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3n4m

E. coli RNA polymerase alpha subunit C-terminal domain in complex with CAP and DNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Catabolite gene activator

Escherichia coli

UniProt P0ACJ8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 4 DNA-directed RNA polymerase subunit alpha × 4 （P0A7Z4） ;DNA (5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3') ; × 2 ;DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3') ; × 2 ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 DI(HYDROXYETHYL)ETHER × 4 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
4bh9 4bhp

2 assemblies

Homodimer
1g6n 1hw5 1i5z 1i6x 2gzw 2gzw 3fwe 3kcc 3qop 3rdi 3rou 3rpq

25 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1cgp 1j59 1lb2 1o3q 1o3r 1o3s 1o3t 1run 1ruo 1zrc 1zrd 1zre

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CRP_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–209； UniProt 2–210

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt P0A7Z4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 6 DNA 4 Catabolite gene activator × 2 （P0ACJ8） ;DNA (5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3') ; × 2 ;DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3') ; × 2 ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 DI(HYDROXYETHYL)ETHER × 4 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1coo 3k4g 3k4g 3k4g 3k4g 3k4g 3k4g 3k4g 3k4g

9 assemblies

Homodimer

None

Homotetramer
1bdf

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
10ma 10mb 10mc 10md 1lb2 1xs9 2jzb 3iyd 3lu0 3n4m 3n97 4jk1

296 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RPOA_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–84； UniProt 246–329 Author chain C； PDBConstruct 1–84； UniProt 246–329

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_id3n4m
Deposition date deposition_date2010-05-21
Structure title titleE. coli RNA polymerase alpha subunit C-terminal domain in complex with CAP and DNA
Keywords keywordsprotein-protein interactions, protein-DNA interactions, GENE REGULATION-DNA complex; GENE REGULATION/DNA
Experimental Method methodX-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.

3n4m__assembly_1__model_1

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

Download this curve (.dat)

3n4m__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3n4m__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）37.37 Å
Rg (electron density)37.30 Å
Total Rg37.47 Å
Atom count7404
Residues788
Excluded volume127090 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3n4m__assembly_1__model_1 decameric （10） 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 (7)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3n4ma1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.3 — cAMP-binding domain-like
Family Family familyb.82.3.2 — cAMP-binding domain
Domain ID domain_idd3n4ma2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.4 — CAP C-terminal domain-like
Domain ID domain_idd3n4mb_
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family familya.60.3.1 — C-terminal domain of RNA polymerase alpha subunit
Domain ID domain_idd3n4mc_
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.3 — C-terminal domain of RNA polymerase alpha subunit
Family Family familya.60.3.1 — C-terminal domain of RNA polymerase alpha subunit

CATH v4.4 (4 domains)

Domain ID domain_id3n4mA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id3n4mA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id3n4mB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id3n4mC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
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7. Citations (2)