4rdo

Structure of YTH-YTHDF2 in the free state

Method: X-RAY DIFFRACTION

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

YTH domain-containing family protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YTHD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–167； UniProt 408–552 Author chain B； PDBConstruct 23–167； UniProt 408–552 Author chain C； PDBConstruct 23–167； UniProt 408–552 Author chain D； PDBConstruct 23–167； UniProt 408–552 Author chain E； PDBConstruct 23–167； UniProt 408–552 Author chain F； PDBConstruct 23–167； UniProt 408–552

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	4rdo
Deposition date deposition_date	2014-09-19
Structure title title	Structure of YTH-YTHDF2 in the free state
Keywords keywords	RNA binding, atypical Beta-Propeller, m6A methylated RNA, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

4rdo__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4rdo__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4rdo__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	16.40 Å
Rg (electron density)	15.02 Å
Total Rg	16.22 Å
Atom count	1217
Residues	148
Excluded volume	21457 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4rdo__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4rdo__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4rdo__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4rdo__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4rdo__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4rdo__assembly_6__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	YTH domain-containing family protein 2
Molecular weight formula_weight	19367.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7542

MGSSYHHHHHHSSGENLYFQHMKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTS

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	422

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d4rdoa1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.0 — automated matches

Domain ID domain_id	d4rdoa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4rdob1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.0 — automated matches

Domain ID domain_id	d4rdob2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4rdoc1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.0 — automated matches

Domain ID domain_id	d4rdoc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4rdod1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.0 — automated matches

Domain ID domain_id	d4rdod2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4rdoe1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.0 — automated matches

Domain ID domain_id	d4rdoe2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4rdof_
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	4rdoA00
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	4rdoB00
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	4rdoC00
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	4rdoD00
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	4rdoE00
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	4rdoF00
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	139.280 Å
Unit-cell length b length_b	139.280 Å
Unit-cell length c length_c	112.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	42.280 Å
R factor r_factor	0.2156
R_work r_work	0.2128
R_free r_free	0.2702

Structure of YTH-YTHDF2 in the free state

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

YTH domain-containing family protein 2

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

4rdo__assembly_3__model_1

4rdo__assembly_3__model_1 | I(q)

4rdo__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (11 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of YTH-YTHDF2 in the free state

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

YTH domain-containing family protein 2

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

4rdo__assembly_3__model_1

4rdo__assembly_3__model_1 | I(q)

4rdo__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (11 domains)

CATH v4.4 (6 domains)

7. Citations (1)