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6ieg

Crystal structure of human MTR4

Method: X-RAY DIFFRACTION Dmax: 157.4 Å Quality: GOOD
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 71–1042 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；15 mM Tricine pH 8.5, 12% (w/v) PEG 4000 Resolution 3.55 Å R-free 0.305
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 71–1042 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；15 mM Tricine pH 8.5, 12% (w/v) PEG 4000 Resolution 3.55 Å R-free 0.305

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 6IEG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6C90 Human Mtr4 helicase in complex with ZCCHC8-CTD Deposited 2018-01-25 Different construct Different mutation/modification 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 71–600（530 aa）
Chain A 842–1042（201 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 MLI MALONATE ION × 4 TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.6 M sodium-potassium (L)-tartrate, 0.1 M Bis-Tris pH 6.5
Resolution 2.20 Å R-free 0.221
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain M 1–1042（1042 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；30 sec wait time, 2.5 sec blot time
Resolution 3.45 Å
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain M 1–1042（1042 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；30 sec wait time, 2.5 sec blot time
Resolution 3.45 Å
6IEH Crystal structures of the hMTR4-NRDE2 complex Deposited 2018-09-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 71–1042（972 aa）
Not recorded CL CHLORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；50 mM Glycine pH 9.0, 100 mM NaCl, 33% (w/v) polyethylene glycol 300 (PEG 300)
Resolution 2.89 Å R-free 0.252
6RO1 X-ray crystal structure of the MTR4 NVL complex Deposited 2019-05-10 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 70–1042（973 aa）
Not recorded 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
7S7B Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1) Deposited 2021-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric
Chain A 1–1042（1042 aa）
Chain E 1–1042（1042 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630
cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging
Resolution 4.06 Å
7S7C Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) Deposited 2021-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain A 1–1042（1042 aa）
Chain E 1–1042（1042 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging
Resolution 3.62 Å
7Z4Y Human NEXT dimer - overall reconstruction of the core complex Deposited 2022-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1042（1042 aa）
Chain D 1–1042（1042 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.50 Å
7Z4Z Human NEXT dimer - focused reconstruction of the dimerization module Deposited 2022-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1042（1042 aa）
Chain D 1–1042（1042 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.00 Å
7Z52 Human NEXT dimer - focused reconstruction of the single MTR4 Deposited 2022-03-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain B 1–1042（1042 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å

10 other PDB entries and 10 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 31–1002； UniProt 71–1042 Author chain B； PDBConstruct 31–1002； UniProt 71–1042

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 6ieg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6ieg
Deposition date deposition_date2018-09-14
Structure title titleCrystal structure of human MTR4
Keywords keywordsRNA helicase, MTR4, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.66 Å
Radius of gyration Rg (electron density) rg_electron47.39 Å
Forward intensity I(0) i0498392000.00
Molecular weight molecular_weight184540.0 kDa
Excluded volume excluded_volume230900 ų
Envelope volume envelope_volume366510 ų
Hydration-shell volume shell_volume65228 ų
Envelope diameter envelope_diameter157.3 Å
Shell Rg shell_rg50.81 Å
Envelope Rg envelope_rg45.85 Å
Shape Rg shape_rg47.41 Å
Total Rg total_rg47.47 Å
Total atoms total_atoms12978
Residues n_residues1783
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax157.4 Å
Rg (real space) rg_real47.65 Å
Rg uncertainty (real space) rg_real_error1.99 Å
I(0) (real space) i0_real4.9840e+08
I(0) uncertainty (real space) i0_real_error1.0740e+07
Rg (reciprocal space) rg_reciprocal47.66 Å
I(0) (reciprocal space) i0_reciprocal498400000.0000
Solution quality estimate total_estimate0.8306
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.5 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.613
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28020000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)