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2vmk

Crystal Structure of E. coli RNase E Apoprotein - Catalytic Domain

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

RIBONUCLEASE E

ESCHERICHIA COLI

UniProt P21513

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 SULFATE ION × 3 ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1slj 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c

13 assemblies; showing the first 12

Homodimer
1smx 1sn8

2 assemblies

Homotetramer
2vmk

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2bx2 2c0b 2c4r 2fym 2fym 2fym 2vrt 2vrt 2vrt 2vrt 5f6c 5ohg

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RNE_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–515； UniProt 1–515 Author chain B； PDBConstruct 1–515； UniProt 1–515 Author chain C； PDBConstruct 1–515； UniProt 1–515 Author chain D； PDBConstruct 1–515； UniProt 1–515

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_id2vmk
Deposition date deposition_date2008-01-28
Structure title titleCrystal Structure of E. coli RNase E Apoprotein - Catalytic Domain
Keywords keywordsNUCLEASE, HYDROLASE, CYTOPLASM, RNA-BINDING, RNA TURNOVER, ENDONUCLEASE, RNA PROCESSING; HYDROLASE
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.

2vmk__assembly_1__model_1

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

Download this curve (.dat)

2vmk__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.

2vmk__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）45.67 Å
Rg (electron density)45.64 Å
Total Rg45.58 Å
Atom count14187
Residues1930
Excluded volume251050 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2vmk__assembly_1__model_1 tetrameric （4） 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)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2vmkA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily20 — Ribonuclease E, catalytic domain
Domain ID domain_id2vmkB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily20 — Ribonuclease E, catalytic domain
Domain ID domain_id2vmkC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily20 — Ribonuclease E, catalytic domain
Domain ID domain_id2vmkD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily20 — Ribonuclease E, catalytic domain
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7. Citations (1)