8jnr

Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink

Method: X-RAY DIFFRACTION

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

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	DNA × 2 Synthetic antibody heavy chain × 4 Synthetic antibody light chain × 4 N-OXALYLGLYCINE × 2 MANGANESE (II) ION × 4 [(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALKB3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–238； UniProt 70–286 Author chain C； PDBConstruct 22–238； UniProt 70–286 Author chain D； PDBConstruct 22–238； UniProt 70–286 Author chain E； PDBConstruct 22–238； UniProt 70–286

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	8jnr
Deposition date deposition_date	2023-06-06
Structure title title	Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink
Keywords keywords	RNA m1A demethylase, 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.

8jnr__assembly_1__model_1

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

Download this curve (.dat)

8jnr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8jnr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.37 Å
Rg (electron density)	45.74 Å
Total Rg	46.16 Å
Atom count	19644
Residues	2502
Excluded volume	347240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8jnr__assembly_1__model_1`	tetradecameric （14）	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 (7)

Entity 1 Entity 1 polymer

Description description	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
Molecular weight formula_weight	27693.1 kDa
EC 编号 ec_number	1.14.11.33,1.14.11.54
Mutation mutation	D110S, D189C, C201S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,E
Atom count atom_count	19651

MGSSHHHHHHSSGLVPRGSHMRVIDREGVYEISLSPTGVSRVCLYPGFVDVKEADWILEQLSQDVPWKQRTGIREDITYQQPRLTAWYGELPYTYSRITMEPNPHWHPVLRTLKNRIEENTGHTFNSLLCNLYRNEKDSVCWHSDDEPSLGRSPIIASLSFGATRTFEMRKKPPPEENGDYTYVERVKIPLDHGTLLIMEGATQADWQHRVPKEYHSREPRVNLTFRTVYPDPRGAPW

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	DNA
Molecular weight formula_weight	867.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,F

TXT

Entity 3 Entity 3 polymer

Description description	Synthetic antibody heavy chain
Molecular weight formula_weight	22927.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J

EVQLVESGGGLVQPGGSLRLSCAASGFNFSYSSIHWVRQAPGKGLEWVAYIYSSSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGDSWYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

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 4 Entity 4 polymer

Description description	Synthetic antibody light chain
Molecular weight formula_weight	23667.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,L,M,N

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQPSYIYYPVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 5 Entity 5 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate
Molecular weight formula_weight	322.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	108.615 Å
Unit-cell length b length_b	142.171 Å
Unit-cell length c length_c	130.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.07 °
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	3.660 Å
Low-resolution limit resolution_low	34.380 Å
R factor r_factor	0.2290
R_work r_work	0.2270
R_free r_free	0.2730

Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink

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

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

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

8jnr__assembly_1__model_1

8jnr__assembly_1__model_1 | I(q)

8jnr__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink

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

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

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

8jnr__assembly_1__model_1

8jnr__assembly_1__model_1 | I(q)

8jnr__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)