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6vgd

Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC

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

Friend leukemia integration 1 transcription factor

Homo sapiens

UniProt Q01543

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） Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1fli 1x66 2ytu

3 assemblies

Homodimer
5e8g 5e8g 9cp6

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5e8i 5e8i 5jvt 5jvt 5jvt 6vg2 6vg2 6vg8 6vgd 9mwy 9mx8 9mx9

13 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name FLI1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–104； UniProt 276–375

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 Friend leukemia integration 1 transcription factor × 1 （Q01543） ;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） 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 Friend leukemia integration 1 transcription factor × 1 （Q01543） ;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） 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_id6vgd
Deposition date deposition_date2020-01-07
Structure title titleCrystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), 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.

6vgd__assembly_1__model_1

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

Download this curve (.dat)

6vgd__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.

6vgd__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）26.41 Å
Rg (electron density)26.04 Å
Total Rg26.68 Å
Atom count3359
Residues368
Excluded volume57231 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6vgd__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 (5)

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7. Citations (1)