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3bep

Structure of a sliding clamp on DNA

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

DNA polymerase III subunit beta

Escherichia coli

UniProt P0A988

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3') ; × 1 ;DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3') ; × 1 ;1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium ; × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1mmi 2pol 2xur 3d1g 3f1v 3pwe 3qsb 4k3k 4k3l 4k3s 4mjp 4mjq

20 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jqj 1jqj 1jqj 1jqj 1jqj 1jql 3bep 3d1e 3d1f 3q4j 3q4j 3q4j

41 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPO3B_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–366； UniProt 1–366 Author chain B； PDBConstruct 1–366； UniProt 1–366

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_id3bep
Deposition date deposition_date2007-11-19
Structure title titleStructure of a sliding clamp on DNA
Keywords keywordsbeta subunit, sliding clamp, E. coli polymerase III, DNA complex, TRANSFERASE, TRANSCRIPTION-DNA COMPLEX; TRANSFERASE, TRANSCRIPTION/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.

3bep__assembly_1__model_1

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

Download this curve (.dat)

3bep__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.

3bep__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）31.10 Å
Rg (electron density)30.76 Å
Total Rg31.26 Å
Atom count6193
Residues756
Excluded volume108940 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3bep__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 (5)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3bepa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd3bepa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd3bepa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd3bepb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd3bepb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd3bepb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit

CATH v4.4 (6 domains)

Domain ID domain_id3bepA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id3bepA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id3bepA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id3bepB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id3bepB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id3bepB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
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7. Citations (1)