9EPC | pdb_00009epc

Cryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba

PDB DOI: https://doi.org/10.2210/pdb9EPC/pdb
EM Map EMD-19877: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Sinapis alba
Mutation(s): No

Deposited: 2024-03-18 Released: 2025-06-18
Deposition Author(s): Effantin, G., Blanvillain, R., Cobessi, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba

Effantin, G., Blanvillain, R., Cobessi, D.

To be published.

Macromolecule Content

Total Structure Weight: 1,262.25 kDa
Atom Count: 65,302
Modeled Residue Count: 8,155
Deposited Residue Count: 11,144
Unique protein chains: 19

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	327	Sinapis alba	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q9XQN8 (Sinapis alba) Explore Q9XQN8 Go to UniProtKB: Q9XQN8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9XQN8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RpoB, subunit beta	C	1,072	Sinapis alba	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A6C0M5W1 (Sinapis alba) Explore A0A6C0M5W1 Go to UniProtKB: A0A6C0M5W1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6C0M5W1
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	680	Sinapis alba	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A6C0M5W0 (Sinapis alba) Explore A0A6C0M5W0 Go to UniProtKB: A0A6C0M5W0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6C0M5W0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta''	E	1,373	Sinapis alba	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A6C0M829 (Sinapis alba) Explore A0A6C0M829 Go to UniProtKB: A0A6C0M829
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6C0M829
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP1, pTAC3	F	911	Sinapis alba	Mutation(s): 0

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP2, pTAC2	G	1,174	Sinapis alba	Mutation(s): 0

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP3, pTAC10	H	675	Sinapis alba	Mutation(s): 0
UniProt
Find proteins for F4JF21 (Arabidopsis thaliana) Explore F4JF21 Go to UniProtKB: F4JF21
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F4JF21
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP4, FSD3	I	264	Sinapis alba	Mutation(s): 0 EC: 1.15.1.1
UniProt
Find proteins for A0ABF7PQ09 (Sinapis alba) Explore A0ABF7PQ09 Go to UniProtKB: A0ABF7PQ09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7PQ09
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP5, pTAC12, HEMERA	J	529	Sinapis alba	Mutation(s): 0

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP6, FLN1	K	460	Sinapis alba	Mutation(s): 0

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP7, pTAC14	L	483	Sinapis alba	Mutation(s): 0

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP8, pTAC6	M	334	Sinapis alba	Mutation(s): 0

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP9, FSD2	N	297	Sinapis alba	Mutation(s): 0

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP10, TRXz	O, P	185	Sinapis alba	Mutation(s): 0

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP11, MurE-like	Q	768	Sinapis alba	Mutation(s): 0

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP12, pTAC7	R	162	Sinapis alba	Mutation(s): 0

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
FLN2	S	611	Sinapis alba	Mutation(s): 0
UniProt
Find proteins for A0ABF7PQ06 (Sinapis alba) Explore A0ABF7PQ06 Go to UniProtKB: A0ABF7PQ06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7PQ06
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
pTAC18	T	140	Sinapis alba	Mutation(s): 0
UniProt
Find proteins for A0ABF7PQ07 (Sinapis alba) Explore A0ABF7PQ07 Go to UniProtKB: A0ABF7PQ07
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7PQ07
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
PRIN2, PLASTID REDOX INSENSITIVE 2	U	187	Sinapis alba	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain AA [auth L] MOL2 format, chain AA [auth L] mmCIF format, chain AA [auth L]	AA [auth L]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain AA [auth L] Interactions & Density Focus chain AA [auth L]
DTT (Subject of Investigation/LOI) Query on DTT Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth E] MOL2 format, chain W [auth E] mmCIF format, chain W [auth E]	W [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain W [auth E] Interactions & Density Focus chain W [auth E]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain X [auth I] SDF format, chain BA [auth N] MOL2 format, chain X [auth I] MOL2 format, chain BA [auth N] mmCIF format, chain X [auth I] mmCIF format, chain BA [auth N]	BA [auth N], X [auth I]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth N] Focus chain X [auth I] Interactions & Density Focus chain BA [auth N] Focus chain X [auth I]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain Y [auth K] SDF format, chain CA [auth S] MOL2 format, chain Y [auth K] MOL2 format, chain CA [auth S] mmCIF format, chain Y [auth K] mmCIF format, chain CA [auth S]	CA [auth S], Y [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth S] Focus chain Y [auth K] Interactions & Density Focus chain CA [auth S] Focus chain Y [auth K]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain Z [auth K] MOL2 format, chain Z [auth K] mmCIF format, chain Z [auth K]	Z [auth K]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain Z [auth K] Interactions & Density Focus chain Z [auth K]