← Back to search
1xpo

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin

Method: X-RAY DIFFRACTION
▼

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

Rho transcription termination factor

Escherichia coli

UniProt P22869

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 Consistent with all polymers
2 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BICYCLOMYCIN × 1 Consistent with all polymers
3 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BICYCLOMYCIN × 1 Consistent with all polymers
4 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BICYCLOMYCIN × 1 Consistent with all polymers
5 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BICYCLOMYCIN × 1 Consistent with all polymers
6 Protein–RNA Monomer Protein 1 RNA 1 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' × 1 MAGNESIUM ION × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BICYCLOMYCIN × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1fyz 1fz0 1fz1 1fz2 1fz3 1fz4 1fz5 1fz6 1fz7 1fz8 1fz9 1fzh

48 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name MEMA_METCA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–419； UniProt 1–419 Author chain B； PDBConstruct 1–419； UniProt 1–419 Author chain C； PDBConstruct 1–419； UniProt 1–419 Author chain D； PDBConstruct 1–419； UniProt 1–419 Author chain E； PDBConstruct 1–419； UniProt 1–419 Author chain F； PDBConstruct 1–419； UniProt 1–419

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1xpo
Deposition date deposition_date2004-10-09
Structure title titleStructural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin
Keywords keywordsRho; Bicyclomycin, TRANSCRIPTION-RNA COMPLEX; TRANSCRIPTION/RNA
Experimental Method methodX-RAY DIFFRACTION
▼

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.

1xpo__assembly_1__model_1

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

Download this curve (.dat)

1xpo__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1xpo__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）24.92 Å
Rg (electron density)24.10 Å
Total Rg25.02 Å
Atom count3282
Residues410
Excluded volume58560 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1xpo__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1xpo__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1xpo__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1xpo__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1xpo__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1xpo__assembly_6__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd1xpoa1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1xpoa2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like
Domain ID domain_idd1xpoa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd1xpob1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1xpob2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like
Domain ID domain_idd1xpob3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd1xpoc1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1xpoc2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like
Domain ID domain_idd1xpoc3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd1xpod1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1xpod2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like
Domain ID domain_idd1xpod3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd1xpoe1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1xpoe2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like
Domain ID domain_idd1xpoe3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd1xpof1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.3 — Rho N-terminal domain-like
Family Family familya.140.3.1 — Rho termination factor, N-terminal domain
Domain ID domain_idd1xpof2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like
Domain ID domain_idd1xpof3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (12 domains)

Domain ID domain_id1xpoA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1xpoA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xpoB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1xpoB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xpoC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1xpoC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xpoD01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1xpoD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xpoE01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1xpoE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xpoF01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1xpoF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
▶

7. Citations (1)