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 D_max: 87.4 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcriptional regulator ERG

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 313–426	Fragment：DNA binding domain	;DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3') ; × 1 ;DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3') ; × 1 Runt-related transcription factor 2 × 1 （Q13950） Core-binding factor subunit beta × 1 （Q13951） QWP mithramycin × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg	Resolution 4.31 Å R-free 0.285

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6VGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SXE The solution structure of the Pointed (PNT) domain from the transcrition factor Erg Deposited 2004-03-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–208（94 aa） Fragment：PNT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 70 mM；Pressure ambient NMR sample composition 1mM Erg U-15N,13C, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Erg 100%15N,10%13C, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM Erg 100%15N, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM Erg 100%15N, 20mM phosphate buffer pH 7.0, 50mM NaCl, 2mM DTT, 1% H2O, 99% D2O \| 1% H2O, 99% D2O	Resolution not provided
4IRG Uninhibited DNA-binding domain of the Ets transcription factor ERG Deposited 2013-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 313–412（100 aa） Fragment：Ets Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；290 K；1.4M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.70 Å R-free 0.228
4IRH Auto-inhibited ERG Ets domain Deposited 2013-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 287–412（126 aa） Fragment：Ets Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；290 K；1.4M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.10 Å R-free 0.215
4IRI Auto-inhibited ERG Ets Domain-DNA Complex Deposited 2013-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 287–412（126 aa） Fragment：Ets Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.2M ammonium chloride, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.77 Å R-free 0.210
5YBC X-ray structure of native ETS-domain domain of Ergp55 Deposited 2017-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 317–408（92 aa） Fragment：ETS domain, UNP residues 317-408 Chain C 317–408（92 aa） Fragment：ETS domain, UNP residues 317-408	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；20%(w/v) PEG400, 130mM NaCl, 60mM MgCl2, 100mM sodium citrate pH 5.6	Resolution 2.50 Å R-free 0.257
5YBD X-ray structure of ETS domain of Ergp55 in complex with E74DNA Deposited 2017-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 317–406（90 aa） Fragment：ETS domain, UNP residues 317-406	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20%(w/v) PEG4000, 200mM MgCl2 as precipitant solution	Resolution 2.77 Å R-free 0.282
5YBD X-ray structure of ETS domain of Ergp55 in complex with E74DNA Deposited 2017-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain X 317–406（90 aa） Fragment：ETS domain, UNP residues 317-406	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20%(w/v) PEG4000, 200mM MgCl2 as precipitant solution	Resolution 2.77 Å R-free 0.282
6VGE Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 313–426（114 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.25 Å R-free 0.317

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain D； UniProt 111–287	Fragment：DNA binding domain	Transcriptional regulator ERG × 1 （P11308） ;DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3') ; × 1 ;DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3') ; × 1 Core-binding factor subunit beta × 1 （Q13951） QWP mithramycin × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg	Resolution 4.31 Å R-free 0.285

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6VGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VG8 Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 111–233（123 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；7% w/v PEG 4000, 50 mM Na Citrate, pH 5.6, 4% v/v isopropanol	Resolution 4.31 Å R-free 0.283
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 Deposited 2020-01-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 111–287（177 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.20 Å R-free 0.293
6VGE Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 111–287（177 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.25 Å R-free 0.317

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain G； UniProt 1–142	Not recorded	Transcriptional regulator ERG × 1 （P11308） ;DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3') ; × 1 ;DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3') ; × 1 Runt-related transcription factor 2 × 1 （Q13950） QWP mithramycin × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg	Resolution 4.31 Å R-free 0.285

