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7s7c

Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)

Method: ELECTRON MICROSCOPY Dmax: 156.1 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–RNA Heteromer Protein × 5 RNA 2 PDB declaration: heptameric（7） Consistent with all polymer counts Chain A； UniProt 1–1042 Chain E； UniProt 1–1042 Not recorded Zinc finger CCHC domain-containing protein 8 × 2 （Q6NZY4） RNA-binding protein 7 × 1 （Q9Y580） RNA (30-MER) × 2 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

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 7S7C 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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
7Z4Y Human NEXT dimer - overall reconstruction of the core complex Deposited 2022-03-06 Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 4–1045； UniProt 1–1042 Author chain E； PDBConstruct 4–1045； UniProt 1–1042

Zinc finger CCHC domain-containing protein 8

Homo sapiens

UniProt Q6NZY4

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–RNA Heteromer Protein × 5 RNA 2 PDB declaration: heptameric（7） Consistent with all polymer counts Chain B； UniProt 1–415 Chain B； UniProt 508–707 Chain F； UniProt 1–415 Chain F； UniProt 508–707 Not recorded Exosome RNA helicase MTR4 × 2 （P42285） RNA-binding protein 7 × 1 （Q9Y580） RNA (30-MER) × 2 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

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 7S7C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LXR Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-22 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 × 2 PDB declaration: dimeric
Chain B 285–324（40 aa）
Not recorded SM SAMARIUM (III) ION × 3 BR BROMIDE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane pH 6.5 0.2 M NaBr 18% (v/v) PEG3350 7% (w/v) glycerol
Resolution 2.00 Å R-free 0.229
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 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 × 2 PDB declaration: dimeric
Chain D 285–324（40 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 285–324（40 aa）
Not recorded BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 285–324（40 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 285–324（40 aa）
Not recorded BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 285–324（40 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 285–324（40 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 285–324（40 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 659–707（49 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
7S7B Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1) Deposited 2021-09-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric
Chain B 1–415（415 aa）
Chain B 508–707（200 aa）
Chain F 1–415（415 aa）
Chain F 508–707（200 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
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 41–337（297 aa）
Chain C 41–337（297 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 41–337（297 aa）
Chain C 41–337（297 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain A 1–707（707 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

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ZCHC8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–418； UniProt 1–415 Author chain B； PDBConstruct 419–618； UniProt 508–707 Author chain F； PDBConstruct 4–418； UniProt 1–415 Author chain F； PDBConstruct 419–618； UniProt 508–707

RNA-binding protein 7

Homo sapiens

UniProt Q9Y580

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–RNA Heteromer Protein × 5 RNA 2 PDB declaration: heptameric（7） Consistent with all polymer counts Chain C； UniProt 7–86 Not recorded Exosome RNA helicase MTR4 × 2 （P42285） Zinc finger CCHC domain-containing protein 8 × 2 （Q6NZY4） RNA (30-MER) × 2 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

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 7S7C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2M8H RRM domain of human RBM7 Deposited 2013-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–94（91 aa） Fragment：unp residues 4-94
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；293.15 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition 0.3 mM [U-99% 13C; U-99% 15N] RBM7, 20 mM BISTRIS, 4 mM beta-mercaptoethanol, 200 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5IQQ Crystal structure of the human RBM7 RRM domain Deposited 2016-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–91（91 aa） Fragment：RNA recognition motif, UNP residues 1-91
Chain B 1–91（91 aa） Fragment：RNA recognition motif, UNP residues 1-91
Chain C 1–91（91 aa） Fragment：RNA recognition motif, UNP residues 1-91
Chain D 1–91（91 aa） Fragment：RNA recognition motif, UNP residues 1-91
Chain E 1–91（91 aa） Fragment：RNA recognition motif, UNP residues 1-91
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；292 K；0.1 M Hepes pH 7.5, 150 mM KCl, 1.4 M tri-sodium citrate
Resolution 2.52 Å R-free 0.244
5LXR Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–86（86 aa）
Not recorded SM SAMARIUM (III) ION × 3 BR BROMIDE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane pH 6.5 0.2 M NaBr 18% (v/v) PEG3350 7% (w/v) glycerol
Resolution 2.00 Å R-free 0.229
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–86（86 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–86（86 aa）
Not recorded BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–86（86 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–86（86 aa）
Not recorded BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–86（86 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 1–86（86 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
5LXY Structure of the minimal RBM7 - ZCCHC8 Complex Deposited 2016-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–86（86 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；0.1 M Bis-Tris-Propane 0.2 M NaBr 0.1 M Sodium malonate 20% (w/v) PEG3350
Resolution 2.85 Å R-free 0.300
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 conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 7–86（80 aa）
Chain G 7–86（80 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

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

View Construct and Data Evidence
UniProt name RBM7_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 4–83； UniProt 7–86

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 7s7c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7s7c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7s7c
Deposition date deposition_date2021-09-15
Structure title titleHuman Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)
Keywords keywordsHelicase, ATPase, RNA, Exosome, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.15 Å
Radius of gyration Rg (electron density) rg_electron47.58 Å
Forward intensity I(0) i0599758000.00
Molecular weight molecular_weight197690.0 kDa
Excluded volume excluded_volume245520 ų
Envelope volume envelope_volume367510 ų
Hydration-shell volume shell_volume65544 ų
Envelope diameter envelope_diameter157.6 Å
Shell Rg shell_rg51.24 Å
Envelope Rg envelope_rg46.14 Å
Shape Rg shape_rg47.56 Å
Total Rg total_rg47.83 Å
Total atoms total_atoms13850
Residues n_residues1666
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 dmax156.1 Å
Rg (real space) rg_real48.16 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real5.9980e+08
I(0) uncertainty (real space) i0_real_error9.9500e+06
Rg (reciprocal space) rg_reciprocal48.15 Å
I(0) (reciprocal space) i0_reciprocal599700000.0000
Solution quality estimate total_estimate0.8825
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.3 Å
Skewness Skewness skewness0.217
Kurtosis Kurtosis kurtosis-0.677
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha60740000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.650
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)