5c0w

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

Method: X-RAY DIFFRACTION

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

Exosome complex component RRP45

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP45_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 1–305

Exosome complex component SKI6

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P46948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP41_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–248； UniProt 1–246

Exosome complex component RRP43

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P25359

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP43_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–394； UniProt 1–394

Exosome complex component RRP46

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P53256

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP46_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 23–245； UniProt 1–223

Exosome complex component RRP42

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12277

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP42_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 3–267； UniProt 1–265

Exosome complex component MTR3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P48240

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTR3_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–250； UniProt 1–250

Exosome complex component RRP40

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q08285

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP40_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 4–243； UniProt 1–240

Exosome complex component RRP4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38792

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP4_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 3–361； UniProt 1–359

Exosome complex component CSL4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P53859

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSL4_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 4–295； UniProt 1–292

Exosome complex exonuclease DIS3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q08162

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease RRP6 × 1 （Q12149） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP44_YEAST
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 4–1004； UniProt 1–1001

Exosome complex exonuclease RRP6

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12149

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex protein LRP1 × 1 （P38801） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRP6_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 3–695； UniProt 1–693

Exosome complex protein LRP1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38801

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 12 RNA 2	Exosome complex component RRP45 × 1 （Q05636） Exosome complex component SKI6 × 1 （P46948） Exosome complex component RRP43 × 1 （P25359） Exosome complex component RRP46 × 1 （P53256） Exosome complex component RRP42 × 1 （Q12277） Exosome complex component MTR3 × 1 （P48240） Exosome complex component RRP40 × 1 （Q08285） Exosome complex component RRP4 × 1 （P38792） Exosome complex component CSL4 × 1 （P53859） Exosome complex exonuclease DIS3 × 1 （Q08162） Exosome complex exonuclease RRP6 × 1 （Q12149） RNA synthetic × 2 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LRP1_YEAST
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–184； UniProt 1–184

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	5c0w
Deposition date deposition_date	2015-06-12
Structure title title	Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates
Keywords keywords	hydrolase, RNA, nuclease, hydrolase-RNA complex; HYDROLASE/RNA
Experimental Method method	X-RAY DIFFRACTION

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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.

5c0w__assembly_1__model_1

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

Download this curve (.dat)

5c0w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c0w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.83 Å
Rg (electron density)	55.89 Å
Total Rg	55.97 Å
Atom count	31155
Residues	3993
Excluded volume	554100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c0w__assembly_1__model_1`	tetradecameric （14）	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 (15)

Entity 1 Entity 1 polymer

Description description	Exosome complex component RRP45
Molecular weight formula_weight	34001.9 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	31160

MAKDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLTSENAREI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Exosome complex component SKI6
Molecular weight formula_weight	27794.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMSRLEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRVSNASAR

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Exosome complex component RRP43
Molecular weight formula_weight	44109.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAESTTLETIEIHPITFPPEVLARISPELSLQRHLSLGIRPCLRKYEEFRDVAIENNTLSRYADAGNIDTKNNILGSNVLKSGKTIVITSITGGIIEETSASIKDLDDFGEEELFEVTKEEDIIANYASVYPVVEVERGRVGACTDEEMTISQKLHDSILHSRILPKKALKVKAGVRSANEDGTFSVLYPDELEDDTLNETNLKMKRKWSYVLYAKIVVLSRTGPVFDLCWNSLMYALQSVKLPRAFIDERASDLRMTIRTRGRSATIRETYEIICDQTKSVPLMINAKNIAFASNYGIVELDPECQLQNSDNSEEEEVDIDMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLMGGGAKITPEMIKRSLLLSRVRADDLSTRFNI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Exosome complex component RRP46
Molecular weight formula_weight	26914.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GHGNNKEPNTKNRLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTAEQLKISLSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNISPRLVV

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Exosome complex component RRP42
Molecular weight formula_weight	29294.4 kDa
Mutation mutation	V138I
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GHMSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQVDVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPISLISFAIYSALNSTYLPKLISAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLENL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Exosome complex component MTR3
Molecular weight formula_weight	27559.9 kDa
Mutation mutation	T75S, M161T
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MNVQDRRRLLGPAAAKPMAFSNTTTHVPEKKSTDLTPKGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLISAVYGPRSIRGSFTSQGTISIQLKNGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKMTSSQISSLIPHCITSITLALADAGIELVDMAGAGEANGTVVSFIKNGEEIVGFWKDDGDDEDLLECLDRCKEQYNRYRDLMISCLMNQET

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 polymer

Description description	Exosome complex component RRP40
Molecular weight formula_weight	26875.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GPHMSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVKEE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 8 Entity 8 polymer

Description description	Exosome complex component RRP4
Molecular weight formula_weight	39714.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

RSMSEVITITKRNGAFQNSSNLSYNNTGISDDENDEEDIYMHDVNSASKSESDSQIVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNIRQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEKMRGNGN

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 9 Entity 9 polymer

Description description	Exosome complex component CSL4
Molecular weight formula_weight	31911.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GPHMACNFQFPEIAYPGKLICPQYGTENKDGEDIIFNYVPGPGTKLIQYEHNGRTLEAITATLVGTVRCEEEKKTDQEEEREGTDQSTEEEKSVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGSNGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAKPF

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 10 Entity 10 polymer

Description description	Exosome complex exonuclease DIS3
Molecular weight formula_weight	114081.0 kDa
EC 编号 ec_number	3.1.13.-,3.1.26.-
Mutation mutation	D171N, D551N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

GPAMSVPAIAPRRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQIVVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFVERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTFPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 11 Entity 11 polymer

Description description	Exosome complex exonuclease RRP6
Molecular weight formula_weight	79649.4 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	D296N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GAMASENPDVLLSRVINVVRAASSLASQDVDFYKNLDRGFSKDLKSKADKLADMANEIILSIDEHHESFELKEEDISDLWNNFGNIMDNLLEMSDHSLDKLNCAINSKSRGSDLQYLGEFSGKNFSPTKRVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMNIIWLQRDLGLYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNEEATPIPSSETKADGILLETISVPQIRDVMERFSVLCNSNISKSRAKPVTNSSILLGKILPREEHDIAYSKDGLPNKVKTEDIRIRAQNFKSALANLEDIIFEIEKPLVVPVKLEEIKTVDPASAPNHSPEIDNLDDLVVLKKKNIQKKQPAKEKGVTEKDAVDYSKIPNILSNKPG

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 12 Entity 12 polymer

Description description	Exosome complex protein LRP1
Molecular weight formula_weight	21086.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MEDIEKIKPYVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGELKRVKSYMDKAKQYDNRITKSNEKSQAEQEKAKNIISNVLDGNKNQFEPSISRSNFQGKHTKFENDELAESTTTKIIDSTDHIRKASSKKSKRLDKVGKKKGGKK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 13 Entity 13 polymer

Description description	RNA synthetic
Molecular weight formula_weight	5811.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R,N

AAAUAAUAAAUAAAAAAA

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 non-polymer

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

▶

Unit-cell length a length_a	195.380 Å
Unit-cell length b length_b	195.380 Å
Unit-cell length c length_c	463.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	4.600 Å
Low-resolution limit resolution_low	59.090 Å
R factor r_factor	0.2773
R_work r_work	0.2713
R_free r_free	0.2838

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

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 SKI6

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 complex exonuclease DIS3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer