5vzj

STRUCTURE OF A TWELVE COMPONENT MPP6-NUCLEAR RNA EXOSOME COMPLEX BOUND TO RNA

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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 5–250； 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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 3–225； 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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 5–269； 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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 5–244； 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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 5–363； 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 RRP6 × 1 （Q12149） Exosome complex exonuclease DIS3 × 1 （Q08162） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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 5–296； UniProt 1–292

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） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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	10
Chains and sequence ranges	Author chain J； PDBConstruct 4–559； UniProt 129–684

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） M-phase phosphoprotein 6 homolog × 1 （P53725） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	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	11
Chains and sequence ranges	Author chain K； PDBConstruct 3–1003； UniProt 1–1001

M-phase phosphoprotein 6 homolog

Saccharomyces cerevisiae

UniProt P53725

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 exonuclease DIS3 × 1 （Q08162） RNA (11-MER) × 1 RNA (19-MER) × 1 SULFATE ION × 5 GLYCEROL × 2 ZINC ION × 1 water × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MPP6_YEAST
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 3–42； UniProt 81–120

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	5vzj
Deposition date deposition_date	2017-05-28
Structure title title	STRUCTURE OF A TWELVE COMPONENT MPP6-NUCLEAR RNA EXOSOME COMPLEX BOUND TO RNA
Keywords keywords	EXORIBONUCLEASE, COMPLEX, RNA, STRUCTURAL PROTEIN, 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.

5vzj__assembly_1__model_1

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

Download this curve (.dat)

5vzj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vzj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.58 Å
Rg (electron density)	52.29 Å
Total Rg	52.42 Å
Atom count	29434
Residues	3719
Excluded volume	524790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vzj__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 (18)

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	29498

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

Entity 2 Entity 2 polymer

Description description	Exosome complex component SKI6
Molecular weight formula_weight	28007.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPDHMSRLEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRVSNASAR

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

Entity 3 Entity 3 polymer

Description description	Exosome complex component RRP43
Molecular weight formula_weight	44060.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAESTTLETIEIHPITFPPEVLARISPELSLQRHLSLGIRPCLRKYEEFRDVAIENNTLSRYADAGNIDTKNNILGSNVLKSGKTIVITSITGGIIEETSAAIKDLDDFGEEELFEVTKEEDIIANYASVYPVVEVERGRVGACTDEEMTISQKLHDSILHSRILPKKALKVKAGVRSANEDGTFSVLYPDELEDDTLNETNLKMKRKWSYVLYAKIVVLSRTGPVFDLCWNSLMYALQSVKLPRAFIDERASDLRMTIRTRGRSATIRETYEIICDQTKSVPLMINAKNIAFASNYGIVELDPECQLQNSDNSEEEEVDIDMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLVGGGAKITPEMIKRSLLLSRVRADDLSTRFNI

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

Entity 4 Entity 4 polymer

Description description	Exosome complex component RRP46
Molecular weight formula_weight	24574.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTAEQLKISLSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNISPRLVV

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

Entity 5 Entity 5 polymer

Description description	Exosome complex component RRP42
Molecular weight formula_weight	29492.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GDPHMSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQVDVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPVSLISFAIYSALNSTYLPKLISAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLENL

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

Entity 6 Entity 6 polymer

Description description	Exosome complex component MTR3
Molecular weight formula_weight	27604.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MNVQDRRRLLGPAAAKPMAFSNTTTHVPEKKSTDLTPKGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLITAVYGPRSIRGSFTSQGTISIQLKNGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKMMSSQISSLIPHCITSITLALADAGIELVDMAGAGEANGTVVSFIKNGEEIVGFWKDDGDDEDLLECLDRCKEQYNRYRDLMISCLMNQET

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

Entity 7 Entity 7 polymer

Description description	Exosome complex component RRP40
Molecular weight formula_weight	26990.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GDPHMSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVKEE

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

Entity 8 Entity 8 polymer

Description description	Exosome complex component RRP4
Molecular weight formula_weight	39877.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GDPHMSEVITITKRNGAFQNSSNLSYNNTGISDDENDEEDIYMHDVNSASKSESDSQIVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNIRQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEKMRGNGN

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

Entity 9 Entity 9 polymer

Description description	Exosome complex component CSL4
Molecular weight formula_weight	32026.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GDPHMACNFQFPEIAYPGKLICPQYGTENKDGEDIIFNYVPGPGTKLIQYEHNGRTLEAITATLVGTVRCEEEKKTDQEEEREGTDQSTEEEKSVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANNLPKEGDIVLTRVTRLSLQRANVEILAVEDKPSPIDSGIGSNGSGIVAAGGGSGAATFSVSQASSDLGETFRGIIRSQDVRSTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTARNDLGVVFARAANGAGGLMYATDWQMMTSPVTGATEKRKCAKPF

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

Entity 10 Entity 10 polymer

Description description	Exosome complex exonuclease RRP6
Molecular weight formula_weight	64515.6 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	D238N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

SLMVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDLKNTKEIAVNLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNEEATPIPSSETKADGILLETISVPQIRDVMERFSVLCNSNISKSRAKPVTNSSILLGKILPREEHDIAYSKDGLPNKVKTEDIRIRAQNFKSALANLEDIIFEIEKPLVVPVKLEEIKTVDPASAPNHSPEIDNLDDLVVLKKKNIQKKQPAKEKGVTEKDAVDYSKI

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

Entity 11 Entity 11 polymer

Description description	Exosome complex exonuclease DIS3
Molecular weight formula_weight	114056.0 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	K

SLMSVPAIAPRRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQIVVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCFFDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFVERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTFPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK

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

Entity 12 Entity 12 polymer

Description description	M-phase phosphoprotein 6 homolog
Molecular weight formula_weight	4674.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

GSVKRVVYKKRPNLIISNVGYSELRKPEGVISGRKTFGDNSD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	ESCHERICHIA COLI

Entity 13 Entity 13 polymer

Description description	RNA (11-MER)
Molecular weight formula_weight	3438.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	M

UUAUUUUAAAA

Entity 14 Entity 14 polymer

Description description	RNA (19-MER)
Molecular weight formula_weight	5933.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	N

UUUAUUAUUUAUUUUAAAA

Entity 15 Entity 15 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 16 Entity 16 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

▼

6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id	5vzjA00
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	5vzjB00
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	5vzjC00
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	5vzjD00
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	5vzjE00
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	5vzjF00
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	5vzjG01
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	5vzjG02
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	5vzjG03
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	5vzjH01
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	5vzjJ01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	5vzjJ02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	5vzjK03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	700 —

Domain ID domain_id	5vzjK05
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

▶

Unit-cell length a length_a	141.090 Å
Unit-cell length b length_b	213.592 Å
Unit-cell length c length_c	225.909 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	44.247 Å
R factor r_factor	0.2192
R_work r_work	0.2167
R_free r_free	0.2659

STRUCTURE OF A TWELVE COMPONENT MPP6-NUCLEAR RNA EXOSOME COMPLEX BOUND TO RNA

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 RRP6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer