8vdi

Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGAGGAAGTGGG) in Ternary Complex with DB2447

Method: X-RAY DIFFRACTION D_max: 56.5 Å Quality: GOOD

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

Transcription factor PU.1

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain F； UniProt 165–270	Not recorded	;DNA (5'-D(APAPTPAPAPGPAPGPGPAPAPGPTPGPGPG)-3') ; × 1 ;DNA (5'-D(TPCPCPCPAPCPTPTPCPCPTPCPTPTPAPT)-3') ; × 1 A1AAQ 4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM Sodium Acetate, pH=4.6, 2% PEG3350	Resolution 1.93 Å R-free 0.202

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 8VDI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8E3K Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) Deposited 2022-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.28 Å R-free 0.151
8E3R Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAAGTGGG) Deposited 2022-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.45 Å R-free 0.153
8E4H Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGAGGAAGTGGG) Deposited 2022-08-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.39 Å R-free 0.153
8E5Y Human PU.1 ETS-Domain Bound to d(AATAAGCGGAAGTGGG) Acetate Free at pH 5.4 Deposited 2022-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；100 mM Bis-Tris pH 5.4, 2% PEG 3350	Resolution 1.32 Å R-free 0.162
8EBH Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAATGGGG) Deposited 2022-08-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.33 Å R-free 0.174
8EE9 Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAATGGGG) Deposited 2022-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.22 Å R-free 0.156
8EJ6 Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGAGGAATGGGG) Deposited 2022-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.39 Å R-free 0.168
8EJ8 Human PU.1 ETS-Domain (165-270) Q226E Mutant Bound to d(AATAAAAGGAAGTGGG) Deposited 2022-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Mutation：Q226E	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.45 Å R-free 0.172
8EK3 Human PU.1 ETS-Domain (165-270) Q226E Mutant Bound to d(AATAAGCGGAATGGGG) Deposited 2022-09-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain (165-270)	Mutation：Q226E	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.38 Å R-free 0.167
8EK8 Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAGAAGGG) Deposited 2022-09-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；200 mM Ammonium Acetate, 100 mM TRIS, pH=8.5, 25% PEG 3350	Resolution 2.63 Å R-free 0.280
8EK8 Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAGAAGGG) Deposited 2022-09-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain E 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；200 mM Ammonium Acetate, 100 mM TRIS, pH=8.5, 25% PEG 3350	Resolution 2.63 Å R-free 0.280
8EKJ Human PU.1 ETS-Domain (165-270) Bound to d(AATAAATGGAAGTGGG) Deposited 2022-09-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, 2% PEG 3350	Resolution 1.54 Å R-free 0.192
8EKU Human PU.1 ETS-Domain (165-270) Bound to d(AATAAATGGAATGGGG) Deposited 2022-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.52 Å R-free 0.188
8EKV Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGATGTGGG) Deposited 2022-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.62 Å R-free 0.200
8EKZ Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGGAGAAGTAGG) Deposited 2022-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.42 Å R-free 0.166
8EM9 Human PU.1 ETS-Domain (165-270) Bound to d(AATAGGAGAAGTAGGG) Deposited 2022-09-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 2.34 Å R-free 0.270
8EMD Human PU.1 ETS-Domain (165-270) Q226E Mutant Bound to d(AATAAGCGGAAGTGGG) Deposited 2022-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain (165-270)	Mutation：Q226E	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.55 Å R-free 0.202
8ENG Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) with Hemi-methylated CpG (forward strand) Deposited 2022-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.25 Å R-free 0.158
8EO1 Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) with Hemi-methylated CpG (reverse strand) Deposited 2022-10-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.28 Å R-free 0.180
8EO4 Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGCGGAAGTGGG) with Di-methylated CpG sites Deposited 2022-10-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG3350	Resolution 1.24 Å R-free 0.165
8EQG Human PU.1 ETS-Domain (165-270) Bound to d(AATAAA(DU)GGAAGTGGG) Deposited 2022-10-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.39 Å R-free 0.184
8EQK Human PU.1 ETS-Domain (165-270) Bound to d(AATAACCGGAAGTGGG) Deposited 2022-10-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.45 Å R-free 0.179
8EQL Human PU.1 ETS-Domain (165-270) Q226E Mutant Bound to d(AATAACCGGAAGTGGG) Deposited 2022-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.52 Å R-free 0.195
8T9U Human PU.1 ETS-domain (165-270) in complex with d(AATAAGCGIAAGTGGG) Deposited 2023-06-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；100 mM Sodium Acetate, pH=4.6, 2% PEG 3350	Resolution 1.47 Å R-free 0.181
8UFF Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAAGTGGG) in Ternary Complex with DB1976 Deposited 2023-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	Y5U (2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM Sodium Acetate, pH=4.6, 2% PEG 3350 well solution mixed 1:1 with 250uM Protein/DNA Complex	Resolution 1.66 Å R-free 0.201
8UFK Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG) Deposited 2023-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex	Resolution 2.41 Å R-free 0.266
8UFK Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG) Deposited 2023-10-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain E 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex	Resolution 2.41 Å R-free 0.266
8UFZ Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG) in Ternary Complex with DB1976 Deposited 2023-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	Y5U (2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex - Ligand incorporated via soaking at 500uM concentration 24h	Resolution 3.06 Å R-free 0.286
8UFZ Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGCGGAAGTG) in Ternary Complex with DB1976 Deposited 2023-10-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain E 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	Y5U (2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex - Ligand incorporated via soaking at 500uM concentration 24h	Resolution 3.06 Å R-free 0.286
8UHK Human PU.1 ETS-Domain (165-270) Bound to d(AAAATAAAAGGAAGTG) Deposited 2023-10-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex	Resolution 3.08 Å R-free 0.304
8UHK Human PU.1 ETS-Domain (165-270) Bound to d(AAAATAAAAGGAAGTG) Deposited 2023-10-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain E 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM TRIS Base (HCl adjusted), pH=8.5, 200mM Ammonium Acetate, 24% PEG3350 1:1 hanging drop with 250uM protein/DNA complex	Resolution 3.08 Å R-free 0.304
8V9N Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG) Deposited 2023-12-08	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM Sodium Acetate, pH=4.6, 2% PEG3350	Resolution 1.78 Å R-free 0.208
8VDH Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG) in Ternary Complex with DB2447 Deposited 2023-12-15	Different construct Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	A1AAQ 4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM Sodium Acetate, pH=4.6, 2% PEG3350	Resolution 1.64 Å R-free 0.208
9CK2 Human PU.1 minimal ETS Domain (165-258) bound to d(AATAAGCGGAAGTGGG) Deposited 2024-07-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–258（94 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.71 Å R-free 0.184
9CMB Human PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG) Deposited 2024-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100 mM sodium cacodylate, pH 6.5, 200 mM zinc acetate and 2% PEG 600	Resolution 2.15 Å R-free 0.246
9CMB Human PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG) Deposited 2024-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100 mM sodium cacodylate, pH 6.5, 200 mM zinc acetate and 2% PEG 600	Resolution 2.15 Å R-free 0.246
9OA4 Human PU.1 ETS-Domain (165-270) Bound to d(5'-AATAAGCGGAAGTGGG-3') d(5'-TCCCACTTTCGCTTAT-3') with a GT mismatch Deposited 2025-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.42 Å R-free 0.195
9OB0 Human PU.1 ETS-Domain (165-270) Bound to d(5'-AATAAGCGIAAGTGGG-3') d(5'-TCCCACTTTCGCTTAT-3') with an IT mismatch Deposited 2025-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 1.79 Å R-free 0.211
9YNZ Human PU.1 ETS-Domain (165-270) Bound to d(5'-AATAAGCGGAAGTGGG-3') d(5'-TCCCACTCPDCGCTTAT-3') Deposited 2025-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 165–270（106 aa） Fragment：ETS-Domain UNP residues 165-270	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2% PEG 3350, 100 mM Sodium Acetate, pH 4.6	Resolution 2.05 Å R-free 0.244

