SAXSdb — 3wpt

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

Importin subunit alpha-1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 75–497	Fragment：UNP residues 75-497	PEG DI(HYDROXYETHYL)ETHER × 11	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；50MM MES, 100MM AMMONIUM SULFATE, 10MM MGCL, 15-20%(w/v) PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.63 Å R-free 0.216
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 75–497	Fragment：UNP residues 75-497	PEG DI(HYDROXYETHYL)ETHER × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；50MM MES, 100MM AMMONIUM SULFATE, 10MM MGCL, 15-20%(w/v) PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.63 Å R-free 0.216

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 3WPT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EFX STRUCTURE OF A COMPLEX BETWEEN THE HUMAN NATURAL KILLER CELL RECEPTOR KIR2DL2 AND A CLASS I MHC LIGAND HLA-CW3 Deposited 2000-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 204–212（9 aa） Fragment：RESIDUES 204-212	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 20000, calcium chloride, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.294
1QGK STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA Deposited 1999-04-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–54（44 aa） Fragment：IBB DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.273
1QGR STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA (II CRYSTAL FORM, GROWN AT LOW PH) Deposited 1999-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–54（27 aa） Fragment：IBB DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.9；pH 3.9	Resolution 2.30 Å R-free 0.285
3FEX Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 70–529（460 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.55 Å R-free 0.292
3FEX Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 70–529（460 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.55 Å R-free 0.292
3FEY Crystal structure of the CBC-importin alpha complex. Deposited 2008-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 70–529（460 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM MES, pH 6.0, and 8% PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.238
4E4V The crystal structure of the dimeric human importin alpha 1 at 2.5 angstrom resolution. Deposited 2012-03-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–529（460 aa） Fragment：Importin alpha 1 lacking IBB domain (UNP residues 70-529)	Mutation：K486R	GOL GLYCEROL × 8 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；298 K；0.5 CITRATE PH 5.4 10 MM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.53 Å R-free 0.203
4E4V The crystal structure of the dimeric human importin alpha 1 at 2.5 angstrom resolution. Deposited 2012-03-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 70–529（460 aa） Fragment：Importin alpha 1 lacking IBB domain (UNP residues 70-529)	Mutation：K486R	GOL GLYCEROL × 5 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；298 K；0.5 CITRATE PH 5.4 10 MM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.53 Å R-free 0.203
4WV6 Heterodimer of Importin alpha 1 with nuclear localization signal of TAF8 Deposited 2014-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 60–529（470 aa） Fragment：UNP residues 60-529	Not recorded	EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；281.15 K；HEPES-NaOH, polyethylene glycole 3350, L-proline	Resolution 1.75 Å R-free 0.180
5H43 Structural and mechanistical studies of the nuclear import by Importin-alpha Deposited 2016-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 70–497（428 aa） Fragment：UNP residues 70-497	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；3%(v/v) Tacsimate pH5.0, 0.1M Sodium citrate tribasic dehydrate pH5.6, 16%(w/v) PEG 3350	Resolution 2.30 Å R-free 0.243
7CRU hnRNPK NLS in complex with Importin alpha 1 (KPNA2) Deposited 2020-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 73–529（457 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000	Resolution 2.80 Å R-free 0.240
7CRU hnRNPK NLS in complex with Importin alpha 1 (KPNA2) Deposited 2020-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 73–529（457 aa）	Not recorded	ACT ACETATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000	Resolution 2.80 Å R-free 0.240
7N8J Human importin alpha 1 in complex with Bimax2 peptide Deposited 2021-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 76–529（454 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.4 M Ammonium phosphate monobasic	Resolution 3.20 Å R-free 0.244
7N9H Structure of the mammalian importin a1 bound to the TDP-43 NLS Deposited 2021-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 70–497（428 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.5M sodium citrate, 10 mM mercaptoethanol	Resolution 2.20 Å R-free 0.215
8FZK Dimeric human importin alpha subunit Deposited 2023-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 71–529（459 aa） Chain B 71–529（459 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；14% PEG 8000, 0.2M Magnesium chloride, 0.1M MES	Resolution 2.10 Å R-free 0.247
8FZK Dimeric human importin alpha subunit Deposited 2023-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 71–529（459 aa） Chain D 71–529（459 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；14% PEG 8000, 0.2M Magnesium chloride, 0.1M MES	Resolution 2.10 Å R-free 0.247
8GCN CRYO-EM STRUCTURE OF IMPORTIN ALPHA1/BETA HETERODIMER Deposited 2023-03-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–53（43 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
9B4Y Cryo-EM structure of importin alpha-1/beta bound to TDP-43 Deposited 2024-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–53（43 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
9BFC Cryo-EM structure of importin alpha-1/beta bound to FG repeats Deposited 2024-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: hexameric	Chain I 1–53（53 aa）	Not recorded	PHE PHENYLALANINE × 2 GLY GLYCINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9N86 Cryo-EM structure of human importin beta:importin alpha (IBB) complex Deposited 2025-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–53（53 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–423； UniProt 75–497 Author chain B； PDBConstruct 1–423； UniProt 75–497

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	3wpt
Deposition date deposition_date	2014-01-17
Structure title title	Crystal structure of closed dimer of human importin-alpha1 (Rch1)
Keywords keywords	;Arm repeat, All Alpha protein, Armadillo repeat, Closed dimer, Nuclear transport, importin-beta, NLS-carring proteins, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
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	30.71 Å
Radius of gyration Rg (electron density) rg_electron	30.02 Å
Forward intensity I(0) i0	128232000.00
Molecular weight molecular_weight	93128.0 kDa
Excluded volume excluded_volume	118080 Å³
Envelope volume envelope_volume	144510 Å³
Hydration-shell volume shell_volume	40535 Å³
Envelope diameter envelope_diameter	104.0 Å
Shell Rg shell_rg	37.09 Å
Envelope Rg envelope_rg	29.73 Å
Shape Rg shape_rg	30.03 Å
Total Rg total_rg	30.64 Å
Total atoms total_atoms	13292
Residues n_residues	845
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	100.5 Å
Rg (real space) rg_real	30.75 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	1.2820e+08
I(0) uncertainty (real space) i0_real_error	1.7340e+06
Rg (reciprocal space) rg_reciprocal	30.73 Å
I(0) (reciprocal space) i0_reciprocal	128200000.0000
Solution quality estimate total_estimate	0.8766
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	32950000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.851

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Importin subunit alpha-1
Molecular weight formula_weight	45773.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13491

NWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYFS

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wpta_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.1 — Armadillo repeat

Domain ID domain_id	d3wptb_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.1 — Armadillo repeat

CATH v4.4 (2 domains)

Domain ID domain_id	3wptA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	3wptB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	139.299 Å
Unit-cell length b length_b	139.299 Å
Unit-cell length c length_c	141.288 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.629 Å
Low-resolution limit resolution_low	46.505 Å
R factor r_factor	0.1910
R_work r_work	0.1896
R_free r_free	0.2160

fit	/app/data/saxs_computation/wp/3wpt/3wpt.fit
pddf	/app/data/pr_computation/wp/3wpt/3wpt.pr.out
profile	/app/data/saxs_computation/wp/3wpt/3wpt.dat

Crystal structure of closed dimer of human importin-alpha1 (Rch1)

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

Importin subunit alpha-1

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