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- PDB-28rf: Cryo-EM single particle structure of the Plastid-Encoded RNA Poly... -

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Basic information

Entry
Database: PDB / ID: 28rf
TitleCryo-EM single particle structure of the Plastid-Encoded RNA Polymerase (PEP)from Chlamydomonas reinhardtii.
Components
  • (DNA-directed RNA polymerase ...) x 4
  • (Uncharacterized ...) x 5
  • Coenzyme Q-binding protein COQ10 START domain-containing protein
  • DNA-directed RNA polymerase
  • Glucose-6-phosphate 1-epimerase
  • Mur ligase central domain-containing protein
  • Rubisco LSMT substrate-binding domain-containing protein
  • S1 motif domain-containing protein
  • SAP domain-containing protein
  • UDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsRNA / Chlamydomonas reinhardtii / Plastid-Encoded RNA / Polymerase / Cryo-EM
Function / homology
Function and homology information


lipid X metabolic process / plastid-encoded plastid RNA polymerase complex / carboxylic acid biosynthetic process / acid-amino acid ligase activity / glucose-6-phosphate 1-epimerase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / ligase activity / lipid A biosynthetic process / catalytic activity ...lipid X metabolic process / plastid-encoded plastid RNA polymerase complex / carboxylic acid biosynthetic process / acid-amino acid ligase activity / glucose-6-phosphate 1-epimerase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / ligase activity / lipid A biosynthetic process / catalytic activity / RNA processing / mitochondrion organization / chloroplast / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / carbohydrate binding / carbohydrate metabolic process / DNA-templated transcription / metal ion binding / DNA binding / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / : / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / DNA-directed RNA polymerase, subunit beta'' / MurE/MurF, N-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / : ...: / : / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / DNA-directed RNA polymerase, subunit beta'' / MurE/MurF, N-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / : / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Branched-chain-amino-acid aminotransferase-like, N-terminal / Mur ligase middle domain / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Glycoside hydrolase-type carbohydrate-binding / START-like domain superfamily / Galactose mutarotase-like domain superfamily / SET domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / S1 domain profile. / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / : / Uncharacterized protein / UDP-3-O-acyl-N-acetylglucosamine deacetylase / SAP domain-containing protein / Uncharacterized protein / Mur ligase central domain-containing protein / Rubisco LSMT substrate-binding domain-containing protein / Coenzyme Q-binding protein COQ10 START domain-containing protein / S1 motif domain-containing protein ...: / : / Uncharacterized protein / UDP-3-O-acyl-N-acetylglucosamine deacetylase / SAP domain-containing protein / Uncharacterized protein / Mur ligase central domain-containing protein / Rubisco LSMT substrate-binding domain-containing protein / Coenzyme Q-binding protein COQ10 START domain-containing protein / S1 motif domain-containing protein / Uncharacterized protein / Glucose-6-phosphate 1-epimerase / Uncharacterized protein / Uncharacterized protein / DNA-directed RNA polymerase subunit beta'' / DNA-directed RNA polymerase subunit beta N-terminal section / DNA-directed RNA polymerase subunit beta C-terminal section
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsKumar, A. / Schuller, S. / Schuller, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Cryo-EM single particle structure of the Plastid-Encoded RNA Polymerase (PEP)from Chlamydomonas reinhardtii.
Authors: Schuller, S. / Kumar, A. / Schuller, J.
History
DepositionFeb 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase
B: DNA-directed RNA polymerase subunit beta N-terminal section
C: DNA-directed RNA polymerase subunit beta C-terminal section
D: DNA-directed RNA polymerase subunit beta''
E: DNA-directed RNA polymerase subunit
F: Glucose-6-phosphate 1-epimerase
G: Rubisco LSMT substrate-binding domain-containing protein
H: UDP-3-O-acyl-N-acetylglucosamine deacetylase
I: UDP-3-O-acyl-N-acetylglucosamine deacetylase
J: Uncharacterized protein A0A2K3DRS4
K: SAP domain-containing protein
M: Uncharacterized protein A0A2K3D3G3
N: Mur ligase central domain-containing protein
Q: Coenzyme Q-binding protein COQ10 START domain-containing protein
R: S1 motif domain-containing protein
S: Uncharacterized protein
T: Uncharacterized protein
X: Uncharacterized protein
Y: Uncharacterized protein
Z: DNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)2,052,12520
Polymers2,052,12520
Non-polymers00
Water00
1


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

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Components

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Protein , 8 types, 10 molecules AZFGHIKNQR

#1: Protein DNA-directed RNA polymerase / Plastid-encoded RNA polymerase subunit alpha


Mass: 83315.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A0A218N9C3, DNA-directed RNA polymerase
#6: Protein Glucose-6-phosphate 1-epimerase


Mass: 69851.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DSM7
#7: Protein Rubisco LSMT substrate-binding domain-containing protein


Mass: 89099.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DDP1
#8: Protein UDP-3-O-acyl-N-acetylglucosamine deacetylase


Mass: 66248.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A0A2K3CSZ9, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#10: Protein SAP domain-containing protein


Mass: 280466.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CWF2
#12: Protein Mur ligase central domain-containing protein


Mass: 86417.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D404
#13: Protein Coenzyme Q-binding protein COQ10 START domain-containing protein


Mass: 43963.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DEZ2
#14: Protein S1 motif domain-containing protein


Mass: 40289.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DL30

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DNA-directed RNA polymerase ... , 4 types, 4 molecules BCDE

#2: Protein DNA-directed RNA polymerase subunit beta N-terminal section / PEP / Plastid-encoded RNA polymerase subunit beta N-terminal section / RNA polymerase subunit beta ...PEP / Plastid-encoded RNA polymerase subunit beta N-terminal section / RNA polymerase subunit beta N-terminal section


Mass: 93313.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HTL6, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta C-terminal section / PEP / Plastid-encoded RNA polymerase subunit beta C-terminal section / RNA polymerase subunit beta ...PEP / Plastid-encoded RNA polymerase subunit beta C-terminal section / RNA polymerase subunit beta C-terminal section


Mass: 70525.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HTL7, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta'' / PEP / Plastid-encoded RNA polymerase subunit beta'' / RNA polymerase subunit beta''


Mass: 358327.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7PCJ6, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit


Mass: 221076.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A0A218N8D6, DNA-directed RNA polymerase

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Uncharacterized ... , 5 types, 6 molecules JMSTXY

#9: Protein Uncharacterized protein A0A2K3DRS4


Mass: 38135.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DRS4
#11: Protein Uncharacterized protein A0A2K3D3G3


Mass: 189894.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D3G3
#15: Protein Uncharacterized protein


Mass: 41104.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HQ14
#16: Protein Uncharacterized protein


Mass: 40748.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CST8
#17: Protein Uncharacterized protein


Mass: 44891.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HT91

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Plastid-Encoded RNA Polymerase (PEP) from Chlamydomonas reinhardtii
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 650394 / Symmetry type: POINT
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00485242
ELECTRON MICROSCOPYf_angle_d0.668115627
ELECTRON MICROSCOPYf_dihedral_angle_d4.89811512
ELECTRON MICROSCOPYf_chiral_restr0.04313068
ELECTRON MICROSCOPYf_plane_restr0.00614965

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