SAXSdb — 1bk5

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

KARYOPHERIN ALPHA

Saccharomyces cerevisiae

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 89–510 Chain B； UniProt 89–510	Fragment：ARMADILLO DOMAIN	CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.20 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 1BK5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BK6 KARYOPHERIN ALPHA (YEAST) + SV40 T ANTIGEN NLS Deposited 1998-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 89–510（422 aa） Fragment：ARMADILLO DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.80 Å R-free 0.307
1BK6 KARYOPHERIN ALPHA (YEAST) + SV40 T ANTIGEN NLS Deposited 1998-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 89–510（422 aa） Fragment：ARMADILLO DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.80 Å R-free 0.307
1EE4 CRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A C-MYC NLS PEPTIDE Deposited 2000-01-30	Different construct Different mutation/modification 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 87–509（423 aa） Fragment：ARMADILLO DOMAIN	Mutation：Y397D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.277
1EE4 CRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A C-MYC NLS PEPTIDE Deposited 2000-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 87–509（423 aa） Fragment：ARMADILLO DOMAIN	Mutation：Y397D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.277
1EE5 YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A NUCLEOPLASMIN NLS PEPTIDE Deposited 2000-01-30	Different construct Different mutation/modification 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 87–510（424 aa） Fragment：ARMADILLLO-REPEAT DOMAIN	Mutation：Y397D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.265
1UN0 Crystal Structure of Yeast Karyopherin (Importin) alpha in complex with a Nup2p N-terminal fragment Deposited 2003-09-03	Different construct Different mutation/modification 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 88–530（443 aa） Fragment：ARMADILLO REPEAT DOMAIN, RESIDUES 88-530	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；50 MM HEPES PH 6.8, 0.15 M NACL, 24 % PEG3350, 2 % PEG400	Resolution 2.60 Å R-free 0.257
1UN0 Crystal Structure of Yeast Karyopherin (Importin) alpha in complex with a Nup2p N-terminal fragment Deposited 2003-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 88–530（443 aa） Fragment：ARMADILLO REPEAT DOMAIN, RESIDUES 88-530	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；50 MM HEPES PH 6.8, 0.15 M NACL, 24 % PEG3350, 2 % PEG400	Resolution 2.60 Å R-free 0.257
2C1T Structure of the Kap60p:Nup2 complex Deposited 2005-09-20	Different construct Different mutation/modification 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 88–541（454 aa） Fragment：ARM DOMAIN, RESIDUES 88-541	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；EXPERIMENTAL DETALS GIVEN IN ENTRY 1UN0 AND IN MATSUURA ET AL, EMBO J, 22, 5358, 2003., pH 6.80	Resolution 2.60 Å R-free 0.251
2C1T Structure of the Kap60p:Nup2 complex Deposited 2005-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 88–541（454 aa） Fragment：ARM DOMAIN, RESIDUES 88-541	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；EXPERIMENTAL DETALS GIVEN IN ENTRY 1UN0 AND IN MATSUURA ET AL, EMBO J, 22, 5358, 2003., pH 6.80	Resolution 2.60 Å R-free 0.251
4PVZ Structure of yeast importin a bound to the membrane protein Nuclear Localization Signal sequence of INM protein Heh2 Deposited 2014-03-18	Different construct Different mutation/modification 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 88–509（422 aa） Fragment：unp residues 88-509	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100 mM ammonium acetate, 20% PEG 8000, 100 mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.226
4PVZ Structure of yeast importin a bound to the membrane protein Nuclear Localization Signal sequence of INM protein Heh2 Deposited 2014-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 88–509（422 aa） Fragment：unp residues 88-509	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100 mM ammonium acetate, 20% PEG 8000, 100 mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.226
4XZR Structure of yeast importin a bound to the membrane protein Nuclear Localization Signal sequence of INM protein Heh1 Deposited 2015-02-04	Different construct Different mutation/modification 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 88–509（422 aa） Fragment：unp residues 88-509	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM ammonium acetate, 20% PEG 8000, 100 mM BisTris	Resolution 2.25 Å R-free 0.215
5H2W Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340) Deposited 2016-10-18	Different construct Different mutation/modification 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 88–510（423 aa） Fragment：UNP residues 88-510	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M MES, 0.1M calcium acetate, 12% PEG8000	Resolution 2.50 Å R-free 0.247
5H2W Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340) Deposited 2016-10-18	Different construct Different mutation/modification 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 88–510（423 aa） Fragment：UNP residues 88-510	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M MES, 0.1M calcium acetate, 12% PEG8000	Resolution 2.50 Å R-free 0.247
5H2X Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172) Deposited 2016-10-18	Different construct Different mutation/modification 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 88–510（423 aa） Fragment：UNP residues 88-510	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium phosphate, 12% PEG8000	Resolution 2.20 Å R-free 0.228
5T94 Crystal structure of Kap60 bound to yeast RCC1 (Prp20) Deposited 2016-09-09	Different construct Different mutation/modification 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 1–542（542 aa）	Mutation：T205A, D276E, K400R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Na cacodylate, 0.1 M NaCl and 1.1 M ammonium sulfate	Resolution 2.63 Å R-free 0.259

