SAXSdb — 1xk5

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

snurportin-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 97–300	Fragment：m3G-cap-binding domain comprising amino acids 97-300	TPG 2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；8% PEG20K, 100mM MES pH6.0 for initial crystals and 200mM sodium citrate pH5.5 for larger crystals after seeding, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.276

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 1XK5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2P8Q Crystal Structure of human Importin beta bound to the Snurportin1 IBB-domain Deposited 2007-03-22	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 25–64（40 aa） Fragment：N-terminal domain (25-64)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；285 K；22%PEG 8000, 0.05M Sodium Chloride, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.35 Å R-free 0.250
2Q5D Crystal Structure of Human Importin Beta bound to the Snurportin1 IBB-domain second crystal form Deposited 2007-05-31	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 25–64（40 aa） Fragment：N-terminal domain (25-64)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；285 K；22%PEG 8000, 0.05M SODIUM CHLORIDE 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.20 Å R-free 0.328
2Q5D Crystal Structure of Human Importin Beta bound to the Snurportin1 IBB-domain second crystal form Deposited 2007-05-31	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 D 25–64（40 aa） Fragment：N-terminal domain (25-64)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；285 K；22%PEG 8000, 0.05M SODIUM CHLORIDE 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.20 Å R-free 0.328
2QNA Crystal structure of human Importin-beta (127-876) in complex with the IBB-domain of Snurportin1 (1-65) Deposited 2007-07-18	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 1–66（66 aa） Fragment：residues 1-66	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.55；283 K；sodium citrate, Ammonium SO4, Ethanol, NaCl, Tris, pH 5.55, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.84 Å R-free 0.282
3GB8 Crystal structure of CRM1/Snurportin-1 complex Deposited 2009-02-19	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 1–328（328 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；8% PEG 8000, 0.2M Magnesium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.90 Å R-free 0.267
3GJX Crystal Structure of the Nuclear Export Complex CRM1-Snurportin1-RanGTP Deposited 2009-03-09	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 B 1–360（360 aa）	Not recorded	NA SODIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 1000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 1000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.281
3GJX Crystal Structure of the Nuclear Export Complex CRM1-Snurportin1-RanGTP Deposited 2009-03-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–360（360 aa）	Not recorded	NA SODIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 1000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 1000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.281
3LWW Structure of an open and closed conformation of Human Importin Beta bound to the Snurportin1 IBB-domain trapped in the same crystallographic asymmetric unit Deposited 2010-02-24	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 25–64（40 aa） Fragment：Snurportin1 N-terminal domain (25-64)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18% PEG 8000, 50 mM sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.313
3LWW Structure of an open and closed conformation of Human Importin Beta bound to the Snurportin1 IBB-domain trapped in the same crystallographic asymmetric unit Deposited 2010-02-24	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 D 25–64（40 aa） Fragment：Snurportin1 N-terminal domain (25-64)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18% PEG 8000, 50 mM sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.313
3NBY Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex Deposited 2010-06-04	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 B 15–360（346 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.1 M Tris/HCl pH range 8.08-8.30, 10-14% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.42 Å R-free 0.315
3NBY Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex Deposited 2010-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 15–360（346 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.1 M Tris/HCl pH range 8.08-8.30, 10-14% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.42 Å R-free 0.315
3NBZ Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal I) Deposited 2010-06-04	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 B 15–360（346 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；289 K；0.1 M Tris/HCl, 16% (w/v) PEG 1000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.285
3NBZ Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal I) Deposited 2010-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 15–360（346 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；289 K；0.1 M Tris/HCl, 16% (w/v) PEG 1000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.285
3NC0 Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II) Deposited 2010-06-04	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 B 15–360（346 aa）	Not recorded	GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.295
3NC0 Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II) Deposited 2010-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 15–360（346 aa） Chain E 15–360（346 aa）	Not recorded	GOL GLYCEROL × 10 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.295
5DIS Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214 Deposited 2015-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–287（287 aa）	Not recorded	PRO PROLINE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；5% PEG 8000, 0.2M L-proline, 0.1M Tris pH 7.5, 4 mM D-maltose, 180 mM LiCl	Resolution 2.85 Å R-free 0.249

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

View Construct and Data Evidence

UniProt name	O95149_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 97–300

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	1xk5
Deposition date deposition_date	2004-09-27
Structure title title	Crystal structure of the m3G-cap-binding domain of snurportin1 in complex with a m3GpppG-cap dinucleotide
Keywords keywords	Protein-RNA-complex, 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	18.17 Å
Radius of gyration Rg (electron density) rg_electron	16.99 Å
Forward intensity I(0) i0	10528000.00
Molecular weight molecular_weight	23956.0 kDa
Excluded volume excluded_volume	29856 Å³
Envelope volume envelope_volume	33639 Å³
Hydration-shell volume shell_volume	16690 Å³
Envelope diameter envelope_diameter	60.9 Å
Shell Rg shell_rg	23.05 Å
Envelope Rg envelope_rg	17.29 Å
Shape Rg shape_rg	16.97 Å
Total Rg total_rg	18.00 Å
Total atoms total_atoms	1683
Residues n_residues	204
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	60.0 Å
Rg (real space) rg_real	18.10 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.0530e+07
I(0) uncertainty (real space) i0_real_error	1.2940e+05
Rg (reciprocal space) rg_reciprocal	18.11 Å
I(0) (reciprocal space) i0_reciprocal	10530000.0000
Solution quality estimate total_estimate	0.8760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.224
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2177000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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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	snurportin-1
Molecular weight formula_weight	23149.4 kDa
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	1765

HYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRRNSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDVLGVAVPAGPLTTKPD

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	2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
Molecular weight formula_weight	832.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1xk5a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family family	d.142.2.5 — m3G-cap binding domain of snurportin-1

CATH v4.4 (1 domains)

Domain ID domain_id	1xk5A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

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8. Citations (3)

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Unit-cell length a length_a	57.470 Å
Unit-cell length b length_b	57.470 Å
Unit-cell length c length_c	130.090 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2270
R_free r_free	0.2760

fit	/app/data/saxs_computation/xk/1xk5/1xk5.fit
pddf	/app/data/pr_computation/xk/1xk5/1xk5.pr.out
profile	/app/data/saxs_computation/xk/1xk5/1xk5.dat

Crystal structure of the m3G-cap-binding domain of snurportin1 in complex with a m3GpppG-cap dinucleotide

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

snurportin-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