6d6q

Human nuclear exosome-MTR4 RNA complex - overall reconstruction

Method: ELECTRON MICROSCOPY D_max: 191.0 Å Quality: GOOD

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

Exosome complex component RRP45

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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain A； UniProt 1–456	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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

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 6D6Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different construct Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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	Q06265-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–473； UniProt 1–456

Exosome complex component RRP41

Homo sapiens

UniProt Q9NPD3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain B； UniProt 1–245	Not recorded	Exosome complex component RRP45 × 1 （Q06265） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–249； 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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain C； UniProt 1–276	Not recorded	Exosome complex component RRP45 × 1 （Q06265） Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–278； 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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain D； UniProt 1–235	Not recorded	Exosome complex component RRP45 × 1 （Q06265） Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP42 × 1 （Q15024） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–237； 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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain E； UniProt 1–291	Not recorded	Exosome complex component RRP45 × 1 （Q06265） Exosome complex component RRP41 × 1 （Q9NPD3） Exosome complex component RRP43 × 1 （Q96B26） Exosome complex component RRP46 × 1 （Q9NQT4） Exosome complex component MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	5
Chains and sequence ranges	Author chain E； PDBConstruct 3–293； UniProt 1–291

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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain F； UniProt 1–272	Not recorded	Exosome complex component RRP45 × 1 （Q06265） 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 RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–272； UniProt 1–272

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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain G； UniProt 1–275	Not recorded	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	7
Chains and sequence ranges	Author chain G； PDBConstruct 3–277； UniProt 1–275

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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain H； UniProt 1–293	Not recorded	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	8
Chains and sequence ranges	Author chain H； PDBConstruct 4–296； UniProt 1–293

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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain I； UniProt 1–195	Not recorded	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	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 ligand/ion 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	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 ligand/ion Different experimental conditions 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 experimental conditions 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
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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	9
Chains and sequence ranges	Author chain I； PDBConstruct 3–197； UniProt 1–195

Exosome component 10

Homo sapiens

UniProt Q01780

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain J； UniProt 1–648 Chain J； UniProt 705–804	Mutation：D313N	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CPR Solution structure of the HRDC domain of human Exosome component 10 Deposited 2005-05-19	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 A 483–593（111 aa） Fragment：HRDC	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.45mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
3SAF Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	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 A 180–606（427 aa） Fragment：UNP residues 180-606	Mutation：D313N	MG MAGNESIUM ION × 1 YT3 YTTRIUM (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.240
3SAF Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	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 B 180–606（427 aa） Fragment：UNP residues 180-606	Mutation：D313N	MG MAGNESIUM ION × 1 YT3 YTTRIUM (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.240
3SAG Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	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 A 180–606（427 aa） Fragment：UNP residues 180-606	Mutation：D313N	YT3 YTTRIUM (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.262
3SAG Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site Deposited 2011-06-02	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 B 180–606（427 aa） Fragment：UNP residues 180-606	Mutation：D313N	YT3 YTTRIUM (III) ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.262
3SAH Crystal structure of the human RRP6 catalytic domain with Y436A mutation in the catalytic site Deposited 2011-06-02	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 A 180–606（427 aa） Fragment：UNP residues 180-606	Mutation：Y436A	YT3 YTTRIUM (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.65 Å R-free 0.265
3SAH Crystal structure of the human RRP6 catalytic domain with Y436A mutation in the catalytic site Deposited 2011-06-02	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 B 180–606（427 aa） Fragment：UNP residues 180-606	Mutation：Y436A	YT3 YTTRIUM (III) ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.65 Å R-free 0.265
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain J 1–648（648 aa） Chain J 705–804（100 aa）	Mutation：D313N Mutation：D313N	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
7MQA Cryo-EM structure of the human SSU processome, state post-A1 Deposited 2021-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain NV 1–885（885 aa）	Not recorded	MG MAGNESIUM ION × 64 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EXOSX_HUMAN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 2–649； UniProt 1–648 Author chain J； PDBConstruct 662–761； UniProt 705–804

Exosome complex exonuclease RRP44

Homo sapiens

UniProt Q9Y2L1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain K； UniProt 1–958	Mutation：D146N, D487N	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） M-phase phosphoprotein 6 × 1 （Q99547） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain K 1–958（958 aa）	Mutation：D146N, D487N	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain J 1–958（958 aa）	Mutation：D146N, D487N	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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RRP44_HUMAN
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 3–960； UniProt 1–958

M-phase phosphoprotein 6

Homo sapiens

UniProt Q99547

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain L； UniProt 1–160	Not recorded	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） Exosome RNA helicase MTR4 × 1 （P42285） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain L 1–160（160 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: dodecameric	Chain K 1–160（160 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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MPH6_HUMAN
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 3–162； UniProt 1–160

