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9qno

Ternary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 - focussed refinement on Importin-9 and Akirin-2

Method: ELECTRON MICROSCOPY Dmax: 99.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Akirin-2

Homo sapiens

UniProt Q53H80

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 1–203 Chain E； UniProt 1–203 Not recorded Importin-9 × 1 （Q96P70） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.20 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 9QNO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7NHT Akirin2 bound human proteasome Deposited 2021-02-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain c 1–203（203 aa）
Chain d 1–203（203 aa）
Not recorded K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9QON Ternary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 - focussed refinement on the alpha subunits, Ipo-9 and Ak2 Deposited 2025-03-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric
Chain B 1–203（203 aa）
Chain C 1–203（203 aa）
Chain D 1–203（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9QOO Composite model: Ternary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 Deposited 2025-03-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain B 1–203（203 aa）
Chain C 1–203（203 aa）
Chain D 1–203（203 aa）
Chain I 1–203（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9QOP Binary complex of human Importin-9 with one homodimer of Akirin-2 Deposited 2025-03-26 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–203（203 aa）
Chain C 1–203（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AKIR2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain D； PDBConstruct 1–203； UniProt 1–203 Author chain E； PDBConstruct 1–203； UniProt 1–203

Importin-9

Homo sapiens

UniProt Q96P70

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1041 Not recorded Akirin-2 × 2 （Q53H80） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.20 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 9QNO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10SM Importin-9 bound to ETS homologous factor (EHF) Deposited 2026-02-05 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–1041（1041 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1041（1041 aa） Fragment：IMPORTIN-9
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
Resolution 2.70 Å R-free 0.238
6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–1041（1041 aa） Fragment：IMPORTIN-9
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
Resolution 2.70 Å R-free 0.238
8F7A Cryo-EM structure of Importin-9 bound to RanGTP Deposited 2022-11-18 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1041（1041 aa） Fragment：IMPORTIN-9
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
9QON Ternary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 - focussed refinement on the alpha subunits, Ipo-9 and Ak2 Deposited 2025-03-26 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric
Chain A 1–1041（1041 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9QOO Composite model: Ternary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 Deposited 2025-03-26 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 1–1041（1041 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9QOP Binary complex of human Importin-9 with one homodimer of Akirin-2 Deposited 2025-03-26 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1041（1041 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IPO9_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–1041； UniProt 1–1041

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9qno

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qno
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qno
Deposition date deposition_date2025-03-25
Structure title titleTernary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 - focussed refinement on Importin-9 and Akirin-2
Keywords keywords20S proteasome, 20S, proteasome, nuclear iport, akirin, akirin2, importin 9, importin, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.11 Å
Radius of gyration Rg (electron density) rg_electron33.65 Å
Forward intensity I(0) i067555500.00
Molecular weight molecular_weight55679.0 kDa
Excluded volume excluded_volume65770 ų
Envelope volume envelope_volume127110 ų
Hydration-shell volume shell_volume32175 ų
Envelope diameter envelope_diameter98.1 Å
Shell Rg shell_rg40.23 Å
Envelope Rg envelope_rg31.20 Å
Shape Rg shape_rg33.61 Å
Total Rg total_rg34.41 Å
Total atoms total_atoms6271
Residues n_residues747
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax99.9 Å
Rg (real space) rg_real33.95 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real6.7560e+07
I(0) uncertainty (real space) i0_real_error8.8240e+05
Rg (reciprocal space) rg_reciprocal34.06 Å
I(0) (reciprocal space) i0_reciprocal67560000.0000
Solution quality estimate total_estimate0.8988
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary56.5 Å
Skewness Skewness skewness-0.075
Kurtosis Kurtosis kurtosis-0.916
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9194000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.951
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)