SAXSdb — 7qe0

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

Helicase SKI2W

Homo sapiens

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 Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–1246	Not recorded	;RNA (5'-R(PUPUPUPUPUPUPUPUP*U)-3') ; × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE	Resolution 6.50 Å

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 7QE0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7QDR Apo human SKI complex in the closed state Deposited 2021-11-29	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1246（1246 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 3.70 Å
7QDS Apo human SKI complex in the open state Deposited 2021-11-30	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1246（1246 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 3.80 Å
7QDY RNA-bound human SKI complex Deposited 2021-12-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain A 1–1246（1246 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 3.10 Å
7QDZ 80S-bound human SKI complex in the closed state Deposited 2021-12-01	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain A 1–1246（1246 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 3.60 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric	Chain A 1–1246（1246 aa）	Not recorded	MG MAGNESIUM ION × 232 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
9G8N 80S-bound human Ski2-exosome complex Deposited 2024-07-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain A 1–1246（1246 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 3.70 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain A 1–1246（1246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
9G8P 40S-bound human SKI2-exosome complex Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 13-meric	Chain A 1–1246（1246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.00 Å
9G8Q 40S-bound human SKI238 complex in the open state (Gatekeeping module) Deposited 2024-07-23	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1246（1246 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.10 Å
9G8R human SKI7-SKI238 complex in the open state Deposited 2024-07-23	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–774（774 aa） Chain A 1049–1246（198 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

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SKIV2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1246； UniProt 1–1246

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	7qe0
Deposition date deposition_date	2021-12-01
Structure title title	80S-bound human SKI complex in the open state
Keywords keywords	multiprotein complex, RNA helicase, DExH-box helicase, ATPase, RNA binding, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	37.63 Å
Radius of gyration Rg (electron density) rg_electron	37.49 Å
Forward intensity I(0) i0	186643000.00
Molecular weight molecular_weight	108670.0 kDa
Excluded volume excluded_volume	135790 Å³
Envelope volume envelope_volume	201590 Å³
Hydration-shell volume shell_volume	45732 Å³
Envelope diameter envelope_diameter	117.4 Å
Shell Rg shell_rg	42.65 Å
Envelope Rg envelope_rg	36.76 Å
Shape Rg shape_rg	37.50 Å
Total Rg total_rg	37.82 Å
Total atoms total_atoms	7618
Residues n_residues	958
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	117.2 Å
Rg (real space) rg_real	37.70 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.8660e+08
I(0) uncertainty (real space) i0_real_error	2.9480e+06
Rg (reciprocal space) rg_reciprocal	37.66 Å
I(0) (reciprocal space) i0_reciprocal	186600000.0000
Solution quality estimate total_estimate	0.8615
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.3 Å
Skewness Skewness skewness	0.290
Kurtosis Kurtosis kurtosis	-0.686
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	37220000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.352

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Helicase SKI2W
Molecular weight formula_weight	137913.7 kDa
EC 编号 ec_number	3.6.4.-
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	7618

MMETERLVLPPPDPLDLPLRAVELGCTGHWELLNLPGAPESSLPHGLPPCAPDLQQEAEQLFLSSPAWLPLHGVEHSARKWQRKTDPWSLLAVLGAPVPSDLQAQRHPTTGQILGYKEVLLENTNLSATTSLSLRRPPGPASQSLWGNPTQYPFWPGGMDEPTITDLNTREEAEEEIDFEKDLLTIPPGFKKGMDFAPKDCPTPAPGLLSLSCMLEPLDLGGGDEDENEAVGQPGGPRGDTVSASPCSAPLARASSLEDLVLKEASTAVSTPEAPEPPSQEQWAIPVDATSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEASCLIMTTEILRSMLYSGSDVIRDLEWVIFDEVHYINDVERGVVWEEVLIMLPDHVSIILLSATVPNALEFADWIGRLKRRQIYVISTVTRPVPLEHYLFTGNSSKTQGELFLLLDSRGAFHTKGYYAAVEAKKERMSKHAQTFGAKQPTHQGGPAQDRGVYLSLLASLRTRAQLPVVVFTFSRGRCDEQASGLTSLDLTTSSEKSEIHLFLQRCLARLRGSDRQLPQVLHMSELLNRGLGVHHSGILPILKEIVEMLFSRGLVKVLFATETFAMGVNMPARTVVFDSMRKHDGSTFRDLLPGEYVQMAGRAGRRGLDPTGTVILLCKGRVPEMADLHRMMMGKPSQLQSQFRLTYTMILNLLRVDALRVEDMMKRSFSEFPSRKDSKAHEQALAELTKRLGALEEPDMTGQLVDLPEYYSWGEELTETQHMIQRRIMESVNGLKSLSAGRVVVVKNQEHHNALGVILQVSSNSTSRVFTTLVLCDKPLSQDPQDRGPATAEVPYPDDLVGFKLFLPEGPCDHTVVKLQPGDMAAITTKVLRVNGEKILEDFSKRQQPKFKKDPPLAAVTTAVQELLRLAQAHPAGPPTLDPVNDLQLKDMSVVEGGLRARKLEELIQGAQCVHSPRFPAQYLKLRERMQIQKEMERLRFLLSDQSLLLLPEYHQRVEVLRTLGYVDEAGTVKLAGRVACAMSSHELLLTELMFDNALSTLRPEEIAALLSGLVCQSPGDAGDQLPNTLKQGIERVRAVAKRIGEVQVACGLNQTVEEFVGELNFGLVEVVYEWARGMPFSELAGLSGTPEGLVVRCIQRLAEMCRSLRGAARLVGEPVLGAKMETAATLLRRDIVFAASLYTQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUP*U)-3') ;
Molecular weight formula_weight	2710.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

UUUUUUUUU

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8. Citations (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	6.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	76838

fit	/app/data/saxs_computation/qe/7qe0/7qe0.fit
pddf	/app/data/pr_computation/qe/7qe0/7qe0.pr.out
profile	/app/data/saxs_computation/qe/7qe0/7qe0.dat

80S-bound human SKI complex in the open state

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

Helicase SKI2W

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)