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	Other combination Heteromer Protein × 13 DNA 1 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain M； UniProt 1–1042	Not recorded	Exosome complex component RRP45 × 1 （Q06265） 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 MTR3 × 1 （Q5RKV6） Exosome complex component RRP40 × 1 （Q9NQT5） Exosome complex component RRP4 × 1 （Q13868） Exosome complex component CSL4 × 1 （Q9Y3B2） Exosome component 10 × 1 （Q01780） Exosome complex exonuclease RRP44 × 1 （Q9Y2L1） M-phase phosphoprotein 6 × 1 （Q99547） ;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ; × 1 DNA/RNA (62-MER) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D6Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6C90 Human Mtr4 helicase in complex with ZCCHC8-CTD Deposited 2018-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental 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
6D6R Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction Deposited 2018-04-22	Parsed fields agree	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain M 1–1042（1042 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；30 sec wait time, 2.5 sec blot time	Resolution 3.45 Å
6IEG Crystal structure of human MTR4 Deposited 2018-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental 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 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 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 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 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 A 1–1042（1042 aa） Chain E 1–1042（1042 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 4.06 Å
7S7C Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–1042（1042 aa） Chain E 1–1042（1042 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 3.62 Å
7Z4Y Human NEXT dimer - overall reconstruction of the core complex Deposited 2022-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1042（1042 aa） Chain D 1–1042（1042 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.50 Å
7Z4Z Human NEXT dimer - focused reconstruction of the dimerization module Deposited 2022-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental 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 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	13
Chains and sequence ranges	Author chain M； PDBConstruct 4–1045； UniProt 1–1042

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

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	6d6q
Deposition date deposition_date	2018-04-22
Structure title title	Human nuclear exosome-MTR4 RNA complex - overall reconstruction
Keywords keywords	RNA exosome, RNA degradation, ribonuclease, helicase, SF2, RNA-protein complex, translocase, nuclear, HYDROLASE; HYDROLASE
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	57.51 Å
Radius of gyration Rg (electron density) rg_electron	57.09 Å
Forward intensity I(0) i0	3121380000.00
Molecular weight molecular_weight	452430.0 kDa
Excluded volume excluded_volume	560550 Å³
Envelope volume envelope_volume	832000 Å³
Hydration-shell volume shell_volume	123080 Å³
Envelope diameter envelope_diameter	205.7 Å
Shell Rg shell_rg	58.92 Å
Envelope Rg envelope_rg	56.32 Å
Shape Rg shape_rg	57.09 Å
Total Rg total_rg	57.14 Å
Total atoms total_atoms	31639
Residues n_residues	3950
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	191.0 Å
Rg (real space) rg_real	57.72 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	3.1210e+09
I(0) uncertainty (real space) i0_real_error	6.6570e+07
Rg (reciprocal space) rg_reciprocal	57.32 Å
I(0) (reciprocal space) i0_reciprocal	3119000000.0000
Solution quality estimate total_estimate	0.8408
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.7 Å
Skewness Skewness skewness	0.536
Kurtosis Kurtosis kurtosis	0.033
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	301900000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.444

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Description description	Exosome complex component RRP45
Molecular weight formula_weight	52828.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	31639

MGSSHHHHHHSQDPNSHMKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEKAPIDTSDVEEKAEEIIAEAEPPSEVVSTPVLWTPGTAQIGEGVENSWGDLEDSEKEDDEGGGDQAIILDGIKMDTGVEVSDIGSQELGFHHVGQTGLEFLTSDAPIILSDSEEEEMIILEPDKNPKKIRTQTTSAKQEKAPSKKPVKRRKKKRAAN

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 RRP41
Molecular weight formula_weight	26831.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADPMAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASILLGD

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 RRP43
Molecular weight formula_weight	30285.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DPMAAGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKLMDEVIKSMKPK

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 RRP46
Molecular weight formula_weight	25480.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SLMEEETHTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSKS

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 RRP42
Molecular weight formula_weight	32072.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

DPMASVTLSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEESLGPKRQKVGFLG

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 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	F

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 7 Entity 7 polymer

Description description	Exosome complex component RRP40
Molecular weight formula_weight	29796.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

DPMAEPASVAAESLAGSRARAARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLHPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES

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 8 Entity 8 polymer

Description description	Exosome complex component RRP4
Molecular weight formula_weight	33184.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DPHMAMEMRLPVARKPLSERLGRDTKKHLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRLLEQEG

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 CSL4
Molecular weight formula_weight	21691.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

DPMAPPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKVARVQPEFLQT

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 component 10
Molecular weight formula_weight	86754.9 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	D313N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

