SAXSdb — 5znr

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

SHORT LIFE family protein

Populus trichocarpa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	17-mer peptide from Histone H3.2 × 1 （P59226） ZINC ION × 2 SULFATE ION × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	17-mer peptide from Histone H3.2 × 1 （P59226） ZINC ION × 2 SULFATE ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B9H0V2_POPTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–216； UniProt 1–215 Author chain B； PDBConstruct 2–216； UniProt 1–215

17-mer peptide from Histone H3.2

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	SHORT LIFE family protein × 1 （B9H0V2） ZINC ION × 2 SULFATE ION × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SHORT LIFE family protein × 1 （B9H0V2） ZINC ION × 2 SULFATE ION × 5	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 1–17； UniProt 21–37 Author chain Q； PDBConstruct 1–17； UniProt 21–37

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	5znr
Deposition date deposition_date	2018-04-10
Structure title title	Crystal structure of PtSHL in complex with an H3K27me3 peptide
Keywords keywords	BAH, PHD, SHL, plant, H3K27me3, epigenetics, 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.

5znr__assembly_1__model_1

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

Download this curve (.dat)

5znr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5znr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.53 Å
Rg (electron density)	20.81 Å
Total Rg	21.81 Å
Atom count	1591
Residues	196
Excluded volume	27837 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5znr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5znr__assembly_2__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	SHORT LIFE family protein
Molecular weight formula_weight	24890.0 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	3165

SMAKAKAPRRTLDSYTVKPINKTVKPGDCVLMRPSDPSKPSYVAKIERIESDGRGPNVRVRVRWYYRPEESIGGRRQFHGSKEVFLSDHYDTQSADTIEGKCMVHSFKNYTKLDAVGNDDFFCRFEYNSSTGAFNPDRVAVYCKCEMPYNPDDLMVQCEGCSDWFHPACIEMSAEEAKRLDHFFCENCSSEGQKKLQNSHNTRQSDAKAETKRRRR

Source Source

Source organism organism	Populus trichocarpa
Common name common_name	Western balsam poplar
NCBI taxonomy ID ncbi_taxonomy_id	3694
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	17-mer peptide from Histone H3.2
Molecular weight formula_weight	1673.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

LATKAARKSAPATGGVK

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	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5znrB01
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	43.717 Å
Unit-cell length b length_b	110.315 Å
Unit-cell length c length_c	58.643 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.202 Å
Low-resolution limit resolution_low	40.051 Å
R factor r_factor	0.2090
R_work r_work	0.2063
R_free r_free	0.2321

Crystal structure of PtSHL in complex with an H3K27me3 peptide

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

SHORT LIFE family protein

State in the Current Structure

Other States of the Same Protein in the Database

17-mer peptide from Histone H3.2

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

5znr__assembly_1__model_1

5znr__assembly_1__model_1 | I(q)

5znr__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 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of PtSHL in complex with an H3K27me3 peptide

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

SHORT LIFE family protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

17-mer peptide from Histone H3.2

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

5znr__assembly_1__model_1

5znr__assembly_1__model_1 | I(q)

5znr__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 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)