9g8n

80S-bound human Ski2-exosome complex

Method: ELECTRON MICROSCOPY D_max: 218.5 Å Quality: GOOD

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

Exosome complex component RRP41

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–RNA Heteromer Protein × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain L； UniProt 1–245	Not recorded	Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 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 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain B 1–245（245 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain B 1–245（245 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain B 1–245（245 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain L 1–245（245 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain N 1–245（245 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain L 1–245（245 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–245； UniProt 1–245

Exosome complex component RRP43

Homo sapiens

UniProt Q96B26

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain N； UniProt 1–276	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 1–276（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain C 1–276（276 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain C 1–276（276 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain C 1–276（276 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain N 1–276（276 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain L 1–276（276 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain N 1–276（276 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS8_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain N； PDBConstruct 5–280； UniProt 1–276

Exosome complex component RRP46

Homo sapiens

UniProt Q9NQT4

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain O； UniProt 1–235	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–235（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain D 1–235（235 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain D 1–235（235 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain D 1–235（235 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain O 1–235（235 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain O 1–235（235 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain O 1–235（235 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain O； PDBConstruct 5–239； UniProt 1–235

Exosome complex component RRP42

Homo sapiens

UniProt Q15024

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain F； UniProt 1–291	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain E 1–291（291 aa）	Mutation：L274V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain E 1–291（291 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain E 1–291（291 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain E 1–291（291 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain F 1–291（291 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain F 1–291（291 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain F 1–291（291 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS7_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 5–295； UniProt 1–291

Exosome complex component RRP40

Homo sapiens

UniProt Q9NQT5

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain H； UniProt 1–275	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 0–274（275 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain G 1–275（275 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain G 1–275（275 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain G 1–275（275 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain H 1–275（275 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain H 1–275（275 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain H 1–275（275 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS3_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain H； PDBConstruct 5–279； UniProt 1–275

Exosome complex component CSL4

Homo sapiens

UniProt Q9Y3B2

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain J； UniProt 1–195	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain I 1–195（195 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain I 1–195（195 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain I 1–195（195 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain J 1–195（195 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain J 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain J 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS1_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain J； PDBConstruct 5–199； UniProt 1–195

Helicase SKI2W

Homo sapiens

UniProt Q15477

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain A； UniProt 1–1246	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7QDR Apo human SKI complex in the closed state Deposited 2021-11-29	Different oligomeric state	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1246（1246 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 3.70 Å
7QDS Apo human SKI complex in the open state Deposited 2021-11-30	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1246（1246 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 3.80 Å
7QDY RNA-bound human SKI complex Deposited 2021-12-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain A 1–1246（1246 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 3.10 Å
7QDZ 80S-bound human SKI complex in the closed state Deposited 2021-12-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain A 1–1246（1246 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 3.60 Å
7QE0 80S-bound human SKI complex in the open state Deposited 2021-12-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–1246（1246 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 6.50 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain A 1–1246（1246 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain A 1–1246（1246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain A 1–1246（1246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å
9G8Q 40S-bound human SKI238 complex in the open state (Gatekeeping module) Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1246（1246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.10 Å
9G8R human SKI7-SKI238 complex in the open state Deposited 2024-07-23	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–774（774 aa） Chain A 1049–1246（198 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 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	SKIV2_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain A； PDBConstruct 1–1246； UniProt 1–1246

Exosome complex component MTR3

Homo sapiens

UniProt Q5RKV6

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain G； UniProt 1–272	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain F 1–272（272 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain F 1–272（272 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain F 1–272（272 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain F 1–272（272 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain G 1–272（272 aa） Chain H 181–272（92 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain G 1–272（272 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain G 1–272（272 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS6_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain G； PDBConstruct 1–272； UniProt 1–272

Exosome complex component RRP4

Homo sapiens

UniProt Q13868

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain I； UniProt 1–293	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NN6 Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 Deposited 2006-10-23	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 1–293（293 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.344
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain H 1–293（293 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain H 1–293（293 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain H 1–293（293 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain I 1–293（293 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain I 1–293（293 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain I 1–293（293 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

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

View Construct and Data Evidence

UniProt name	EXOS2_HUMAN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain I； PDBConstruct 5–297； UniProt 1–293