SMAPPSTREPRVLSATSATKSDGEMVLPGFPDADSFVKFALGSVVAVTKASGGLPQFGDEYDFYRSFPGFQAFCETQGDRLLQCMSRVMQYHGCRSNIKDRSKVTELEDKFDLLVDANDVILERVGILLDEASGVNKNQQPVLPAGLQVPKTVVSSWNRKAAEYGKKAKSETFRLLHAKNIIRPQLKFREKIDNSNTPFLPKIFIKPNAQKPLPQALSKERRERPQDRPEDLDVPPALADFIHQQRTQQVEQDMFAHPYQYELNHFTPADAVLQKPQPQLYRPIEETPCHFISSLDELVELNEKLLNCQEFAVNLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWERGNGQPVQLQVVWQRSRDICLKKFIKPIFTDESYLELYRKQKKHLNTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREMPLLKSEVAAGVKKSGPLPSAERLENVLFGPHDCSHAPPDGYPIIPTSGSVPVQKQASLFPDEKEDNLLGSRGSGSGSGSGSVSQAAKFDPSTKIYEISNRWKLAQVQVQKDSKEAVKKKAAEQTAAREQAKEACKAAAEQAISVRQQVVLENAAKKRERATSDPRTTEQKQEKKRLKISKK

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	Exosome complex exonuclease RRP44
Molecular weight formula_weight	109267.9 kDa
EC 编号 ec_number	3.1.13.-,3.1.26.-
Mutation mutation	D146N, D487N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GSMLKSKTFLKKTRAGGVMKIVREHYLRDDIGCGAPGCAACGGAHEGPALEPQPQDPASSVCPQPHYLLPDTNVLLHQIDVLEDPAIRNVIVLQTVLQEVRNRSAPVYKRIRDVTNNQEKHFYTFTNEHHRETYVEQEQGENANDRNNRAIRVAAKWYNEHLKKMSADNQLQVIFITNDRRNKEKAIEEGIPAFTCEEYVKSLTANPELIDRLACLSEEGNEIESGKIIFSEHLPLSKLQQGIKSGTYLQGTFRASRENYLEATVWIHGDSEENKEIILQGLKHLNRAVHEDIVAVELLPKSQWVAPSSVVLHDEGQNEEDVEKEEETERMLKTAVSEKMLKPTGRVVGIIKRNWRPYCGMLSKSDIKESRRHLFTPADKRIPRIRIETRQASTLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDINDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLAESLDQAESPTFPYLNTLLRILATRCMMQAVYFCSGMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTDKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSNGIVSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTVFHVFDKVKVKIMLDSSNLQHQKIRMSLVEPQIPGISIPTDTSNMDLNGPKKKKMKLGK

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	M-phase phosphoprotein 6
Molecular weight formula_weight	19268.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DPMAAERKTRLSKNLLRMKFMQRGLDSETKKQLEEEEKKIISEEHWYLDLPELKEKESFIIEEQSFLLCEDLLYGRMSFRGFNPEVEKLMLQMNAKHKAEEVEDETVELDVSDEEMARRYETLVGTIGKKFARKRDHANYEEDENGDITPIKAKKMFLKPQD

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	Exosome RNA helicase MTR4
Molecular weight formula_weight	118225.0 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

SGDMADAFGDELFSVFEGDSTTAAGTKKDKEKDKGKWKGPPGSADKAGKRFDGKLQSESTNNGKNKRDVDFEGTDEPIFGKKPRIEESITEDLSLADLMPRVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDAGDLAKGDQKGRKGGTKGPSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVKNEGDDFGWGVVVNFSKKSNVKPNSGELDPLYVVEVLLRCSKESLKNSATEAAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQKVEAFEHRMYSHPLHNDPNLETVYTLCEKKAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVFAASLYL

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 14 Entity 14 polymer

Description description	;RNA (5'-R(APGPCPAPCPCPGPUPAPAPAPGPAPCPGPC)-3') ;
Molecular weight formula_weight	5143.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	N

AGCACCGUAAAGACGC

Entity 15 Entity 15 polymer

Description description	DNA/RNA (62-MER)
Molecular weight formula_weight	19487.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide/polyribonucleotide hybrid
Chain IDs strand_id	O

GCGTCTTTACGGTGCTCACCACACCACACCACACCACACCACACCACACCACACAAAAAAAA

Entity 16 Entity 16 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 17 Entity 17 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 18 Entity 18 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6d6qA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	6d6qB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	6d6qC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	6d6qD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	6d6qE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	6d6qF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	70 — GHMP Kinase, N-terminal domain

Domain ID domain_id	6d6qG01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6d6qG02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	6d6qG03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	6d6qH01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6d6qI01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6d6qK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

▶

8. Citations (1)

▶

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	—

Resolution resolution	3.45 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	122703

fit	/app/data/saxs_computation/d6/6d6q/6d6q.fit
pddf	/app/data/pr_computation/d6/6d6q/6d6q.pr.out
profile	/app/data/saxs_computation/d6/6d6q/6d6q.dat

Human nuclear exosome-MTR4 RNA complex - overall reconstruction

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

Exosome complex component RRP45

State in the Current Structure

Other States of the Same Protein in the Database

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 MTR3

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 RRP4

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

Exosome component 10

State in the Current Structure

Other States of the Same Protein in the Database

Exosome complex exonuclease RRP44

State in the Current Structure

Other States of the Same Protein in the Database

M-phase phosphoprotein 6

State in the Current Structure

Other States of the Same Protein in the Database

Exosome RNA helicase MTR4

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 (18)

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

来源 Source

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