SAXSdb — 3im1

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

Pre-mRNA-splicing helicase BRR2

Saccharomyces cerevisiae

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 1839–2163	Fragment：Sec63 unit (UNP residues 1839-2163)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM sodium cacodylate, pH 6.0, 100mM Li2SO4, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.232

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 3IM1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3HIB Crystal structure of the second Sec63 domain of yeast Brr2 Deposited 2009-05-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1851–2163（313 aa） Fragment：Second Sec63 domain: UNP residues 1851-2163	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M Sodium citrate, 17% PEG 8000, 0.2M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.257
3IM2 Structure of the C-terminal Sec63 unit of yeast Brr2, P41212 Form Deposited 2009-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1839–2163（325 aa） Fragment：Sec63 unit (UNP residues 1839-2163)	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM sodium cacodylate, pH 6.0, 100mM Li2SO4, 15 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.99 Å R-free 0.237
3JCM Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric	Chain N 1–2163（2163 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 M7M N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) × 1	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
4BGD Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8 Deposited 2013-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 442–2163（1722 aa） Fragment：RESIDUES 442-2163	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM HEPESNA PH 7.5, 200 MM MGCL2, 32-40% PEG400	Resolution 3.10 Å R-free 0.270
5DCA Crystal structure of yeast full length Brr2 in complex with Prp8 Jab1 domain Deposited 2015-08-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 113–2163（2051 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES-NaOH, pH 6.5, 9 % (w/v) PEG 3350, 0.2 M MgCl2	Resolution 2.80 Å R-free 0.255
5GAN The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom Deposited 2015-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric	Chain B 1–2163（2163 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.70 Å
5GAO Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP Deposited 2015-12-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: 11-meric	Chain B 1–2163（2163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 4.20 Å
5GAP Body region of the U4/U6.U5 tri-snRNP Deposited 2015-12-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: Dodecameric	Chain B 1–2163（2163 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted at 4 deg C for 2 seconds before plunging.	Resolution 3.60 Å
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 B 1–2163（2163 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
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 B 1–2163（2163 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 31-meric	Chain C 1–2163（2163 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
5M52 Crystal structure of yeast Brr2 full-lenght in complex with Prp8 Jab1 domain Deposited 2016-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–2163（2163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M Tris-HCl pH 7.5, 10.5 % (w/v) PEG 3350, 0.2 M MgCl	Resolution 3.40 Å R-free 0.296
5M52 Crystal structure of yeast Brr2 full-lenght in complex with Prp8 Jab1 domain Deposited 2016-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–2163（2163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M Tris-HCl pH 7.5, 10.5 % (w/v) PEG 3350, 0.2 M MgCl	Resolution 3.40 Å R-free 0.296
5M5P S. cerevisiae spliceosomal helicase Brr2 (271-end) in complex with the Jab/MPN domain of S. cerevisiae Prp8 Deposited 2016-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 271–2163（1893 aa） Fragment：UNP residues 271-2163	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1 M MES pH 6.5 9.2% (w/v) PEG 4000 0.4 M MgCl2	Resolution 4.20 Å R-free 0.335
5M5P S. cerevisiae spliceosomal helicase Brr2 (271-end) in complex with the Jab/MPN domain of S. cerevisiae Prp8 Deposited 2016-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 271–2163（1893 aa） Fragment：UNP residues 271-2163	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1 M MES pH 6.5 9.2% (w/v) PEG 4000 0.4 M MgCl2	Resolution 4.20 Å R-free 0.335
5NRL Structure of a pre-catalytic spliceosome Deposited 2017-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric	Chain B 1–2163（2163 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；Buffer pH: HEPES, 7.9; EDTA, 8.0 cryo-EM vitrification conditions Cryogen ETHANE；Grids were glow-discharged for 15 s before deposition of 3 microliter sample (~1.5 mg mL-1), and subsequently incubated for 2-3.5 s before blotting and vitrification by plunging into liquid ethane with a Vitrobot Mark III (FEI) operated at 4 degrees Celsius and 100% humidity.	Resolution 7.20 Å
5ZWM Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part) Deposited 2018-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain D 1–2163（2163 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5ZWO Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom Deposited 2018-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric	Chain D 1–2163（2163 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7B9V Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound Deposited 2020-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 50-meric	Chain B 1–2163（2163 aa）	Not recorded	MG MAGNESIUM ION × 6 K POTASSIUM ION × 1 KGN D-chiro inositol hexakisphosphate × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

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

View Construct and Data Evidence

UniProt name	BRR2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–328； UniProt 1839–2163

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	3im1
Deposition date deposition_date	2009-08-09
Structure title title	Structure of the C-terminal Sec63 unit of yeast Brr2, P212121 Form
Keywords keywords	;ATPase, RNA helicase, RNPase, RNA unwindase, molecular modeling, pre-mRNA splicing, spliceosome catalytic activation, U5-200K protein/Brr2, ATP-binding, Helicase, Hydrolase, mRNA processing, mRNA splicing, Nucleotide-binding, Nucleus, Phosphoprotein, Spliceosome ;; HYDROLASE
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	22.79 Å
Radius of gyration Rg (electron density) rg_electron	21.63 Å
Forward intensity I(0) i0	21905100.00
Molecular weight molecular_weight	36847.0 kDa
Excluded volume excluded_volume	46725 Å³
Envelope volume envelope_volume	56817 Å³
Hydration-shell volume shell_volume	22229 Å³
Envelope diameter envelope_diameter	76.7 Å
Shell Rg shell_rg	28.02 Å
Envelope Rg envelope_rg	21.92 Å
Shape Rg shape_rg	21.61 Å
Total Rg total_rg	22.59 Å
Total atoms total_atoms	2598
Residues n_residues	325
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	76.7 Å
Rg (real space) rg_real	22.73 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.1910e+07
I(0) uncertainty (real space) i0_real_error	3.6150e+05
Rg (reciprocal space) rg_reciprocal	22.75 Å
I(0) (reciprocal space) i0_reciprocal	21910000.0000
Solution quality estimate total_estimate	0.8862
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.247
Kurtosis Kurtosis kurtosis	-0.453
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5937000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3im1A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — Sec63 N-terminal domain-like domain

Domain ID domain_id	3im1A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	3im1A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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8. Citations (1)

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Unit-cell length a length_a	55.235 Å
Unit-cell length b length_b	76.504 Å
Unit-cell length c length_c	84.585 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	1.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1951
R_work r_work	0.1930
R_free r_free	0.2316

Description description	Pre-mRNA-splicing helicase BRR2
Molecular weight formula_weight	37155.2 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3152

Structure of the C-terminal Sec63 unit of yeast Brr2, P212121 Form

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

Pre-mRNA-splicing helicase BRR2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	412

fit	/app/data/saxs_computation/im/3im1/3im1.fit
pddf	/app/data/pr_computation/im/3im1/3im1.pr.out
profile	/app/data/saxs_computation/im/3im1/3im1.dat