Exosome RNA helicase MTR4
Homo sapiens
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.
| Other PDB | Difference from Current Entry 6RO1 | 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 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 |
| 6IEG Crystal structure of human MTR4 Deposited 2018-09-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain B
71–1042(972 aa)
|
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 |
| 6IEG Crystal structure of human MTR4 Deposited 2018-09-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
71–1042(972 aa)
|
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 |
| 6IEH Crystal structures of the hMTR4-NRDE2 complex Deposited 2018-09-14 | Different construct 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 |
| 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 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 |