3k4g

Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–86； UniProt 245–329 Author chain B； PDBConstruct 2–86； UniProt 245–329 Author chain C； PDBConstruct 2–86； UniProt 245–329 Author chain D； PDBConstruct 2–86； UniProt 245–329 Author chain E； PDBConstruct 2–86； UniProt 245–329 Author chain F； PDBConstruct 2–86； UniProt 245–329 Author chain G； PDBConstruct 2–86； UniProt 245–329 Author chain H； PDBConstruct 2–86； UniProt 245–329

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3k4g
Deposition date deposition_date	2009-10-05
Structure title title	Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain
Keywords keywords	BACTERIAL TRANSCRIPTION REGULATION, DNA-directed RNA polymerase, Nucleotidyltransferase, Transcription, Transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3k4g__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3k4g__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k4g__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	14.36 Å
Rg (electron density)	13.32 Å
Total Rg	14.71 Å
Atom count	646
Residues	77
Excluded volume	11803 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k4g__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3k4g__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3k4g__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3k4g__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3k4g__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3k4g__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3k4g__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3k4g__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	9787.4 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	5585

MEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	317

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3k4ga_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4gb_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4gc_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4gd_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4ge_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4gf_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4gg_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

Domain ID domain_id	d3k4gh_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family family	a.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

CATH v4.4 (8 domains)

Domain ID domain_id	3k4gA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3k4gH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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Unit-cell length a length_a	51.342 Å
Unit-cell length b length_b	67.612 Å
Unit-cell length c length_c	116.553 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	47.023 Å
R factor r_factor	0.1940
R_work r_work	0.1930
R_free r_free	0.2360

Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3k4g__assembly_2__model_1

3k4g__assembly_2__model_1 | I(q)

3k4g__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3k4g__assembly_2__model_1

3k4g__assembly_2__model_1 | I(q)

3k4g__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)