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

View Construct and Data Evidence

UniProt name	IMA1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–422； UniProt 89–510 Author chain B； PDBConstruct 1–422； UniProt 89–510

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	1bk5
Deposition date deposition_date	1998-07-14
Structure title title	KARYOPHERIN ALPHA FROM SACCHAROMYCES CEREVISIAE
Keywords keywords	PROTEIN TRANSPORT, NLS NUCLEAR IMPORT, ARMADILLO REPEAT CONTAINING PROTEIN; 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	35.09 Å
Radius of gyration Rg (electron density) rg_electron	34.83 Å
Forward intensity I(0) i0	132047000.00
Molecular weight molecular_weight	93413.0 kDa
Excluded volume excluded_volume	117590 Å³
Envelope volume envelope_volume	149190 Å³
Hydration-shell volume shell_volume	37265 Å³
Envelope diameter envelope_diameter	135.5 Å
Shell Rg shell_rg	39.31 Å
Envelope Rg envelope_rg	34.70 Å
Shape Rg shape_rg	34.82 Å
Total Rg total_rg	35.19 Å
Total atoms total_atoms	6552
Residues n_residues	844
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	127.7 Å
Rg (real space) rg_real	35.36 Å
Rg uncertainty (real space) rg_real_error	1.21 Å
I(0) (real space) i0_real	1.3200e+08
I(0) uncertainty (real space) i0_real_error	2.3220e+06
Rg (reciprocal space) rg_reciprocal	35.19 Å
I(0) (reciprocal space) i0_reciprocal	132000000.0000
Solution quality estimate total_estimate	0.6169
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.7 Å
Skewness Skewness skewness	0.561
Kurtosis Kurtosis kurtosis	-0.016
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23100000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.792; Smooth: 0.903

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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	KARYOPHERIN ALPHA
Molecular weight formula_weight	46718.4 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	6782

LPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQCNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDANLIPPLVKLLEVAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIADNRIIEVTLDALENILKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIETYFG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bk5a_
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	d1bk5b_
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	1bk5A00
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	1bk5B00
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	157.980 Å
Unit-cell length b length_b	74.140 Å
Unit-cell length c length_c	84.050 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	2.200 Å
Low-resolution limit resolution_low	19.500 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2760

fit	/app/data/saxs_computation/bk/1bk5/1bk5.fit
pddf	/app/data/pr_computation/bk/1bk5/1bk5.pr.out
profile	/app/data/saxs_computation/bk/1bk5/1bk5.dat

KARYOPHERIN ALPHA FROM SACCHAROMYCES CEREVISIAE

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

KARYOPHERIN ALPHA

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