6ro1

X-ray crystal structure of the MTR4 NVL complex

Method: X-RAY DIFFRACTION Dmax: 124.6 Å Quality: GOOD

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

Exosome RNA helicase MTR4

Homo sapiens

UniProt P42285

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 70–1042 Not recorded Nuclear valosin-containing protein-like × 1 (O15381) SO4 SULFATE ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris/HCl pH 8.0, 1.8M Ammonium Sulphate Resolution 3.07 Å R-free 0.257

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.

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTREX_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–973; UniProt 70–1042

Nuclear valosin-containing protein-like

Homo sapiens

UniProt O15381

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 167–216 Not recorded Exosome RNA helicase MTR4 × 1 (P42285) SO4 SULFATE ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris/HCl pH 8.0, 1.8M Ammonium Sulphate Resolution 3.07 Å R-free 0.257

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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NVL_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 6–55; UniProt 167–216

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 6ro1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ro1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ro1
Deposition date deposition_date2019-05-10
Structure title titleX-ray crystal structure of the MTR4 NVL complex
Keywords keywordsDExH helicase, Complex, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.52
Radius of gyration Rg (electron density) rg_electron37.37
Forward intensity I(0) i0160068000.00
Molecular weight molecular_weight101660.0 kDa
Excluded volume excluded_volume127250 ų
Envelope volume envelope_volume188570 ų
Hydration-shell volume shell_volume43396 ų
Envelope diameter envelope_diameter121.9
Shell Rg shell_rg42.00
Envelope Rg envelope_rg37.04
Shape Rg shape_rg37.41
Total Rg total_rg37.59
Total atoms total_atoms13925
Residues n_residues937
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 dmax124.6
Rg (real space) rg_real37.70
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real1.6010e+08
I(0) uncertainty (real space) i0_real_error2.8930e+06
Rg (reciprocal space) rg_reciprocal37.60
I(0) (reciprocal space) i0_reciprocal160100000.0000
Solution quality estimate total_estimate0.8783
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-0.655
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27790000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6ro1A01
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_id6ro1A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)