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6VGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CL3 MOLECULAR INSIGHTS INTO PEBP2/CBF-SMMHC ASSOCIATED ACUTE LEUKEMIA REVEALED FROM THE THREE-DIMENSIONAL STRUCTURE OF PEBP2/CBF BETA Deposited 1999-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–141（138 aa） Fragment：BETA SUBUNIT	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K NMR sample composition 96% WATER/4% D2O	Resolution not provided
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1H9D Aml1/cbf-beta/dna complex Deposited 2001-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.271
1H9D Aml1/cbf-beta/dna complex Deposited 2001-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.271
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain a 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 6 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain k 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain c 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain i 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain o 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain u 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 0 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
6NIL cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex Deposited 2018-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–151（151 aa） Chain E 1–151（151 aa） Chain H 1–151（151 aa） Chain K 1–151（151 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6P59 Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex Deposited 2019-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–165（165 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；MES (pH 6), PEG 6000, Dichloromethane	Resolution 2.94 Å R-free 0.268
6P59 Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex Deposited 2019-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–165（165 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；MES (pH 6), PEG 6000, Dichloromethane	Resolution 2.94 Å R-free 0.268
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 Deposited 2020-01-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.20 Å R-free 0.293
6VGE Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.25 Å R-free 0.317
8CX0 Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric	Chain C 1–182（182 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8CX1 Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1 Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain C 1–182（182 aa） Chain H 1–182（182 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8CX2 Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2 Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain C 1–182（182 aa） Chain H 1–182（182 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8E40 Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA Deposited 2022-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–157（157 aa） Fragment：UNP residues 1-157	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
8FVI Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain 0 1–157（157 aa） Fragment：UNP residues 1-157	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8FVJ Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain 0 1–157（157 aa） Fragment：UNP residues 1-157 Chain 5 1–157（157 aa） Fragment：UNP residues 1-157	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8H0I Cryo-EM structure of APOBEC3G-Vif complex Deposited 2022-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain D 1–156（156 aa） Chain F 1–156（156 aa） Chain H 1–156（156 aa） Chain J 1–156（156 aa）	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.80 Å
8J62 Cryo-EM structure of APOBEC3G-Vif complex Deposited 2023-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain D 1–156（156 aa） Chain F 1–156（156 aa） Chain H 1–156（156 aa） Chain J 1–156（156 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.50 Å
8SZK The cryo-EM structure of PPP2R5A/HIV-1 Vif/CBFb/EloB/EloC complex Deposited 2023-05-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E93 Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: decameric	Chain o 1–170（170 aa） Chain s 1–170（170 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E9V Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: 13-meric	Chain o 1–170（170 aa） Chain s 1–170（170 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

19 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vgg
Deposition date deposition_date	2020-01-08
Structure title title	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
Keywords keywords	Ewing sarcoma, enhancer, transcription factor, oncogenesis, prostate cancer, ETS-family, Runt-family, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.31 Å
Radius of gyration Rg (electron density) rg_electron	25.87 Å
Forward intensity I(0) i0	54815500.00
Molecular weight molecular_weight	50528.0 kDa
Excluded volume excluded_volume	60192 Å³
Envelope volume envelope_volume	80596 Å³
Hydration-shell volume shell_volume	26695 Å³
Envelope diameter envelope_diameter	91.8 Å
Shell Rg shell_rg	32.29 Å
Envelope Rg envelope_rg	25.65 Å
Shape Rg shape_rg	25.87 Å
Total Rg total_rg	26.53 Å
Total atoms total_atoms	3513
Residues n_residues	368
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	87.4 Å
Rg (real space) rg_real	26.36 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	5.4820e+07
I(0) uncertainty (real space) i0_real_error	7.7150e+05
Rg (reciprocal space) rg_reciprocal	26.35 Å
I(0) (reciprocal space) i0_reciprocal	54810000.0000
Solution quality estimate total_estimate	0.8874
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.327
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5244000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.947

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Transcriptional regulator ERG
Molecular weight formula_weight	14927.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3515

GPHMPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSYHAHPQKMN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3') ;
Molecular weight formula_weight	4954.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CAGAGGATGTGGCTTC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3') ;
Molecular weight formula_weight	4843.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GAAGCCACATCCTCTG

Entity 4 Entity 4 polymer

Description description	Runt-related transcription factor 2
Molecular weight formula_weight	19542.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

AELVRTDSPNFLCSVLPSHWRCNKTLPVAFKVVALGEVPDGTVVTVMAGNDENYSAELRNASAVMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKVTVDGPREPRRHRQKLDDSKPSLFSDRLSDLGRIPHPSMRVGVPPQNPRPSLNSAPSPFNPQGQSQITD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Core-binding factor subunit beta
Molecular weight formula_weight	18263.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MGSSHHHHHHSQDPMPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 non-polymer

Description description	mithramycin
Molecular weight formula_weight	1085.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

▶

8. Citations (1)

▶

Unit-cell length a length_a	104.678 Å
Unit-cell length b length_b	104.678 Å
Unit-cell length c length_c	322.836 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	4.310 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2531
R_work r_work	0.2514
R_free r_free	0.2846

fit	/app/data/saxs_computation/vg/6vgg/6vgg.fit
pddf	/app/data/pr_computation/vg/6vgg/6vgg.pr.out
profile	/app/data/saxs_computation/vg/6vgg/6vgg.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcriptional regulator ERG

State in the Current Structure

Other States of the Same Protein in the Database

Runt-related transcription factor 2

State in the Current Structure

Other States of the Same Protein in the Database

Core-binding factor subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)