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2bh2

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

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

23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA

ESCHERICHIA COLI

UniProt P55135

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 23S RIBOSOMAL RNA 1932-1968 × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 IRON/SULFUR CLUSTER × 1 water × 2 Consistent with all polymers
2 Protein–RNA Monomer Protein 1 RNA 1 23S RIBOSOMAL RNA 1932-1968 × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 IRON/SULFUR CLUSTER × 1 water × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1uwv

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2bh2 2bh2

2 assemblies

View Construct and Data Evidence
UniProt name RUMA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–433； UniProt 1–432 Author chain B； PDBConstruct 2–433； UniProt 1–432

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_id2bh2
Deposition date deposition_date2005-01-06
Structure title titleCrystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.
Keywords keywords;IRON-SULFUR CLUSTER, METHYLTRANSFERASE, RNA MODIFICATION, RNA PROCESSING, TRANSFERASE, RUMA, BASE FLIPPING, SAM, OB-FOLD, PROTEIN-RNA COMPLEX, BASE STACKING, SUBSTRATE SELECTIVITY, GENERAL BASE, PRODUCT RELEASE, 4FE-4S, METAL-BINDING ;; TRANSFERASE
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.

2bh2__assembly_2__model_1

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

Download this curve (.dat)

2bh2__assembly_2__model_1 | I(q)

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

2bh2__assembly_2__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）23.94 Å
Rg (electron density)23.25 Å
Total Rg23.91 Å
Atom count3900
Residues445
Excluded volume67147 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2bh2__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2bh2__assembly_2__model_1 dimeric （2） 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 (5)

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2bh2a1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.12 — TRAM domain
Domain ID domain_idd2bh2a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.40 — (Uracil-5-)-methyltransferase
Domain ID domain_idd2bh2b1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.12 — TRAM domain
Domain ID domain_idd2bh2b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.40 — (Uracil-5-)-methyltransferase

CATH v4.4 (6 domains)

Domain ID domain_id2bh2A01
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_id2bh2A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id2bh2A03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily1070 —
Domain ID domain_id2bh2B01
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_id2bh2B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id2bh2B03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily1070 —
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7. Citations (2)