SAXSdb — 5j3e

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

Thymocyte nuclear protein 1

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	5-methylcytosine containing DNA × 2 UNKNOWN ATOM OR ION × 3 water × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5-methylcytosine containing DNA × 2 UNKNOWN ATOM OR ION × 5 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–225； UniProt 1–225 Author chain B； PDBConstruct 1–225； UniProt 1–225

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	5j3e
Deposition date deposition_date	2016-03-30
Structure title title	Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA
Keywords keywords	;protein-DNA complex, modified DNA, 5-methylcytosine containing DNA, Structural Genomics Consortium, SGC, NUCLEAR PROTEIN-DNA complex ;; NUCLEAR 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j3e__assembly_1__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`5j3e__assembly_2__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	Thymocyte nuclear protein 1
Molecular weight formula_weight	25740.4 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	3764

MSRPRKRLAGTSGSDKGLSGKRTKTENSGEALAKVEDSNPQKTSATKNCLKNLSSHWLMKSEPESRLEKGVDVKFSIEDLKAQPKQTTCWDGVRNYQARNFLRAMKLGEEAFFYHSNCKEPGIAGLMKIVKEAYPDHTQFEKNNPHYDPSSKEDNPKWSMVDVQFVRMMKRFIPLAELKSYHQAHKATGGPLKNMVLFTRQRLSIQPLTQEEFDFVLSLEEKEPS

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

Entity 2 Entity 2 polymer

Description description	5-methylcytosine containing DNA
Molecular weight formula_weight	3677.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D,E,F

GCCAACGTTGGC

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5j3eA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	590 — ph1033 like fold
Homologous superfamily homologous superfamily	10 — ph1033 like domains

Domain ID domain_id	5j3eB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	590 — ph1033 like fold
Homologous superfamily homologous superfamily	10 — ph1033 like domains

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Unit-cell length a length_a	40.327 Å
Unit-cell length b length_b	73.232 Å
Unit-cell length c length_c	108.201 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	43.510 Å
R factor r_factor	0.2106
R_work r_work	0.2087
R_free r_free	0.2488

Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA

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

Thymocyte nuclear protein 1

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

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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA

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

Thymocyte nuclear protein 1

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

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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)