5yeh

Crystal structure of CTCF ZFs4-8-eCBS

Method: X-RAY DIFFRACTION D_max: 98.4 Å Quality: GOOD

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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 349–490	Fragment：UNP residues 349-490	;DNA (5'-D(APCPGPGPTPTPTPCPCPGPCPTPAPGPAPGPGPGPCPG)-3') ; × 1 ;DNA (5'-D(TPCPGPCPCPCPTPCPTPAPGPCPGPGPAPAPAPCPCPG)-3') ; × 1 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
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 349–490	Fragment：UNP residues 349-490	;DNA (5'-D(APCPGPGPTPTPTPCPCPGPCPTPAPGPAPGPGPGPCPG)-3') ; × 1 ;DNA (5'-D(TPCPGPCPCPCPTPCPTPAPGPCPGPGPAPAPAPCPCPG)-3') ; × 1 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

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 5YEH	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 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 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 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 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 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 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 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 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 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 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
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
8SSQ ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 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 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	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
8SSQ ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 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 319–606（288 aa） Fragment：Zinc finger domains 3-11	Not recorded	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
8SSR ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20 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 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 construct 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 1–142； UniProt 349–490 Author chain B； PDBConstruct 1–142； UniProt 349–490

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	5yeh
Deposition date deposition_date	2017-09-17
Structure title title	Crystal structure of CTCF ZFs4-8-eCBS
Keywords keywords	;zinc fingers, insulators, enhancers, promoters, 3D genome, topological domains, contact loops, higher-order chromatin structure, DNA BINDING PROTEIN-DNA complex ;; DNA BINDING PROTEIN/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	27.26 Å
Radius of gyration Rg (electron density) rg_electron	26.87 Å
Forward intensity I(0) i0	92440600.00
Molecular weight molecular_weight	55893.0 kDa
Excluded volume excluded_volume	61417 Å³
Envelope volume envelope_volume	87702 Å³
Hydration-shell volume shell_volume	28068 Å³
Envelope diameter envelope_diameter	103.1 Å
Shell Rg shell_rg	33.04 Å
Envelope Rg envelope_rg	26.80 Å
Shape Rg shape_rg	26.85 Å
Total Rg total_rg	27.42 Å
Total atoms total_atoms	3782
Residues n_residues	358
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	98.4 Å
Rg (real space) rg_real	27.23 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	9.2440e+07
I(0) uncertainty (real space) i0_real_error	1.3550e+06
Rg (reciprocal space) rg_reciprocal	27.24 Å
I(0) (reciprocal space) i0_reciprocal	92440000.0000
Solution quality estimate total_estimate	0.8635
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.9 Å
Skewness Skewness skewness	0.290
Kurtosis Kurtosis kurtosis	-0.309
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6268000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.998

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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	Transcriptional repressor CTCF
Molecular weight formula_weight	16825.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3853

KPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHK

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 K-12

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPGPGPTPTPTPCPCPGPCPTPAPGPAPGPGPGPCPG)-3') ;
Molecular weight formula_weight	6191.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E

ACGGTTTCCGCTAGAGGGCG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPCPGPCPCPCPTPCPTPAPGPCPGPGPAPAPAPCPCPG)-3') ;
Molecular weight formula_weight	6079.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

TCGCCCTCTAGCGGAAACCG

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	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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8. Citations (1)

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Unit-cell length a length_a	45.845 Å
Unit-cell length b length_b	54.876 Å
Unit-cell length c length_c	66.938 Å
Unit-cell angle α angle_alpha	81.17 °
Unit-cell angle β angle_beta	80.11 °
Unit-cell angle γ angle_gamma	79.72 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.328 Å
Low-resolution limit resolution_low	32.706 Å
R factor r_factor	0.2243
R_work r_work	0.2219
R_free r_free	0.2695

fit	/app/data/saxs_computation/ye/5yeh/5yeh.fit
pddf	/app/data/pr_computation/ye/5yeh/5yeh.pr.out
profile	/app/data/saxs_computation/ye/5yeh/5yeh.dat

Crystal structure of CTCF ZFs4-8-eCBS

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 (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 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)