Isoform 2 of HBS1-like protein

Homo sapiens

UniProt Q9Y450

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain E； UniProt 369–632	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component RRP45 × 1 （Q06265） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10AY Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961 Deposited 2026-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 478–684（207 aa） Fragment：domain 2 + domain 3 Chain D 478–684（207 aa） Fragment：domain 2 + domain 3	Not recorded	A1C4S N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
11MR Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement) Deposited 2026-03-05	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 478–684（207 aa） Fragment：domain 2 + domain 3 Chain C 478–684（207 aa） Fragment：domain 2 + domain 3	Not recorded	ZN ZINC ION × 2 A1C9W N-[(3S)-2,6-dioxopiperidin-3-yl]-2-fluoro-3-[(2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}propan-2-yl)carbamamido]benzamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES (pH 7.5), 240 mM NaCl, 3 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
5LZW Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a truncated mRNA. Deposited 2016-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric	Chain jj 1–684（684 aa）	Not recorded	MG MAGNESIUM ION × 281 ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.	Resolution 3.53 Å
5LZX Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a UGA stop codon. Deposited 2016-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric	Chain jj 1–684（684 aa）	Not recorded	MG MAGNESIUM ION × 264 ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.	Resolution 3.67 Å
5LZY Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA. Deposited 2016-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric	Chain jj 1–684（684 aa）	Not recorded	MG MAGNESIUM ION × 236 ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.	Resolution 3.99 Å
5LZZ Structure of the mammalian rescue complex with Pelota and Hbs1l (combined) Deposited 2016-10-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric	Chain jj 1–684（684 aa）	Not recorded	MG MAGNESIUM ION × 264 ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；3 ul aliquots were applied to the grid and incubated for 30 s, before blotting for 3s to remove excess solution.	Resolution 3.47 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain E 369–632（264 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain E 369–632（264 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain E 369–632（264 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å
9G8R human SKI7-SKI238 complex in the open state Deposited 2024-07-23	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 372–546（175 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 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	HBS1L_HUMAN
Isoform	Q9Y450-2
PDB entities	11
Chains and sequence ranges	Author chain E； PDBConstruct 5–268； UniProt 369–632

Exosome complex component RRP45

Homo sapiens

UniProt Q06265

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain K； UniProt 1–439	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） DIS3-like exonuclease 1 × 1 （Q8TF46）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6D6Q Human nuclear exosome-MTR4 RNA complex - overall reconstruction Deposited 2018-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain A 1–456（456 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 conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain A 1–456（456 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
6H25 Human nuclear RNA exosome EXO-10-MPP6 complex Deposited 2018-07-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain A 1–439（439 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 3.80 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain K 1–439（439 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain K 1–439（439 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain K 1–439（439 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EXOS9_HUMAN
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain K； PDBConstruct 5–443； UniProt 1–439

DIS3-like exonuclease 1

Homo sapiens

UniProt Q8TF46

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 × 12 RNA 1 PDB declaration: 13-meric（13） Consistent with all polymer counts	Chain M； UniProt 1–1054	Not recorded	Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） CrPV-IRES RNA × 1 Helicase SKI2W × 1 （Q15477） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Isoform 2 of HBS1-like protein × 1 （Q9Y450） Exosome complex component RRP45 × 1 （Q06265）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9G8N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain M 1–1054（1054 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain M 1–1054（1054 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain M 1–1054（1054 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DI3L1_HUMAN
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain M； PDBConstruct 3–1056； UniProt 1–1054

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9g8n
Deposition date deposition_date	2024-07-23
Structure title title	80S-bound human Ski2-exosome complex
Keywords keywords	Ribosome, RNase, Helicase, RNA-binding, mRNA-degradation, cytoplasm; RIBOSOME
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	61.18 Å
Radius of gyration Rg (electron density) rg_electron	61.83 Å
Forward intensity I(0) i0	3585910000.00
Molecular weight molecular_weight	491260.0 kDa
Excluded volume excluded_volume	610950 Å³
Envelope volume envelope_volume	988150 Å³
Hydration-shell volume shell_volume	135650 Å³
Envelope diameter envelope_diameter	248.3 Å
Shell Rg shell_rg	61.67 Å
Envelope Rg envelope_rg	62.28 Å
Shape Rg shape_rg	61.88 Å
Total Rg total_rg	61.65 Å
Total atoms total_atoms	34405
Residues n_residues	4348
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	218.5 Å
Rg (real space) rg_real	61.58 Å
Rg uncertainty (real space) rg_real_error	1.69 Å
I(0) (real space) i0_real	3.5840e+09
I(0) uncertainty (real space) i0_real_error	7.6650e+07
Rg (reciprocal space) rg_reciprocal	60.78 Å
I(0) (reciprocal space) i0_reciprocal	3581000000.0000
Solution quality estimate total_estimate	0.8322
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	67.2 Å
Skewness Skewness skewness	0.648
Kurtosis Kurtosis kurtosis	0.294
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0071
Highest regularization parameter α highest_alpha	410500000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.668; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.814

