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2ram

A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER

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

PROTEIN (TRANSCRIPTION FACTOR NF-KB P65)

Mus musculus

UniProt Q04207

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(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3') ; × 2 (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 2 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1bft 1my5 1my7

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ikn 1k3z 1le5 1le5 1le9 1le9 1lei 1oy3 1ram 1vkx 2i9t 2ram

23 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TF65_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–273； UniProt 19–291 Author chain B； PDBConstruct 1–273； UniProt 19–291

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_id2ram
Deposition date deposition_date1997-11-23
Structure title titleA NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER
Keywords keywords;COMPLEX (TRANSCRIPTION FACTOR-DNA), DNA-BINDING, TRANSCRIPTION REGULATION, ACTIVATOR NUCLEAR PROTEIN, PHOSPHORYLATION, CONFORMATION, TRANSCRIPTION-DNA COMPLEX ;; 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.

2ram__assembly_1__model_1

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

Download this curve (.dat)

2ram__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.

2ram__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）29.53 Å
Rg (electron density)30.24 Å
Total Rg30.32 Å
Atom count5186
Residues582
Excluded volume88823 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2ram__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 (4)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2rama1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd2rama2
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.5 — p53-like transcription factors
Family Family familyb.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain
Domain ID domain_idd2ramb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd2ramb2
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.5 — p53-like transcription factors
Family Family familyb.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id2ramA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily340 — Rel homology domain (RHD), DNA-binding domain
Domain ID domain_id2ramA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ramB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily340 — Rel homology domain (RHD), DNA-binding domain
Domain ID domain_id2ramB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)