8ssq

ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4

Method: X-RAY DIFFRACTION D_max: 142.0 Å Quality: GOOD

▼

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

Transcriptional repressor CTCF

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 A； UniProt 319–606	Fragment：Zinc finger domains 3-11	DNA (35-MER) Strand I × 1 DNA (35-MER) Strand 2 × 1 ZN ZINC ION × 9 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350	Resolution 3.12 Å R-free 0.271
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain D； UniProt 319–606	Fragment：Zinc finger domains 3-11	DNA (35-MER) Strand I × 1 DNA (35-MER) Strand 2 × 1 ZN ZINC ION × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350	Resolution 3.12 Å R-free 0.271

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 8SSQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X6H Solution structures of the C2H2 type zinc finger domain of human Transcriptional repressor CTCF Deposited 2005-05-17	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 515–587（73 aa） Fragment：C2H2 type zinc finger domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.5mM C2H2 type zinc finger domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10uM ZnCl2; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CT1 Solution Structure of the zinc finger domain of Transcriptional repressor CTCF protein Deposited 2005-05-23	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 399–462（64 aa） Fragment：zinc finger domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 2.46mM zinc finger domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5K5H Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure Deposited 2016-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 348–464（117 aa） Fragment：unp residues 348-464	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% (w/v) polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris HCl, pH 5.5	Resolution 3.11 Å R-free 0.264
5K5I Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P65 Deposited 2016-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 378–489（112 aa） Fragment：unp residues 378-489	Not recorded	ZN ZINC ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；20% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5	Resolution 2.19 Å R-free 0.245
5K5J Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P41212 Deposited 2016-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 378–489（112 aa） Fragment：unp residues 378-489	Not recorded	ZN ZINC ION × 4 SO4 SULFATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；25% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, and 0.1 M bis-tris HCl, pH 5.5	Resolution 2.29 Å R-free 0.254
5K5L Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure Deposited 2016-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: heptameric	Chain E 405–492（88 aa） Fragment：unp residues 405-492 Chain F 405–492（88 aa） Fragment：unp residues 405-492 Chain G 405–492（88 aa） Fragment：unp residues 405-492	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；289 K；20% (w/v) polyethylene glycol 8,000 0.1 M CHES-NaOH pH 9.5	Resolution 3.12 Å R-free 0.270
5KKQ Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Deposited 2016-06-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 321–465（145 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5	Resolution 1.74 Å R-free 0.199
5KKQ Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Deposited 2016-06-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 321–465（145 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5	Resolution 1.74 Å R-free 0.199
5T00 Human CTCF ZnF3-7 and methylated DNA complex Deposited 2016-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 321–465（145 aa） Fragment：UNP residues 321-465	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5	Resolution 2.19 Å R-free 0.243
5T00 Human CTCF ZnF3-7 and methylated DNA complex Deposited 2016-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 321–465（145 aa） Fragment：UNP residues 321-465	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M HEPES-NaOH, pH 7.5	Resolution 2.19 Å R-free 0.243
5T0U CTCF ZnF2-7 and DNA complex structure Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 294–465（172 aa） Fragment：UNP residues 294-465	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6	Resolution 3.20 Å R-free 0.266
5T0U CTCF ZnF2-7 and DNA complex structure Deposited 2016-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 294–465（172 aa） Fragment：UNP residues 294-465	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6	Resolution 3.20 Å R-free 0.266
5UND Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA Deposited 2017-01-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 348–547（200 aa）	Not recorded	ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；28% PEG 2000 MME 100mM Bis-Tris, pH 6.5	Resolution 2.55 Å R-free 0.237
5UND Crystal Structure of CTCF(ZnF 4-10) With 28-mer DNA Deposited 2017-01-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 348–547（200 aa）	Not recorded	ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；28% PEG 2000 MME 100mM Bis-Tris, pH 6.5	Resolution 2.55 Å R-free 0.237
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEF Crystal structure of CTCF ZFs2-8-Hs5-1aE Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain J 292–490（199 aa） Fragment：UNP residues 292-490	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.81 Å R-free 0.254
5YEG Crystal structure of CTCF ZFs4-8-Hs5-1a complex Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 349–490（142 aa） Fragment：UNP residues 349-490	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289.15 K；0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350	Resolution 2.00 Å R-free 0.204
5YEG Crystal structure of CTCF ZFs4-8-Hs5-1a complex Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 349–489（141 aa） Fragment：UNP residues 349-489	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289.15 K；0.1M Bis-tris pH 5.6-6.0, 0.2M Sodium chloride, 17-24% PEG3350	Resolution 2.00 Å R-free 0.204
5YEH Crystal structure of CTCF ZFs4-8-eCBS Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 349–490（142 aa） Fragment：UNP residues 349-490	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.33 Å R-free 0.270
5YEH Crystal structure of CTCF ZFs4-8-eCBS Deposited 2017-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 349–490（142 aa） Fragment：UNP residues 349-490	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1 M Bis-tris pH 5.6-6.0, 0.2 M Sodium chloride and 17-24% PEG 3350	Resolution 2.33 Å R-free 0.270
5YEL Crystal structure of CTCF ZFs6-11-gb7CSE Deposited 2017-09-18	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 B 405–580（176 aa） Fragment：UNP residues 405-580	Mutation：C504S	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350	Resolution 2.96 Å R-free 0.286
5YEL Crystal structure of CTCF ZFs6-11-gb7CSE Deposited 2017-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 405–580（176 aa） Fragment：UNP residues 405-580	Mutation：C504S	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；0.1M Bis-tris pH 5.6-6.0, 0.1M Sodium chloride, 17-20% PEG3350	Resolution 2.96 Å R-free 0.286
6QNX Structure of the SA2/SCC1/CTCF complex Deposited 2019-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 222–231（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K	Resolution 2.70 Å
7W1M Cryo-EM structure of human cohesin-CTCF-DNA complex Deposited 2021-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain H 1–727（727 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 Deposited 2023-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	ZN ZINC ION × 9 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl	Resolution 3.14 Å R-free 0.284
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 Deposited 2023-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl	Resolution 3.14 Å R-free 0.284
8SSS ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer Deposited 2023-05-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 263–465（203 aa） Fragment：Zinc finger domains 1-7	Not recorded	ZN ZINC ION × 7 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；26.5% PEG3350, 0.26M DL-Malic acid 7.0	Resolution 2.30 Å R-free 0.231
8SSS ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer Deposited 2023-05-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 263–465（203 aa） Fragment：Zinc finger domains 1-7	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；26.5% PEG3350, 0.26M DL-Malic acid 7.0	Resolution 2.30 Å R-free 0.231
8SST ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer Deposited 2023-05-08	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 A 263–465（203 aa） Fragment：Zinc finger domains 1-7	Mutation：K365T	ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.243
8SST ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed with 23mer Deposited 2023-05-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 263–465（203 aa） Fragment：Zinc finger domains 1-7	Mutation：K365T	ZN ZINC ION × 7 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.243
8SSU ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: trimeric	Chain A 320–582（263 aa） Fragment：Zinc finger domains 3-11 of CTCF, Residues 195-258 of LDB1	Not recorded	EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane/pH 6.4, 20% w/v Polyethylene glycol 3,350	Resolution 2.89 Å R-free 0.240

