SAXSdb — 2jkd

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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	GLYCEROL × 2 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 SULFATE ION × 1 water × 1	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 2–181； UniProt 25–204 Author chain B； PDBConstruct 2–181； UniProt 25–204

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	2jkd
Deposition date deposition_date	2008-08-27
Structure title title	Structure of the yeast Pml1 splicing factor and its integration into the RES complex
Keywords keywords	;MRNA PROCESSING, PML1/SNU17/BUD13, PRE-MRNA SPLICING, SACCHAROMYCES CEREVISIAE, PHOSPHO-PEPTIDE RECOGNITION, RES, NUCLEUS, MRNA SPLICING, 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.

2jkd__assembly_1__model_1

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

Download this curve (.dat)

2jkd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jkd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.91 Å
Rg (electron density)	15.56 Å
Total Rg	16.66 Å
Atom count	1208
Residues	150
Excluded volume	21347 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jkd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jkd__assembly_2__model_1`	monomeric （1）	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	PRE-MRNA LEAKAGE PROTEIN 1
Molecular weight formula_weight	21543.2 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	2438

MYIDIMPDFSPSGLLELESNNKEGIALKHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGHSLDTDLDDRTEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNVHHHHHH

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	46

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2jkdA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2jkdB00
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	85.720 Å
Unit-cell length b length_b	85.720 Å
Unit-cell length c length_c	97.840 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.860 Å
R factor r_factor	0.2170
R_work r_work	0.2150
R_free r_free	0.2620

Structure of the yeast Pml1 splicing factor and its integration into the RES complex

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

2jkd__assembly_1__model_1

2jkd__assembly_1__model_1 | I(q)

2jkd__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the yeast Pml1 splicing factor and its integration into the RES complex

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

2jkd__assembly_1__model_1

2jkd__assembly_1__model_1 | I(q)

2jkd__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)