SAXSdb — 3els

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

Pre-mRNA leakage protein 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 CHLORIDE ION × 1 GLYCEROL × 4 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 6 CHLORIDE ION × 6 GLYCEROL × 24 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PML1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–158； UniProt 51–204

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	3els
Deposition date deposition_date	2008-09-23
Structure title title	Crystal Structure of Yeast Pml1p, Residues 51-204
Keywords keywords	;Intrinsically unstructured domain, forkhead-associated domain (FHA) domain, pre-mRNA retention and splicing, protein phosphorylation, RES complex, mRNA processing, mRNA splicing, Nucleus, SPLICING ;; SPLICING
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.

3els__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3els__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3els__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.74 Å
Rg (electron density)	27.50 Å
Total Rg	28.28 Å
Atom count	7160
Residues	870
Excluded volume	126860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3els__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3els__assembly_2__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Pre-mRNA leakage protein 1
Molecular weight formula_weight	18050.3 kDa
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	1432

GAMGKHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGHSLDTDLDDRTEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3elsA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	100.613 Å
Unit-cell length b length_b	100.613 Å
Unit-cell length c length_c	102.196 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1913
R_work r_work	0.1890
R_free r_free	0.2361

Crystal Structure of Yeast Pml1p, Residues 51-204

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

Pre-mRNA leakage protein 1

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

3els__assembly_2__model_1

3els__assembly_2__model_1 | I(q)

3els__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of Yeast Pml1p, Residues 51-204

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

Pre-mRNA leakage protein 1

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

3els__assembly_2__model_1

3els__assembly_2__model_1 | I(q)

3els__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)