20 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTCF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–288； UniProt 319–606 Author chain D； PDBConstruct 1–288； UniProt 319–606

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	8ssq
Deposition date deposition_date	2023-05-08
Structure title title	ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4
Keywords keywords	;PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN, transcription factor, zinc fingers, insulator/chromatin architecture, transcription-dna complex, TRANSCRIPTION ;; TRANSCRIPTION/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	40.48 Å
Radius of gyration Rg (electron density) rg_electron	40.73 Å
Forward intensity I(0) i0	283765000.00
Molecular weight molecular_weight	102370.0 kDa
Excluded volume excluded_volume	113260 Å³
Envelope volume envelope_volume	185150 Å³
Hydration-shell volume shell_volume	41003 Å³
Envelope diameter envelope_diameter	151.7 Å
Shell Rg shell_rg	42.86 Å
Envelope Rg envelope_rg	39.71 Å
Shape Rg shape_rg	40.71 Å
Total Rg total_rg	40.87 Å
Total atoms total_atoms	6926
Residues n_residues	630
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	142.0 Å
Rg (real space) rg_real	40.73 Å
Rg uncertainty (real space) rg_real_error	1.68 Å
I(0) (real space) i0_real	2.8380e+08
I(0) uncertainty (real space) i0_real_error	5.1900e+06
Rg (reciprocal space) rg_reciprocal	40.49 Å
I(0) (reciprocal space) i0_reciprocal	283700000.0000
Solution quality estimate total_estimate	0.8534
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.7 Å
Skewness Skewness skewness	0.487
Kurtosis Kurtosis kurtosis	-0.227
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7193000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.835

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Transcriptional repressor CTCF
Molecular weight formula_weight	34055.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	6941

TRPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYACRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNTMARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKK

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 (35-MER) Strand I
Molecular weight formula_weight	10730.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E

TTAGCGCCCCCTGCTGGTTAAATGTGGTACTGCAC

Entity 3 Entity 3 polymer

Description description	DNA (35-MER) Strand 2
Molecular weight formula_weight	10807.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F

GTGCAGTACCACATTTAACCAGCAGGGGGCGCTAA

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

▶

8. Citations (1)

▶

Unit-cell length a length_a	352.070 Å
Unit-cell length b length_b	67.768 Å
Unit-cell length c length_c	61.194 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	3.120 Å
Low-resolution limit resolution_low	41.860 Å
R factor r_factor	0.2412
R_work r_work	0.2396
R_free r_free	0.2714

fit	/app/data/saxs_computation/ss/8ssq/8ssq.fit
pddf	/app/data/pr_computation/ss/8ssq/8ssq.pr.out
profile	/app/data/saxs_computation/ss/8ssq/8ssq.dat

ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4

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

Transcriptional repressor CTCF

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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)