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Exosome complex component RRP41
Molecular weight formula_weight	26417.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	34405

MAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASILLGD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Exosome complex component RRP43
Molecular weight formula_weight	30429.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

GPDSMAAGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKLMDEVIKSMKPK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Exosome complex component RRP46
Molecular weight formula_weight	25636.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

GPDSMEEETHTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSKS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Exosome complex component RRP42
Molecular weight formula_weight	32216.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GPDSMASVTLSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEESLGPKRQKVGFLG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Exosome complex component RRP40
Molecular weight formula_weight	29940.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GPDSMAEPASVAAESLAGSRARAARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLHPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Exosome complex component CSL4
Molecular weight formula_weight	21835.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

GPDSMAPPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKVARVQPEFLQT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	CrPV-IRES RNA
Molecular weight formula_weight	13422.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	X

UUUUUUUUUUUUUUUUUUUUUUUUUUCUCCUCUUUUUUUUUUUU

Entity 8 Entity 8 polymer

Description description	Helicase SKI2W
Molecular weight formula_weight	137913.7 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MMETERLVLPPPDPLDLPLRAVELGCTGHWELLNLPGAPESSLPHGLPPCAPDLQQEAEQLFLSSPAWLPLHGVEHSARKWQRKTDPWSLLAVLGAPVPSDLQAQRHPTTGQILGYKEVLLENTNLSATTSLSLRRPPGPASQSLWGNPTQYPFWPGGMDEPTITDLNTREEAEEEIDFEKDLLTIPPGFKKGMDFAPKDCPTPAPGLLSLSCMLEPLDLGGGDEDENEAVGQPGGPRGDTVSASPCSAPLARASSLEDLVLKEASTAVSTPEAPEPPSQEQWAIPVDATSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEASCLIMTTEILRSMLYSGSDVIRDLEWVIFDEVHYINDVERGVVWEEVLIMLPDHVSIILLSATVPNALEFADWIGRLKRRQIYVISTVTRPVPLEHYLFTGNSSKTQGELFLLLDSRGAFHTKGYYAAVEAKKERMSKHAQTFGAKQPTHQGGPAQDRGVYLSLLASLRTRAQLPVVVFTFSRGRCDEQASGLTSLDLTTSSEKSEIHLFLQRCLARLRGSDRQLPQVLHMSELLNRGLGVHHSGILPILKEIVEMLFSRGLVKVLFATETFAMGVNMPARTVVFDSMRKHDGSTFRDLLPGEYVQMAGRAGRRGLDPTGTVILLCKGRVPEMADLHRMMMGKPSQLQSQFRLTYTMILNLLRVDALRVEDMMKRSFSEFPSRKDSKAHEQALAELTKRLGALEEPDMTGQLVDLPEYYSWGEELTETQHMIQRRIMESVNGLKSLSAGRVVVVKNQEHHNALGVILQVSSNSTSRVFTTLVLCDKPLSQDPQDRGPATAEVPYPDDLVGFKLFLPEGPCDHTVVKLQPGDMAAITTKVLRVNGEKILEDFSKRQQPKFKKDPPLAAVTTAVQELLRLAQAHPAGPPTLDPVNDLQLKDMSVVEGGLRARKLEELIQGAQCVHSPRFPAQYLKLRERMQIQKEMERLRFLLSDQSLLLLPEYHQRVEVLRTLGYVDEAGTVKLAGRVACAMSSHELLLTELMFDNALSTLRPEEIAALLSGLVCQSPGDAGDQLPNTLKQGIERVRAVAKRIGEVQVACGLNQTVEEFVGELNFGLVEVVYEWARGMPFSELAGLSGTPEGLVVRCIQRLAEMCRSLRGAARLVGEPVLGAKMETAATLLRRDIVFAASLYTQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	Exosome complex component MTR3
Molecular weight formula_weight	28267.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MPGDHRRIRGPEESQPPQLYAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQSLVRAARRRGAAAQP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 10 Entity 10 polymer

