5m5p

S. cerevisiae spliceosomal helicase Brr2 (271-end) in complex with the Jab/MPN domain of S. cerevisiae Prp8

Method: X-RAY DIFFRACTION Dmax: 197.1 Å Quality: REASONABLE

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

Pre-mRNA-splicing helicase BRR2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32639

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 271–2163 Fragment:UNP residues 271-2163 Pre-mRNA-splicing factor 8 × 1 (P33334) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 271–2163 Fragment:UNP residues 271-2163 Pre-mRNA-splicing factor 8 × 1 (P33334) 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

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.

17 other PDB entries and 18 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 5–1897; UniProt 271–2163 Author chain C; PDBConstruct 5–1897; UniProt 271–2163

Pre-mRNA-splicing factor 8

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P33334

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2147–2413 Fragment:UNP residues 2147-2413 Pre-mRNA-splicing helicase BRR2 × 1 (P32639) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 2147–2413 Fragment:UNP residues 2147-2413 Pre-mRNA-splicing helicase BRR2 × 1 (P32639) 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

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.

435 other PDB entries and 442 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRP8_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–270; UniProt 2147–2413 Author chain D; PDBConstruct 4–270; UniProt 2147–2413

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5m5p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5m5p
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5m5p
Deposition date deposition_date2016-10-22
Structure title titleS. cerevisiae spliceosomal helicase Brr2 (271-end) in complex with the Jab/MPN domain of S. cerevisiae Prp8
Keywords keywordssplicing, helicase, complex, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier68.00
Radius of gyration Rg (electron density) rg_electron67.99
Forward intensity I(0) i02991960000.00
Molecular weight molecular_weight477180.0 kDa
Excluded volume excluded_volume603150 ų
Envelope volume envelope_volume950850 ų
Hydration-shell volume shell_volume118090 ų
Envelope diameter envelope_diameter219.3
Shell Rg shell_rg66.21
Envelope Rg envelope_rg65.66
Shape Rg shape_rg67.95
Total Rg total_rg68.07
Total atoms total_atoms67309
Residues n_residues4196
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax197.1
Rg (real space) rg_real68.09
Rg uncertainty (real space) rg_real_error1.58
I(0) (real space) i0_real2.9920e+09
I(0) uncertainty (real space) i0_real_error6.7730e+07
Rg (reciprocal space) rg_reciprocal67.52
I(0) (reciprocal space) i0_reciprocal2988000000.0000
Solution quality estimate total_estimate0.6223
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary68.6
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.722
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha277700000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.994; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)