SAXSdb — 9dso

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

;5'-3' exoribonuclease 2 ;

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Decapping nuclease RAI1 × 1 （P53063） Regulator of Ty1 transposition protein 103 × 1 （Q05543） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRN2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–981； UniProt 1–981

Decapping nuclease RAI1

Saccharomyces cerevisiae

UniProt P53063

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	;5'-3' exoribonuclease 2 ; × 1 （Q02792） Regulator of Ty1 transposition protein 103 × 1 （Q05543） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DXO_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–387； UniProt 1–387

Regulator of Ty1 transposition protein 103

Saccharomyces cerevisiae

UniProt Q05543

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	;5'-3' exoribonuclease 2 ; × 1 （Q02792） Decapping nuclease RAI1 × 1 （P53063） MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RT103_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 21–429； UniProt 1–409

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	9dso
Deposition date deposition_date	2024-09-28
Last revision last_revision	2025-04-16
Structure title title	CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX
Keywords keywords	Nuclease, Complex, Transcription termination, TRANSCRIPTION; TRANSCRIPTION
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.

9dso__assembly_1__model_1

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

Download this curve (.dat)

9dso__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dso__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.30 Å
Rg (electron density)	35.64 Å
Total Rg	36.06 Å
Atom count	8975
Residues	1115
Excluded volume	159970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dso__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	;5'-3' exoribonuclease 2 ;
Molecular weight formula_weight	114204.0 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	A
Atom count atom_count	8975

MGVPSFFRWLSRKYPKIISPVLEEQPQIVDGVILPLDYSASNPNGELDNLYLDMNGIVHPCSHPENKPPPETEDEMLLAVFEYTNRVLNMARPRKVLVMAVDGVAPRAKMNQQRARRFRSARDAQIENEAREEIMRQREEVGEIIDDAVRNKKTWDSNAITPGTPFMDKLAAALRYWTAFKLATDPGWKNLQVIISDATVPGEGEHKIMNFIRSQRADPEYNPNTTHCIYGLDADLIFLGLATHEPHFKILREDVFAQDNRKRNNLKDTINMTEEEKQFLQKQNSEQPFLWLHINVLREYLSAELWVPGLPFTFDLERAIDDWVFMCFFCGNDFLPHLPCLDVRENSIDILLDIWKVVLPKLKTYMTCDGVLNLPSVETLLQHLGSREGDIFKTRHIQEARKKEAFERRKAQKNMSKGQDRHPTVATEQLQMYDTQGNLAKGSWNLTTSDMVRLKKELMLANEGNEEAIAKVKQQSDKNNELMKDISKEEIDDAVSKANKTNFNLAEVMKQKIINKKHRLEKDNEEEEIAKDSKKVKTEKAESECDLDAEIKDEIVADVNDRENSETTEVSRDSPVHSTVNVSEGPKNGVFDTDEFVKLFEPGYHERYYTAKFHVTPQDIEQLRKDMVKCYIEGVAWVLMYYYQGCASWNWFYPYHYAPLATDFHGFSHLEIKFEEGTPFLPYEQLMSVLPAASGHALPKIFRSLMSEPDSEIIDFYPEEFPIDMNGKKMSWQGIALLPFIDQDRLLTAVRAQYPLLSDAERARNIRGEPVLLISNKNANYERFSKKLYSKENNNNNVVVKFQHFKSGLSGIVSKDVEGFELNGKIVCPIQGGSLPNLSTTLILKMSYRLIPLPSRNKSIILNGFIPSEPVLTAYDLDSIMYKYNNQNYSRRWNFGNDLKQNIVPVGPKGITQYKPRTGGYRAFFYFAELSRNNVQPAHNYGRNSYNSQPGFNNSRYDGGNNNYRQNSNYRNNKYSGNRNSLEHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Decapping nuclease RAI1
Molecular weight formula_weight	44571.4 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGVSANLFVKQRGSTTALKQPKEIGFYSRTKDEEYLISDDTNLNYYYLPDAELDRKLDLSSGFQKFKDYYKDFEDRCSLRGLLETIESSERHKGKKINADIITFRGIARKLISCAFDSPSFNTVDLRIVSFNGQLFIKEVPEAVNAAKASSATEAGRNINQDLNVFTGYKFETLATLSNPLQYTPREVIEKRTKRIVSHGDEYISVVRTGVGNCKLILGAEVDCIFDFKENGRDNLKHYAELKCTQQVANISDTHKFERKLFRTWLQCFLVGIPRIIYGFKDDHYVLKTVEEFSTEEVPVLLKNNNPQVGSACLEAIKWYGLLTEWLLKMIPRDEDPHSQIRAFKLVFENNHLRLSEIEESDEEYSGLIDGEHILSNGFKEWRKSLK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Regulator of Ty1 transposition protein 103
Molecular weight formula_weight	48725.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSSGLVPRGSHMPFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSKQVVNDIERSLKTESSPVEALVLPQKLKDFAKDYEKLVKMHHNVCAMKMRFDKSSDELDPSSSVYEENFKTISKIGNMAKDIINESILKRESGIHKLQSTLDDEKRHLDEEQNMLSEIEFVLSAKDPSRLNKNVDEDNIIPTYEVGDGDDDDDDGDNDDDDDDDDDDKNYDDRSNDSNYGVTNISTTDKKNEVVEKTDSEHKNSTHNPSDNQFGMKRTHDMIGHDDANDIPEKKVHLDSKTSEDGTFNSEDGHYELDIEGHVGAQTDEGVENSGGVSSSIQDLLSKLAN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 non-polymer

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

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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	2.85 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	552608

CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX

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

;5'-3' exoribonuclease 2 ;

State in the Current Structure

Other States of the Same Protein in the Database

Decapping nuclease RAI1

State in the Current Structure

Other States of the Same Protein in the Database

Regulator of Ty1 transposition protein 103

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9dso__assembly_1__model_1

9dso__assembly_1__model_1 | I(q)

9dso__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)

CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX

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

;5'-3' exoribonuclease 2 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Decapping nuclease RAI1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Regulator of Ty1 transposition protein 103

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9dso__assembly_1__model_1

9dso__assembly_1__model_1 | I(q)

9dso__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)