SAXSdb — 5sup

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

ATP-dependent RNA helicase SUB2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 61–446	Fragment：residues 61-446	RNA annealing protein YRA1 × 1 （Q12159） ;RNA (5'-R(PUPUPUPUPUPU)-3') ; × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate	Resolution 2.60 Å R-free 0.268
2	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 61–446	Fragment：residues 61-446	RNA annealing protein YRA1 × 1 （Q12159） ;RNA (5'-R(PUPUPUPUPUPU)-3') ; × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate	Resolution 2.60 Å R-free 0.268
3	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 61–446	Fragment：residues 61-446	RNA annealing protein YRA1 × 1 （Q12159） ;RNA (5'-R(PUPUPUPUPUPU)-3') ; × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate	Resolution 2.60 Å R-free 0.268

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5SUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5SUQ Crystal structure of the THO-Sub2 complex Deposited 2016-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–446（446 aa） Chain C 1–446（446 aa）	Not recorded	KEG 12-TUNGSTOPHOSPHATE × 11	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.4；289 K；100 mM Tris-HCl (pH 8.4), 17.5% PEG3350, 2% methanol, 0.3 M NDSB-195	Resolution 6.00 Å R-free 0.434
7APX yeast THO-Sub2 complex Deposited 2020-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 48–446（399 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
7LUV Cryo-EM structure of the yeast THO-Sub2 complex Deposited 2021-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 1–446（446 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7V2Y cryo-EM structure of yeast THO complex with Sub2 Deposited 2021-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 1–446（446 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8U8C Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2 Deposited 2023-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–55（55 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.5, and 20% PEG3350	Resolution 2.40 Å R-free 0.231

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUB2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–390； UniProt 61–446 Author chain B； PDBConstruct 5–390； UniProt 61–446 Author chain C； PDBConstruct 5–390； UniProt 61–446

RNA annealing protein YRA1

Saccharomyces cerevisiae

UniProt Q12159

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain H； UniProt 200–226	Fragment：residues 200-226	ATP-dependent RNA helicase SUB2 × 1 （Q07478） ;RNA (5'-R(PUPUPUPUPUPU)-3') ; × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate	Resolution 2.60 Å R-free 0.268
2	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain G； UniProt 200–226	Fragment：residues 200-226	ATP-dependent RNA helicase SUB2 × 1 （Q07478） ;RNA (5'-R(PUPUPUPUPUPU)-3') ; × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate	Resolution 2.60 Å R-free 0.268
3	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain I； UniProt 200–226	Fragment：residues 200-226	ATP-dependent RNA helicase SUB2 × 1 （Q07478） ;RNA (5'-R(PUPUPUPUPUPU)-3') ; × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；277 K；100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate	Resolution 2.60 Å R-free 0.268

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	YRA1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 6–32； UniProt 200–226 Author chain H； PDBConstruct 6–32； UniProt 200–226 Author chain I； PDBConstruct 6–32； UniProt 200–226

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	5sup
Deposition date deposition_date	2016-08-03
Structure title title	Crystal structure of the Sub2-Yra1 complex in association with RNA
Keywords keywords	mRNA export, HYDROLASE-RNA complex; HYDROLASE/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.97 Å
Radius of gyration Rg (electron density) rg_electron	37.51 Å
Forward intensity I(0) i0	325956000.00
Molecular weight molecular_weight	144000.0 kDa
Excluded volume excluded_volume	179070 Å³
Envelope volume envelope_volume	228870 Å³
Hydration-shell volume shell_volume	51235 Å³
Envelope diameter envelope_diameter	132.4 Å
Shell Rg shell_rg	43.19 Å
Envelope Rg envelope_rg	37.32 Å
Shape Rg shape_rg	37.49 Å
Total Rg total_rg	37.88 Å
Total atoms total_atoms	10100
Residues n_residues	1214
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	125.4 Å
Rg (real space) rg_real	38.04 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	3.2600e+08
I(0) uncertainty (real space) i0_real_error	5.1170e+06
Rg (reciprocal space) rg_reciprocal	38.00 Å
I(0) (reciprocal space) i0_reciprocal	325900000.0000
Solution quality estimate total_estimate	0.8855
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.8 Å
Skewness Skewness skewness	0.323
Kurtosis Kurtosis kurtosis	-0.567
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	177000000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.862

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	ATP-dependent RNA helicase SUB2
Molecular weight formula_weight	44462.9 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	10127

GAMGSTGFKDFLLKPELSRAIIDCGFEHPSEVQQHTIPQSIHGTDVLCQAKSGLGKTAVFVLSTLQQLDPVPGEVAVVVICNARELAYQIRNEYLRFSKYMPDVKTAVFYGGTPISKDAELLKNKDTAPHIVVATPGRLKALVREKYIDLSHVKNFVIDECDKVLEELDMRRDVQEIFRATPRDKQVMMFSATLSQEIRPICRRFLQNPLEIFVDDEAKLTLHGLQQYYIKLEEREKNRKLAQLLDDLEFNQVIIFVKSTTRANELTKLLNASNFPAITVHGHMKQEERIARYKAFKDFEKRICVSTDVFGRGIDIERINLAINYDLTNEADQYLHRVGRAGRFGTKGLAISFVSSKEDEEVLAKIQERFDVKIAEFPEEGIDPSTYLNN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RNA annealing protein YRA1
Molecular weight formula_weight	3679.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

GAMGSNKPKREKPAKKSLEDLDKEMADYFEKK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	4547.5 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,E,F

UUUUUUUUUUUUUUU

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5supA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5supA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5supB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5supB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5supC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5supC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	99.346 Å
Unit-cell length b length_b	99.346 Å
Unit-cell length c length_c	247.469 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	18

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	49.673 Å
R factor r_factor	0.2213
R_work r_work	0.2189
R_free r_free	0.2676

fit	/app/data/saxs_computation/su/5sup/5sup.fit
pddf	/app/data/pr_computation/su/5sup/5sup.pr.out
profile	/app/data/saxs_computation/su/5sup/5sup.dat

Crystal structure of the Sub2-Yra1 complex in association with RNA

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

ATP-dependent RNA helicase SUB2

State in the Current Structure

Other States of the Same Protein in the Database

RNA annealing protein YRA1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)