SAXSdb — 3tj3

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 66–512	Fragment：UNP residues 66-512	Nuclear pore complex protein Nup50 × 1 （Q9UKX7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 66–512	Fragment：UNP residues 66-512	Nuclear pore complex protein Nup50 × 1 （Q9UKX7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.255

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 3TJ3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JDQ C-terminal domain of influenza A virus polymerase PB2 subunit in complex with human importin alpha5 Deposited 2007-01-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–512（447 aa） Fragment：RESIDUES 66-512	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；1 MICROLITRE OF PROTEIN SOLUTION, AT 20 MG/ML IN 30 MM TRIS-HCL, PH 7.5, 150 MM NACL, 3 MM BETA-MERCAPTOETHANOL WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M NAAC, PH 4.6, 5 MM CACL2, 15% MPD)	Resolution 2.20 Å R-free 0.247
2JDQ C-terminal domain of influenza A virus polymerase PB2 subunit in complex with human importin alpha5 Deposited 2007-01-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–512（447 aa） Fragment：RESIDUES 66-512	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；1 MICROLITRE OF PROTEIN SOLUTION, AT 20 MG/ML IN 30 MM TRIS-HCL, PH 7.5, 150 MM NACL, 3 MM BETA-MERCAPTOETHANOL WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M NAAC, PH 4.6, 5 MM CACL2, 15% MPD)	Resolution 2.20 Å R-free 0.247
4B18 The crystal structure of human Importin alpha 5 with TERT NLS peptide Deposited 2012-07-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–512（447 aa） Fragment：RESIDUES 66-512	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.52 Å R-free 0.253
6WX9 SOX2 bound to Importin-alpha 5 Deposited 2020-05-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 73–538（466 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2M sodium/potassium phosphate, 20% (w/v) PEG3350	Resolution 2.80 Å R-free 0.251

3 other PDB entries and 4 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 1–447； UniProt 66–512 Author chain B； PDBConstruct 1–447； UniProt 66–512

Nuclear pore complex protein Nup50

Homo sapiens

UniProt Q9UKX7

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–109	Fragment：N-terminal domain (UNP residues 1-109)	Importin subunit alpha-1 × 1 （P52294）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–109	Fragment：N-terminal domain (UNP residues 1-109)	Importin subunit alpha-1 × 1 （P52294）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.255

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 3TJ3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EC1 Solution structure of the RanBD1 domain from human Nucleoporin 50 kDa Deposited 2007-02-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 351–468（118 aa） Fragment：RanBP domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.14 mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
7MO0 Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 337–468（132 aa） Fragment：RAN-binding domain of NUP50 (UNP residues 337-468)	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；25% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES	Resolution 2.45 Å R-free 0.239
7MO0 Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 337–468（132 aa） Fragment：RAN-binding domain of NUP50 (UNP residues 337-468)	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；25% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES	Resolution 2.45 Å R-free 0.239

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUP50_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–114； UniProt 1–109 Author chain D； PDBConstruct 6–114； UniProt 1–109

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	3tj3
Deposition date deposition_date	2011-08-23
Structure title title	Structure of importin a5 bound to the N-terminus of Nup50
Keywords keywords	ARMADILLO repeat, nuclear import adaptor, NLS-bearing proteins, nucleo-cytoplasmic shuttling, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	34.33 Å
Radius of gyration Rg (electron density) rg_electron	33.92 Å
Forward intensity I(0) i0	170733000.00
Molecular weight molecular_weight	105610.0 kDa
Excluded volume excluded_volume	132730 Å³
Envelope volume envelope_volume	172590 Å³
Hydration-shell volume shell_volume	42366 Å³
Envelope diameter envelope_diameter	113.7 Å
Shell Rg shell_rg	40.49 Å
Envelope Rg envelope_rg	33.50 Å
Shape Rg shape_rg	33.92 Å
Total Rg total_rg	34.43 Å
Total atoms total_atoms	7415
Residues n_residues	953
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	112.6 Å
Rg (real space) rg_real	34.29 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	1.7070e+08
I(0) uncertainty (real space) i0_real_error	2.7770e+06
Rg (reciprocal space) rg_reciprocal	34.32 Å
I(0) (reciprocal space) i0_reciprocal	170700000.0000
Solution quality estimate total_estimate	0.8956
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.1 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52920000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.912

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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	49401.3 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	7545

GFHEAQISNMEMAPGGVITSDMIEMIFSKSPEQQLSATQKFRKLLSKEPNPPIDEVISTPGVVARFVEFLKRKENCTLQFESAWVLTNIASGNSLQTRIVIQAGAVPIFIELLSSEFEDVQEQAVWALGNIAGDSTMCRDYVLDCNILPPLLQLFSKQNRLTMTRNAVWALSNLCRGKSPPPEFAKVSPCLNVLSWLLFVSDTDVLADACWALSYLSDGPNDKIQAVIDAGVCRRLVELLMHNDYKVVSPALRAVGNIVTGDDIQTQVILNCSALQSLLHLLSSPKESIKKEACWTISNITAGNRAQIQTVIDANIFPALISILQTAEFRTRKEAAWAITNATSGGSAEQIKYLVELGCIKPLCDLLTVMDSKIVQVALNGLENILRLGEQEAKRNGTGINPYCALIEEAYGLDKIEFLQSHENQEIYQKAFDLIEHYFGTEDEDSS

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 polymer

Description description	Nuclear pore complex protein Nup50
Molecular weight formula_weight	11806.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GPLGSMAKRNAEKELTDRNWDQEDEAEEVGTFSMASEEVLKNRAIKKAKRRNVGFESDTGGAFKGFKGLVVPSGGGRFSGFGSGAGGKPLEGLSNGNNITSAPPFASAKAAADP

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3tj3a_
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.118.1.0 — automated matches

Domain ID domain_id	d3tj3b_
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.118.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3tj3A00
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	3tj3B00
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	81.683 Å
Unit-cell length b length_b	98.291 Å
Unit-cell length c length_c	135.352 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.702 Å
Low-resolution limit resolution_low	15.028 Å
R factor r_factor	0.2170
R_work r_work	0.2149
R_free r_free	0.2553

fit	/app/data/saxs_computation/tj/3tj3/3tj3.fit
pddf	/app/data/pr_computation/tj/3tj3/3tj3.pr.out
profile	/app/data/saxs_computation/tj/3tj3/3tj3.dat

Structure of importin a5 bound to the N-terminus of Nup50

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

Nuclear pore complex protein Nup50

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)