SAXSdb — 5yel

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	DNA (26-MER) × 1 DNA (26-MER) × 1 ZINC ION × 6	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	DNA (26-MER) × 1 DNA (26-MER) × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTCF_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–176； UniProt 405–580 Author chain B； PDBConstruct 1–176； UniProt 405–580

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5yel
Deposition date deposition_date	2017-09-18
Structure title title	Crystal structure of CTCF ZFs6-11-gb7CSE
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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5yel__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5yel__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yel__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.49 Å
Rg (electron density)	27.91 Å
Total Rg	28.29 Å
Atom count	2392
Residues	220
Excluded volume	38766 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yel__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5yel__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA (26-MER)
Molecular weight formula_weight	7940.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F
Atom count atom_count	4772

ATTGCAGTACCACATTTAACCAGCAG

Entity 2 Entity 2 polymer

Description description	Transcriptional repressor CTCF
Molecular weight formula_weight	20922.2 kDa
Mutation mutation	C504S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

KPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYASRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNTMARHADNCAGP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	DNA (26-MER)
Molecular weight formula_weight	8033.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E

TCTGCTGGTTAAATGTGGTACTGCAA

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	12

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Unit-cell length a length_a	190.993 Å
Unit-cell length b length_b	69.631 Å
Unit-cell length c length_c	84.445 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.25 °
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	—

Resolution resolution	2.960 Å
Low-resolution limit resolution_low	37.874 Å
R factor r_factor	0.2687
R_work r_work	0.2678
R_free r_free	0.2856

Crystal structure of CTCF ZFs6-11-gb7CSE

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5yel__assembly_1__model_1

5yel__assembly_1__model_1 | I(q)

5yel__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

Crystal structure of CTCF ZFs6-11-gb7CSE

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5yel__assembly_1__model_1

5yel__assembly_1__model_1 | I(q)

5yel__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)