6d6r

Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction

Method: ELECTRON MICROSCOPY

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 13 DNA 1 RNA 1	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 ZINC ION × 1 MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6d6r
Deposition date deposition_date	2018-04-22
Structure title title	Human nuclear exosome-MTR4 RNA complex - composite map after focused 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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6d6r__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6d6r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6d6r__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	57.53 Å
Rg (electron density)	57.11 Å
Total Rg	57.16 Å
Atom count	31639
Residues	3950
Excluded volume	560550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6d6r__assembly_1__model_1`	pentadecameric （15）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 17 Entity 17 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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

▼

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	6d6rA00
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	6d6rB01
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	6d6rC00
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	6d6rD00
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	6d6rE00
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	6d6rF00
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	6d6rG01
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	6d6rG02
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	6d6rG03
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	6d6rH01
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	6d6rI01
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	6d6rI02
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	6d6rK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1010 — 5'-nuclease

▶

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Method resolution_method	—
颗粒数 num_particles	122703

Human nuclear exosome-MTR4 RNA complex - composite map after focused 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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component RRP41

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component RRP43

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component RRP46

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component RRP42

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component MTR3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component RRP40

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component RRP4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome complex component CSL4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exosome component 10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer