5dca

Crystal structure of yeast full length Brr2 in complex with Prp8 Jab1 domain

Method: X-RAY DIFFRACTION Dmax: 150.6 Å Quality: GOOD

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 113–2163 Not recorded Pre-mRNA-splicing factor 8 × 1 (P33334) 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

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 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 1–1948; UniProt 113–2163

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 J; UniProt 2148–2398 Not recorded Pre-mRNA-splicing helicase BRR2 × 1 (P32639) 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

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 443 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 J; PDBConstruct 1–251; UniProt 2148–2398

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 5dca

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5dca
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5dca
Deposition date deposition_date2015-08-23
Structure title titleCrystal structure of yeast full length Brr2 in complex with Prp8 Jab1 domain
Keywords keywordsprotein complex, helicase, RNP remodeling, spliceosome activation, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.50
Radius of gyration Rg (electron density) rg_electron44.82
Forward intensity I(0) i0866887000.00
Molecular weight molecular_weight250300.0 kDa
Excluded volume excluded_volume316170 ų
Envelope volume envelope_volume443800 ų
Hydration-shell volume shell_volume81128 ų
Envelope diameter envelope_diameter158.5
Shell Rg shell_rg50.52
Envelope Rg envelope_rg44.46
Shape Rg shape_rg44.81
Total Rg total_rg45.10
Total atoms total_atoms17651
Residues n_residues2199
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 dmax150.6
Rg (real space) rg_real45.40
Rg uncertainty (real space) rg_real_error1.71
I(0) (real space) i0_real8.6690e+08
I(0) uncertainty (real space) i0_real_error1.8330e+07
Rg (reciprocal space) rg_reciprocal45.50
I(0) (reciprocal space) i0_reciprocal867000000.0000
Solution quality estimate total_estimate0.8894
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.6
Skewness Skewness skewness0.258
Kurtosis Kurtosis kurtosis-0.430
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha104600000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5dcaj_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.97 — Cytidine deaminase-like
Superfamily Superfamily superfamilyc.97.3 — JAB1/MPN domain
Family Family familyc.97.3.0 — automated matches

CATH v4.4 (13 domains)

Domain ID domain_id5dcaA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5dcaA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5dcaA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id5dcaA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily10 — Sec63 N-terminal domain-like domain
Domain ID domain_id5dcaA07
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id5dcaA08
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id5dcaA09
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5dcaA10
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5dcaA11
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id5dcaA12
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3380 — Sec63 N-terminal domain-like fold
Homologous superfamily homologous superfamily10 — Sec63 N-terminal domain-like domain
Domain ID domain_id5dcaA13
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id5dcaA14
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id5dcaJ01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily10 — Cytidine Deaminase, domain 2

8. Citations (1)

9. Files and Curves (10)