SAXSdb — 5z8l

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

Chromatin remodeling protein EBS

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	H3K27me3 peptide × 1 （P59226） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EBS_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 1–234

H3K27me3 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	Chromatin remodeling protein EBS × 1 （F4JL28） ZINC ION × 2 water × 2	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 1–16； UniProt 21–36

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	5z8l
Deposition date deposition_date	2018-01-31
Structure title title	crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide
Keywords keywords	EBS, BAH, PHD, H3K27me3, histone reader, GENE REGULATION; GENE REGULATION
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.

5z8l__assembly_1__model_1

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

Download this curve (.dat)

5z8l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5z8l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.14 Å
Rg (electron density)	20.34 Å
Total Rg	21.46 Å
Atom count	1676
Residues	211
Excluded volume	29736 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5z8l__assembly_1__model_1`	dimeric （2）	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	Chromatin remodeling protein EBS
Molecular weight formula_weight	26493.2 kDa
Mutation mutation	K201A,K202A
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	1784

MAKTRPGVASKIKTGRKELDSYTIKGTNKVVRAGDCVLMRPSDAGKPPYVARVEKIEADARNNVKVHCRWYYRPEESLGGRRQFHGAKELFLSDHFDVQSAHTIEGKCIVHTFKNYTRLENVGAEDYYCRFEYKAATGAFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWYHPACVGMTIEEAKKLDHFVCAECSSDDDVAASQNGFTSSPADDVKVRLSLFSHLLYRCSITYL

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	H3K27me3 peptide
Molecular weight formula_weight	1543.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

LATKAARKSAPATGGV

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	108

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5z8lA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	490 — Bromo adjacent homology (BAH) domain

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Unit-cell length a length_a	36.247 Å
Unit-cell length b length_b	60.299 Å
Unit-cell length c length_c	98.038 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	2.005 Å
Low-resolution limit resolution_low	49.019 Å
R factor r_factor	0.2026
R_work r_work	0.2012
R_free r_free	0.2301

crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide

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

Chromatin remodeling protein EBS

State in the Current Structure

Other States of the Same Protein in the Database

H3K27me3 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

5z8l__assembly_1__model_1

5z8l__assembly_1__model_1 | I(q)

5z8l__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

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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide

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

Chromatin remodeling protein EBS

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H3K27me3 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

5z8l__assembly_1__model_1

5z8l__assembly_1__model_1 | I(q)

5z8l__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

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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)