SAXSdb — 3u1m

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

Pre-mRNA-splicing factor CWC2

Saccharomyces cerevisiae

UniProt Q12046

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–240	Fragment：UNP residues 1-240	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；pH 6.5, 21% PEG 3350, 200mM (NH4)2HCitrate, 100mM Na3Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.95 Å R-free 0.191

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3U1M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TP2 Crystal Structure of the Splicing Factor Cwc2 from yeast Deposited 2011-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–227（227 aa） Fragment：UNP residues 1-227	Not recorded	NA SODIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG5000 MME, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.256
3TP2 Crystal Structure of the Splicing Factor Cwc2 from yeast Deposited 2011-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–227（227 aa） Fragment：UNP residues 1-227	Not recorded	NA SODIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG5000 MME, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.256
3U1L Structure of the mRNA splicing complex component Cwc2 Deposited 2011-09-30	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–240（240 aa） Fragment：UNP residues 1-240	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；pH 6.5, 21% PEG 3350, 200mM (NH4)2HCitrate, 100mM Na3Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.64 Å R-free 0.189
5GM6 Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution Deposited 2016-07-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 46-meric	Chain R 1–339（339 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5 ZN ZINC ION × 13 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
5GMK Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution Deposited 2016-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 45-meric	Chain R 1–339（339 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8；The CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5LJ5 Overall structure of the yeast spliceosome immediately after branching. Deposited 2016-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 45-meric	Chain M 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；3 microlitres sample were applied to the grid, left for 30 seconds and then blotted for 2.5-3.0 seconds before plunging.	Resolution 10.00 Å
5LQW yeast activated spliceosome Deposited 2016-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 31-meric	Chain F 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
5MPS Structure of a spliceosome remodeled for exon ligation Deposited 2016-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 30-meric	Chain M 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 3 K POTASSIUM ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；NP-40 is also called IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging.	Resolution 3.85 Å
5MQ0 Structure of a spliceosome remodeled for exon ligation Deposited 2016-12-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 46-meric	Chain M 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 3 K POTASSIUM ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；NP-40 is also called IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging.	Resolution 4.17 Å
5WSG Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution Deposited 2016-12-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 45-meric	Chain R 1–339（339 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8；10mM Tris-HCl, pH 8.0, 75mM NaCl, 1mM Mg(OAc)2, 1mM imidazole, 0.01% NP40, 1mM TCEP, 0.5mM EGTA cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
5Y88 Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom Deposited 2017-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 44-meric	Chain N 1–339（339 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
5YLZ Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom Deposited 2017-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 43-meric	Chain N 1–339（339 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6BK8 S. cerevisiae spliceosomal post-catalytic P complex Deposited 2017-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 46-meric	Chain G 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 5 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6EXN Post-catalytic P complex spliceosome with 3' splice site docked Deposited 2017-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 40-meric	Chain M 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；3 uL sample was applied to the grid, left for 30s, then blotted for 3s and immediately plunged into liquid ethane.	Resolution 3.70 Å
6J6G Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom Deposited 2019-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 41-meric	Chain R 1–339（339 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6J6H Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom Deposited 2019-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 41-meric	Chain R 1–339（339 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6J6N Cryo-EM structure of the yeast B*-b1 complex at an average resolution of 3.86 angstrom Deposited 2019-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 41-meric	Chain R 1–339（339 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.86 Å
6J6Q Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom Deposited 2019-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 42-meric	Chain R 1–339（339 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DTR Structure of the yeast post-catalytic P complex spliceosome at 2.3 Angstrom resolution Deposited 2024-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 47-meric	Chain M 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 K POTASSIUM ION × 4 IHP INOSITOL HEXAKISPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.31 Å

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CWC2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–240； UniProt 1–240

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	3u1m
Deposition date deposition_date	2011-09-30
Structure title title	Structure of the mRNA splicing complex component Cwc2
Keywords keywords	CSMP, Zinc Finger, mRNA splicing, SPLICING; SPLICING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.45 Å
Radius of gyration Rg (electron density) rg_electron	17.22 Å
Forward intensity I(0) i0	11711400.00
Molecular weight molecular_weight	25216.0 kDa
Excluded volume excluded_volume	31470 Å³
Envelope volume envelope_volume	37150 Å³
Hydration-shell volume shell_volume	17794 Å³
Envelope diameter envelope_diameter	56.3 Å
Shell Rg shell_rg	23.57 Å
Envelope Rg envelope_rg	17.53 Å
Shape Rg shape_rg	17.19 Å
Total Rg total_rg	18.32 Å
Total atoms total_atoms	1774
Residues n_residues	221
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	56.7 Å
Rg (real space) rg_real	18.32 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.1710e+07
I(0) uncertainty (real space) i0_real_error	1.2830e+05
Rg (reciprocal space) rg_reciprocal	18.35 Å
I(0) (reciprocal space) i0_reciprocal	11710000.0000
Solution quality estimate total_estimate	0.9018
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.080
Kurtosis Kurtosis kurtosis	-0.509
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2540000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Pre-mRNA-splicing factor CWC2
Molecular weight formula_weight	27373.1 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	2111

MTSWRDKSAKVQVKESELPSSIPAQTGLTFNIWYNKWSQGFAGNTRFVSPFALQPQLHSGKTRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDPAAQKRLQE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	326

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3u1ma1
Class class	g — Small proteins
Fold Fold fold	g.66 — CCCH zinc finger
Superfamily Superfamily superfamily	g.66.1 — CCCH zinc finger
Family Family family	g.66.1.2 — Pre-mRNA splicing factor Cwc2 / Cwf2 / Prp3, zinc finger domain

Domain ID domain_id	d3u1ma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

CATH v4.4 (1 domains)

Domain ID domain_id	3u1mA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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8. Citations (1)

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Unit-cell length a length_a	44.719 Å
Unit-cell length b length_b	54.340 Å
Unit-cell length c length_c	111.381 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	1.950 Å
Low-resolution limit resolution_low	29.347 Å
R factor r_factor	0.1606
R_work r_work	0.1590
R_free r_free	0.1910

fit	/app/data/saxs_computation/u1/3u1m/3u1m.fit
pddf	/app/data/pr_computation/u1/3u1m/3u1m.pr.out
profile	/app/data/saxs_computation/u1/3u1m/3u1m.dat

Structure of the mRNA splicing complex component Cwc2

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

Pre-mRNA-splicing factor CWC2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction