4oo1

Structure of an Rrp6-RNA exosome complex bound to poly(A) 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

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt P46948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt P25359

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt P53256

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt Q12277

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt P48240

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt Q08285

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt P38792

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt P53859

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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

UniProt Q12149

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 10 RNA 1	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） POLY A RNA × 1 MAGNESIUM ION × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PHOSPHATE ION × 2	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 4–560； UniProt 129–685

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	4oo1
Deposition date deposition_date	2014-01-29
Structure title title	Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA
Keywords keywords	RNA EXOSOME COMPLEX, RNA PROCESSING/DECAY, NUCLEUS, RNA BINDING PROTEIN-RNA complex, 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.

4oo1__assembly_1__model_1

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

Download this curve (.dat)

4oo1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4oo1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.75 Å
Rg (electron density)	43.11 Å
Total Rg	43.47 Å
Atom count	21590
Residues	2747
Excluded volume	385520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4oo1__assembly_1__model_1`	undecameric （11）	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	21590

MAKDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLTSENAREI

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 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
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
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
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
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
EC 编号 ec_number	3.1.13.-
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
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
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
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
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	64612.7 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

SLMVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESMLEDLKNTKEIAVNLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIEKESPWKILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNTNEEATPIPSSETKADGILLETISVPQIRDVMERFSVLCNSNISKSRAKPVTNSSILLGKILPREEHDIAYSKDGLPNKVKTEDIRIRAQNFKSALANLEDIIFEIEKPLVVPVKLEEIKTVDPASAPNHSPEIDNLDDLVVLKKKNIQKKQPAKEKGVTEKDAVDYSKIP

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 11 Entity 11 polymer

Description description	POLY A RNA
Molecular weight formula_weight	7856.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	S

AAAAAAAAAAAAAAAAAAAAAAAA

Entity 12 Entity 12 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id	4oo1A00
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	4oo1B00
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	4oo1C00
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	4oo1D00
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	4oo1E00
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	4oo1F00
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	4oo1G01
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	4oo1G02
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	4oo1G03
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	4oo1H01
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	4oo1I01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	880 —

Domain ID domain_id	4oo1I02
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	4oo1J01
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	4oo1J02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

▶

Unit-cell length a length_a	193.292 Å
Unit-cell length b length_b	200.083 Å
Unit-cell length c length_c	97.405 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	48.426 Å
R factor r_factor	0.2288
R_work r_work	0.2268
R_free r_free	0.2649

Structure of an Rrp6-RNA exosome complex bound to poly(A) 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