34 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPI1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–106； UniProt 165–270

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	8vdi
Deposition date deposition_date	2023-12-15
Structure title title	Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGAGGAAGTGGG) in Ternary Complex with DB2447
Keywords keywords	;Minor groove binder, DNA binding small molecule, diamidine, PU.1, transcription factor, transcriptional inhibition, TRANSCRIPTION, TRANSCRIPTION-DNA complex ;; TRANSCRIPTION/DNA
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	17.53 Å
Radius of gyration Rg (electron density) rg_electron	16.35 Å
Forward intensity I(0) i0	12469600.00
Molecular weight molecular_weight	20588.0 kDa
Excluded volume excluded_volume	23250 Å³
Envelope volume envelope_volume	28834 Å³
Hydration-shell volume shell_volume	15076 Å³
Envelope diameter envelope_diameter	56.8 Å
Shell Rg shell_rg	21.99 Å
Envelope Rg envelope_rg	16.62 Å
Shape Rg shape_rg	16.26 Å
Total Rg total_rg	17.29 Å
Total atoms total_atoms	2560
Residues n_residues	123
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	56.5 Å
Rg (real space) rg_real	17.45 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.2470e+07
I(0) uncertainty (real space) i0_real_error	1.5840e+05
Rg (reciprocal space) rg_reciprocal	17.46 Å
I(0) (reciprocal space) i0_reciprocal	12470000.0000
Solution quality estimate total_estimate	0.8213
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1229000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	;DNA (5'-D(APAPTPAPAPGPAPGPGPAPAPGPTPGPGPG)-3') ;
Molecular weight formula_weight	5060.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2761

AATAAGAGGAAGTGGG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPCPCPAPCPTPTPCPCPTPCPTPTPAPT)-3') ;
Molecular weight formula_weight	4735.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TCCCACTTCCTCTTAT

Entity 3 Entity 3 polymer

Description description	Transcription factor PU.1
Molecular weight formula_weight	12436.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GSKKKIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYQKMARALRNYGKTGEVKKVKKKLTYQFSGEVLGRGGLAERRHPPH

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

Entity 4 Entity 4 non-polymer

Description description	4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide)
Molecular weight formula_weight	375.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

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8. Citations (1)

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Unit-cell length a length_a	42.996 Å
Unit-cell length b length_b	60.583 Å
Unit-cell length c length_c	44.297 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	33.140 Å
R factor r_factor	0.1683
R_work r_work	0.1664
R_free r_free	0.2018

fit	/app/data/saxs_computation/vd/8vdi/8vdi.fit
pddf	/app/data/pr_computation/vd/8vdi/8vdi.pr.out
profile	/app/data/saxs_computation/vd/8vdi/8vdi.dat

Human PU.1 ETS-Domain (165-270) Bound to d(AATAAGAGGAAGTGGG) in Ternary Complex with DB2447

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

Transcription factor PU.1

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)