pix.
= 306.432 Å		0.85 Å/pix.
x 360 pix.
= 306.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.038927805 - 0.071099915
Average (Standard dev.)0.0002686747 (±0.0026960569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.432 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85120.85120.8512
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z306.432306.432306.432
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ138139230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0390.0710.000

-
Supplemental data

-
Additional map: #1

Fileemd_11028_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : NosRca-deltaC:Rubisco complex

EntireName: NosRca-deltaC:Rubisco complex
Components
  • Complex: NosRca-deltaC:Rubisco complex
    • Complex: AAA-core of the Rca hexamer from Nostoc sp. PCC7120 in complex with ATP/ATPgammaS
      • Protein or peptide: Ribulose bisphosphate carboxylase/oxygenase activase
    • Complex: Rubisco complex from Nostoc sp. PCC7120 in complex with inhibitor CABP
      • Protein or peptide: Ribulose bisphosphate carboxylase large chain
      • Protein or peptide: Ribulose bisphosphate carboxylase small chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

+
Supramolecule #1: NosRca-deltaC:Rubisco complex

SupramoleculeName: NosRca-deltaC:Rubisco complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The Rca hexamer captured in the complex with its substrate Rubisco from Nostoc sp. PCC 7120.
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

+
Supramolecule #2: AAA-core of the Rca hexamer from Nostoc sp. PCC7120 in complex wi...

SupramoleculeName: AAA-core of the Rca hexamer from Nostoc sp. PCC7120 in complex with ATP/ATPgammaS
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

+
Supramolecule #3: Rubisco complex from Nostoc sp. PCC7120 in complex with inhibitor CABP

SupramoleculeName: Rubisco complex from Nostoc sp. PCC7120 in complex with inhibitor CABP
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

+
Macromolecule #1: Ribulose bisphosphate carboxylase/oxygenase activase

MacromoleculeName: Ribulose bisphosphate carboxylase/oxygenase activase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Molecular weightTheoretical: 32.773316 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: SYYIAPRFLD KLAVHITKNF LNIPGVRVPL ILGIHGRKGE GKTFQCELAF EKMGIEVTLI SGGELESPDA GDPARLIRLR YRETAELIK VRGKMCVLMI NDLDAGAGRF DEGTQYTVNT QLVNATLMNI ADNPTDVQLP GSYDSNPIRR VPIIVTGNDF S TLYAPLIR ...String:
SYYIAPRFLD KLAVHITKNF LNIPGVRVPL ILGIHGRKGE GKTFQCELAF EKMGIEVTLI SGGELESPDA GDPARLIRLR YRETAELIK VRGKMCVLMI NDLDAGAGRF DEGTQYTVNT QLVNATLMNI ADNPTDVQLP GSYDSNPIRR VPIIVTGNDF S TLYAPLIR DGRMEKFYWE PNRDDKVGIV GGIFAEDGLS QREIEQLVDT FPKQSIDFFS ALRSRIYDIQ IRDFIHKVGF ER ISLRVVN SLEAPPEFKK PDFSLAHLIE SGNLVLGEQQ RVDNSQLVDE YNR

UniProtKB: Ribulose bisphosphate carboxylase/oxygenase activase

+
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: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Molecular weightTheoretical: 53.155125 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTTV WTDLLTDLDR YKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT SIVGNVFGFK ALRALRLEDI RFPVAYIKTF QGPPHGIQVE R DKLNKYGR ...String:
MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTTV WTDLLTDLDR YKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT SIVGNVFGFK ALRALRLEDI RFPVAYIKTF QGPPHGIQVE R DKLNKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFT(KCX)DDENIN SAPFQRWRDR FLFVADAITK AQAETGEI K GHYLNVTAPT CEEMLKRAEY AKELKQPIIM HDYLTAGFTA NTTLARWCRD NGVLLHIHRA MHAVIDRQKN HGIHFRVLA KALRLSGGDH IHTGTVVGKL EGERGITMGF VDLLRENYVE QDKSRGIYFT QDWASLPGVM AVASGGIHVW HMPALVEIFG DDSVLQFGG GTLGHPWGNA PGATANRVAL EACVQARNEG RNLAREGNDV IREAAKWSPE LAVACELWKE IKFEFEAMDT V

UniProtKB: Ribulose bisphosphate carboxylase large chain

+
Macromolecule #3: Ribulose bisphosphate carboxylase small chain

MacromoleculeName: Ribulose bisphosphate carboxylase small chain / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Molecular weightTheoretical: 12.840725 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MQTLPKERRY ETLSYLPPLT DVQIEKQVQY ILSQGYIPAV EFNEVSEPTE LYWTLWKLPL FGAKTSREVL AEVQSCRSQY PGHYIRVVG FDNIKQCQIL SFIVHKPSRY

UniProtKB: Ribulose bisphosphate carboxylase small subunit

+
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

+
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #7: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 7 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

ChemComp-CAP:
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.2 mg/mL
BufferpH: 8.4
Component:
ConcentrationFormulaName
10.0 mMC4H6O5Malic acid
20.0 mMC6H13NO4S2-ethanesulfonic acid
20.0 mMC4H11NO32-Amino-2-hydroxymethyl-propane-1,3-diol
50.0 mMKClPotassium chloride
10.0 mMMgCl2Magnesium chloride
5.0 mMNaHCO3Sodium bicarbonate
0.004 mMC6H14O13P22-Carboxyarabinitol-1,5-diphosphate
2.0 mMC10H16N5O13P3Adenosine triphosphate sodium salt
2.0 mMC10H12Li4N5O12P3SAdenosine 5'-(3-thiotriphosphate) tetralithium salt
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsNosRubisco (1 uM) was incubated with NaHCO3 (10 mM) at 298 K for 10 min followed by addition of CABP (8 uM). CABP-inhibited NosRubisco (0.5 uM) was then incubated with NosRcaDC (10 uM) in the presence of ATP (2 mM) for 10 s, followed by the addition of ATP-gammaS (2 mM), and incubated at 298 K for another 10 min before preparing the cryo-grids.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9042 / Average exposure time: 2.8 sec. / Average electron dose: 60.0 e/Å2 / Details: 31 frames per image
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 519151
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1rbl

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21149
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-6z1f:
CryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120)

+
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