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 D_max: 86.6 Å Quality: GOOD

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

Friend leukemia integration 1 transcription factor

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 276–375	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）	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

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 6VGD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLI DNA-BINDING DOMAIN OF FLI-1 Deposited 1994-09-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 276–373（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1X66 Solution structure of the SAM_PNT-domain of the human friend LEUKEMIAINTEGRATION 1 transcription factor Deposited 2005-05-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–198（85 aa） Fragment：SAM_PNT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient NMR sample composition 1.17mM SAM_PNT DOMAIN, 20mM TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2YTU Solution structure of the SAM_PNT-domain of the human friend LEUKEMIAINTEGRATION 1 transcription factor Deposited 2007-04-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–220（121 aa） Fragment：SAM_PNT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120 mM；Pressure AMBIENT NMR sample composition 0.24mM SAM_PNT DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5E8G Crystal structure of the DNA binding domain of human transcription factor FLI1 Deposited 2015-10-14	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 276–399（124 aa） Fragment：UNP residues 276-399 Chain C 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M sodium acetate pH 5.5, 0.1 M Co2+ sulfate heptahydrate, 24% PEG 4000	Resolution 2.70 Å R-free 0.248
5E8G Crystal structure of the DNA binding domain of human transcription factor FLI1 Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 276–399（124 aa） Fragment：UNP residues 276-399 Chain D 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M sodium acetate pH 5.5, 0.1 M Co2+ sulfate heptahydrate, 24% PEG 4000	Resolution 2.70 Å R-free 0.248
5E8I Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA ACCGGAAGTG Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 276–399（124 aa） Fragment：UNP residues 276-399 Chain G 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Na cacodylate pH 6.5, 0.2 M CaCl2, 14% w/v PEG 8000	Resolution 3.45 Å R-free 0.271
5E8I Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA ACCGGAAGTG Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain D 276–399（124 aa） Fragment：UNP residues 276-399 Chain J 276–399（124 aa） Fragment：UNP residues 276-399	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Na cacodylate pH 6.5, 0.2 M CaCl2, 14% w/v PEG 8000	Resolution 3.45 Å R-free 0.271
5JVT Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG Deposited 2016-05-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 276–375（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6	Resolution 3.10 Å R-free 0.237
5JVT Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG Deposited 2016-05-11	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 D 276–375（100 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6	Resolution 3.10 Å R-free 0.237
5JVT Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG Deposited 2016-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 276–375（100 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6	Resolution 3.10 Å R-free 0.237
6VG2 Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 276–375（100 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；1.6 M ammonium sulfate	Resolution 3.90 Å R-free 0.294
6VG2 Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 276–375（100 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；1.6 M ammonium sulfate	Resolution 3.90 Å R-free 0.294
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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 276–375（100 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
9CP6 Crystal structure of the DNA binding domain of FLI1 (residues 259-371) Deposited 2024-07-17	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 259–371（113 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Hepes, pH 6.5, 1 M Na citrate	Resolution 1.66 Å R-free 0.235
9MWY Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing four contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain C 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain D 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain L 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399)	Mutation：F362A Mutation：F362A Mutation：F362A Mutation：F362A	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Tris, pH 6.5, 0.7 M sodium acetate	Resolution 3.28 Å R-free 0.281
9MX8 Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing three contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 259–375（117 aa） Fragment：DNA-binding domain (residues 259-375) Chain C 259–375（117 aa） Fragment：DNA-binding domain (residues 259-375) Chain D 259–375（117 aa） Fragment：DNA-binding domain (residues 259-375)	Mutation：F362A Mutation：F362A Mutation：F362A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M sodium cacodylate, pH 7.0, 1.6 M sodium acetate, added cryoprotectant: 34% sucrose	Resolution 3.15 Å R-free 0.278
9MX9 Crystal structure of the DNA binding domain of FLI1 (F362A) in complex with a DNA containing two contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain D 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399)	Mutation：F362A Mutation：F362A	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 18% PEG8000	Resolution 2.55 Å R-free 0.250
9MXA Crystal structure of the DNA binding domain of FLI1 (wild-type) in complex with a DNA containing two contiguous GGAA sites Deposited 2025-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399) Chain D 259–399（141 aa） Fragment：DNA-binding domain (residues 259-399)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1 M Tris, pH 8.5, 2 M ammonium phosphate	Resolution 2.59 Å R-free 0.287

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

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	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	Friend leukemia integration 1 transcription factor × 1 （Q01543） ;DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3') ; × 1 ;DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3') ; × 1 Core-binding factor subunit beta × 1 （Q13951）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6VGD	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 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
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 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
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 Deposited 2020-01-08	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	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

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	Friend leukemia integration 1 transcription factor × 1 （Q01543） ;DNA (5'-D(PCPAPGPAPGPGPAPTPGPTPGPGPCPTPTPC)-3') ; × 1 ;DNA (5'-D(PGPAPAPGPCPCPAPCPAPTPCPCPTPCPTPG)-3') ; × 1 Runt-related transcription factor 2 × 1 （Q13950）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6VGD	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 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 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 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 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 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 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 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
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 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
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 Deposited 2020-01-08	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	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
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 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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vgd
Deposition date deposition_date	2020-01-07
Structure title title	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
Keywords keywords	Ewing sarcoma, enhancer, transcription factor, oncogenesis, prostate cancer, ETS-family, Runt-family, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	26.41 Å
Radius of gyration Rg (electron density) rg_electron	26.04 Å
Forward intensity I(0) i0	51800700.00
Molecular weight molecular_weight	48318.0 kDa
Excluded volume excluded_volume	57231 Å³
Envelope volume envelope_volume	77479 Å³
Hydration-shell volume shell_volume	25704 Å³
Envelope diameter envelope_diameter	90.4 Å
Shell Rg shell_rg	32.32 Å
Envelope Rg envelope_rg	25.74 Å
Shape Rg shape_rg	26.04 Å
Total Rg total_rg	26.68 Å
Total atoms total_atoms	3359
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

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

Maximum dimension Dmax dmax	86.6 Å
Rg (real space) rg_real	26.47 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	5.1800e+07
I(0) uncertainty (real space) i0_real_error	7.1850e+05
Rg (reciprocal space) rg_reciprocal	26.46 Å
I(0) (reciprocal space) i0_reciprocal	51800000.0000
Solution quality estimate total_estimate	0.8916
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	85.2 Å
Skewness Skewness skewness	0.397
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4690000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.943

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Friend leukemia integration 1 transcription factor
Molecular weight formula_weight	12098.7 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	3359

GPHMPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPTE

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)

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8. Citations (1)

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Unit-cell length a length_a	104.513 Å
Unit-cell length b length_b	104.513 Å
Unit-cell length c length_c	322.040 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	4.200 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2947
R_work r_work	0.2948
R_free r_free	0.2932

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

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

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

Friend leukemia integration 1 transcription factor

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 (5)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)