SAXSdb — 5yko

▼

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

Probable lysine-specific demethylase JMJ14

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	H3(1-10)K4me3 peptide × 1 （P59226） NICKEL (II) ION × 1 ZINC ION × 2 N-OXALYLGLYCINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	JMJ14_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–564； UniProt 35–597

H3(1-10)K4me3 peptide

OrganismNot specified

UniProt P59226

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Probable lysine-specific demethylase JMJ14 × 1 （Q8GUI6） NICKEL (II) ION × 1 ZINC ION × 2 N-OXALYLGLYCINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 2–11

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5yko
Deposition date deposition_date	2017-10-15
Structure title title	Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide
Keywords keywords	JMJ14, jumonji domain, C5HC2 zinc finger, H3K4me3 demethylase, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5yko__assembly_1__model_1

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

Download this curve (.dat)

5yko__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yko__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.40 Å
Rg (electron density)	24.46 Å
Total Rg	25.41 Å
Atom count	4031
Residues	493
Excluded volume	71663 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yko__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Probable lysine-specific demethylase JMJ14
Molecular weight formula_weight	65001.8 kDa
EC 编号 ec_number	1.14.11.-
Mutation mutation	E180A, E181A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4031

SSSPKITARWNPSEACRPLVDDAPIFYPTNEDFDDPLGYIEKLRSKAESYGICRIVPPVAWRPPCPLKEKKIWENSKFPTRIQFIDLLQNREPIKKSTKTKKRKRRRISKIGYTRRKRDSGCDTASSGSSDSEGKFGFQTGPDFTLAAFQKYDEYFKECYFQSEDHPGSKASENKKFKPKVKDLEGEYWRIVEQATDEVEVYYGADLETKKFGSGFPKYKPGYPISEADQYSQCGWNLNNLSRLPGSVLAFESCDISGVIVPWLYVGMCFSTFCWHVEDHHLYSMNYLHTGDPKVWYGIPGNHAESFENVMKKRLPDLFEEQPDLLHQLVTQLSPRILKEEGVPVYRAVQRSGEFILTFPKAYHSGFNCGFNCAEAVNVAPVDWLVHGQNAVEGYSKQRRKSSLSHDKLLLGAAMEATYCLWELSLSKKKTPVIARWKRVCSEDGLLTKAVKKRVQMEEERLNHLQDGFSLRKMEGDFDNKRERECFLCFYDLHMSASSCKCSPNRFACLIHAKDLCSCESKDRYILIRHTLDELWALVRALEGDLDAIDLWASKCRDQYPSQH

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	H3(1-10)K4me3 peptide
Molecular weight formula_weight	1192.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ARTKQTARKS

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

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	2

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	1

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5ykoA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

▶

Unit-cell length a length_a	68.639 Å
Unit-cell length b length_b	100.113 Å
Unit-cell length c length_c	109.405 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	39.338 Å
R factor r_factor	0.2057
R_work r_work	0.2037
R_free r_free	0.2438

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

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

Probable lysine-specific demethylase JMJ14

State in the Current Structure

Other States of the Same Protein in the Database

H3(1-10)K4me3 peptide

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

5yko__assembly_1__model_1

5yko__assembly_1__model_1 | I(q)

5yko__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 (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

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

Probable lysine-specific demethylase JMJ14

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H3(1-10)K4me3 peptide

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

5yko__assembly_1__model_1

5yko__assembly_1__model_1 | I(q)

5yko__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 (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)