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6vgg

Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC

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

Transcriptional regulator ERG

Homo sapiens

UniProt P11308

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 3 DNA 2 ;DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') ; × 1 ;DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') ; × 1 Runt-related transcription factor 2 × 1 （Q13950） Core-binding factor subunit beta × 1 （Q13951） mithramycin × 2 MAGNESIUM ION × 1 water × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1sxe

1 assemblies

Homodimer
4irg 4irh 5ybc

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4iri 5ybd 5ybd 6vge 6vgg

5 assemblies

View Construct and Data Evidence
UniProt name ERG_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–118； UniProt 313–426

Runt-related transcription factor 2

Homo sapiens

UniProt Q13950

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 3 DNA 2 Transcriptional regulator ERG × 1 （P11308） ;DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') ; × 1 ;DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') ; × 1 Core-binding factor subunit beta × 1 （Q13951） mithramycin × 2 MAGNESIUM ION × 1 water × 2 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
6vg8 6vgd 6vge 6vgg

4 assemblies

View Construct and Data Evidence
UniProt name RUNX2_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–177； UniProt 111–287

Core-binding factor subunit beta

Homo sapiens

UniProt Q13951

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 3 DNA 2 Transcriptional regulator ERG × 1 （P11308） ;DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') ; × 1 ;DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') ; × 1 Runt-related transcription factor 2 × 1 （Q13950） mithramycin × 2 MAGNESIUM ION × 1 water × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1cl3

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1e50 1e50 1e50 1e50 1h9d 1h9d 4n9f 4n9f 4n9f 4n9f 4n9f 4n9f

35 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PEBB_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain G； PDBConstruct 15–156； UniProt 1–142

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_id6vgg
Deposition date deposition_date2020-01-08
Structure title titleCrystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC
Keywords keywordsEwing sarcoma, enhancer, transcription factor, oncogenesis, prostate cancer, ETS-family, Runt-family, TRANSCRIPTION; TRANSCRIPTION
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.

6vgg__assembly_1__model_1

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

Download this curve (.dat)

6vgg__assembly_1__model_1 | I(q)

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

6vgg__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）26.31 Å
Rg (electron density)25.87 Å
Total Rg26.53 Å
Atom count3513
Residues368
Excluded volume60192 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6vgg__assembly_1__model_1 pentameric （5） 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 (8)

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7. Citations (1)