Description description	Exosome complex component RRP4
Molecular weight formula_weight	33190.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GPDSMAMEMRLPVARKPLSERLGRDTKKHLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRLLEQEG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 11 Entity 11 polymer

Description description	Isoform 2 of HBS1-like protein
Molecular weight formula_weight	30196.1 kDa
EC 编号 ec_number	3.6.5.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPDSSQCESPSLTELFQEHKENNISQCFTLSDLCNQSSASFTDLSLGSFPLSQLANRCQSSPGISELTGSLSSLAFHKASPTRDLENLSLSELIAETIDVDNSQIKKESFEVSLSEVRSPGIDSNIDLSVLIKNPDFVPKPVVDPSIAPSSRTKVLSSKLGKNSNFAKDNKKNNKGSLTRKPPFSLSWTKALAARPSAFASTLCLRYPLKSCKRRTLDLYKTFLYSRQVQDVKDKEISPLVAITPFDFKSASPDDIVKANQKKAFTRELEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 12 Entity 12 polymer

Description description	Exosome complex component RRP45
Molecular weight formula_weight	49370.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GPDSMKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEKAPIDTSDVEEKAEEIIAEAEPPSEVVSTPVLWTPGTAQIGEGVENSWGDLEDSEKEDDEGGGDQAIILDGIKMDTGVEVSDIGSQDAPIILSDSEEEEMIILEPDKNPKKIRTQTTSAKQEKAPSKKPVKRRKKKRAAN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 13 Entity 13 polymer

Description description	DIS3-like exonuclease 1
Molecular weight formula_weight	121108.6 kDa
EC 编号 ec_number	3.1.13.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

GPMLQKREKVLLLRTFQGRTLRIVREHYLRPCVPCHSPLCPQPAACSHDGKLLSSDVTHYVIPDWKVVQDYLEILEFPELKGIIFMQTACQAVQHQRGRRQYNKLRNLLKDARHDCILFANEFQQCCYLPRERGESMEKWQTRSIYNAAVWYYHHCQDRMPIVMVTEDEEAIQQYGSETEGVFVITFKNYLDNFWPDLKAAHELCDSILQSRRERENESQESHGKEYPEHLPLEVLEAGIKSGRYIQGILNVNKHRAQIEAFVRLQGASSKDSDLVSDILIHGMKARNRSIHGDVVVVELLPKNEWKGRTVALCENDCDDKASGESPSEPMPTGRVVGILQKNWRDYVVTFPSKEEVQSQGKNAQKILVTPWDYRIPKIRISTQQAETLQDFRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSISVIPFSEAQMCEMPVNTPESPWKVSPEEEQKRKDLRKSHLVFSIDPKGCEDVNDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLSADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNLSVVDDIPEFKDLDEKSRQAKLEELVWAIGKLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKIWESFPHQALLRQHPPPHQEFFSELRECAKAKGFFIDTRSNKTLADSLDNANDPHDPIVNRLLRSMATQAMSNALYFSTGSCAEEEFHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKGNLFSNKDLEELCRHINNRNQAAQHSQKQSTELFQCMYFKDKDPATEERCISDGVIYSIRTNGVLLFIPRFGIKGAAYLKNKDGLVISCGPDSCSEWKPGSLQRFQNKITSTTTDGESVTFHLFDHVTVRISIQASRCHSDTIRLEIISNKPYKIPNTELIHQSSPLLKSELVKEVTKSVEEAQLAQEVKVNIIQEEYQEYRQTKGRSLYTLLEEIRDLALLDVSNNYGI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	79353

fit	/app/data/saxs_computation/g8/9g8n/9g8n.fit
pddf	/app/data/pr_computation/g8/9g8n/9g8n.pr.out
profile	/app/data/saxs_computation/g8/9g8n/9g8n.dat

80S-bound human Ski2-exosome complex

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

Exosome complex component RRP41

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component RRP43

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component RRP46

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component RRP42

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component RRP40

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component CSL4

State in the Current Structure

Other States of the Same Protein in the Database

Helicase SKI2W

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component MTR3

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component RRP4

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 2 of HBS1-like protein

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex component RRP45

State in the Current Structure

Other States of the Same Protein in the Database

DIS3-like exonuclease 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

来源 Source

Entity 9 Entity 9 polymer

Polymer Polymer

来源 Source

Entity 10 Entity 10 polymer

Polymer Polymer

来源 Source

Entity 11 Entity 11 polymer

Polymer Polymer

来源 Source