4bgd

Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8

Method: X-RAY DIFFRACTION Dmax: 145.0 Å Quality: GOOD

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

PRE-MRNA-SPLICING HELICASE BRR2

SACCHAROMYCES CEREVISIAE

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 442–2163 Fragment:RESIDUES 442-2163 PRE-MRNA-SPLICING FACTOR 8 × 1 (P33334) 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

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 1–1722; UniProt 442–2163

PRE-MRNA-SPLICING FACTOR 8

SACCHAROMYCES CEREVISIAE

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 C; UniProt 2148–2395 Fragment:RESIDUES 2148-2395 PRE-MRNA-SPLICING HELICASE BRR2 × 1 (P32639) 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

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 C; PDBConstruct 1–248; UniProt 2148–2395

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 4bgd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4bgd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4bgd
Deposition date deposition_date2013-03-25
Structure title titleCrystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8
Keywords keywordsTRANSCRIPTION, SPLICEOSOME, RNA HELICASE, U5 SNRNP, RETINITIS PIGMENTOSA; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.22
Radius of gyration Rg (electron density) rg_electron43.62
Forward intensity I(0) i0692125000.00
Molecular weight molecular_weight222950.0 kDa
Excluded volume excluded_volume281490 ų
Envelope volume envelope_volume377720 ų
Hydration-shell volume shell_volume71477 ų
Envelope diameter envelope_diameter148.2
Shell Rg shell_rg48.87
Envelope Rg envelope_rg43.13
Shape Rg shape_rg43.61
Total Rg total_rg43.89
Total atoms total_atoms15718
Residues n_residues1955
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 dmax145.0
Rg (real space) rg_real44.14
Rg uncertainty (real space) rg_real_error1.39
I(0) (real space) i0_real6.9210e+08
I(0) uncertainty (real space) i0_real_error1.4070e+07
Rg (reciprocal space) rg_reciprocal44.22
I(0) (reciprocal space) i0_reciprocal692200000.0000
Solution quality estimate total_estimate0.8961
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.3
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.557
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85790000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.904

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4bgdc_
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_id4bgdA01
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_id4bgdA02
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_id4bgdA03
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_id4bgdA04
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_id4bgdA05
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_id4bgdA06
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id4bgdA07
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_id4bgdA08
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_id4bgdA09
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_id4bgdA10
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_id4bgdA11
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_id4bgdA12
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id4bgdC01
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)