SAXSdb — 5xbk

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

Importin-4

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 D； UniProt 668–1081	Fragment：UNP residues 668-1081	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；Sodium tartrate, PEG3350	Resolution 3.22 Å R-free 0.281
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 668–1081	Fragment：UNP residues 668-1081	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；Sodium tartrate, PEG3350	Resolution 3.22 Å R-free 0.281
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 668–1081	Fragment：UNP residues 668-1081	histone H3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；Sodium tartrate, PEG3350	Resolution 3.22 Å R-free 0.281
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 668–1081	Fragment：UNP residues 668-1081	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；Sodium tartrate, PEG3350	Resolution 3.22 Å R-free 0.281

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 5XBK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5XAH Crystal structure of human Importin4 Deposited 2017-03-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 668–1081（414 aa） Fragment：UNP residues 668-1081	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291 K；Sodium Tartrate, PEG3350	Resolution 3.00 Å R-free 0.280
5XAH Crystal structure of human Importin4 Deposited 2017-03-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 668–1081（414 aa） Fragment：UNP residues 668-1081	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291 K；Sodium Tartrate, PEG3350	Resolution 3.00 Å R-free 0.280
5XAH Crystal structure of human Importin4 Deposited 2017-03-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 668–1081（414 aa） Fragment：UNP residues 668-1081	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291 K；Sodium Tartrate, PEG3350	Resolution 3.00 Å R-free 0.280
5XAH Crystal structure of human Importin4 Deposited 2017-03-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 668–1081（414 aa） Fragment：UNP residues 668-1081	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291 K；Sodium Tartrate, PEG3350	Resolution 3.00 Å R-free 0.280
7UNK Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex Deposited 2022-04-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1081（1081 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
8DYO Cryo-EM structure of Importin-4 bound to RanGTP Deposited 2022-08-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1081（1081 aa）	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 7.10 Å

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

View Construct and Data Evidence

UniProt name	IPO4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–416； UniProt 668–1081 Author chain B； PDBConstruct 3–416； UniProt 668–1081 Author chain C； PDBConstruct 3–416； UniProt 668–1081 Author chain D； PDBConstruct 3–416； UniProt 668–1081

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	5xbk
Deposition date deposition_date	2017-03-20
Structure title title	Crystal structure of human Importin4
Keywords keywords	Histone, Chromatin, Assembly, 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	41.93 Å
Radius of gyration Rg (electron density) rg_electron	41.71 Å
Forward intensity I(0) i0	359726000.00
Molecular weight molecular_weight	159020.0 kDa
Excluded volume excluded_volume	201280 Å³
Envelope volume envelope_volume	282590 Å³
Hydration-shell volume shell_volume	58653 Å³
Envelope diameter envelope_diameter	143.1 Å
Shell Rg shell_rg	45.06 Å
Envelope Rg envelope_rg	40.82 Å
Shape Rg shape_rg	41.70 Å
Total Rg total_rg	41.92 Å
Total atoms total_atoms	11162
Residues n_residues	1480
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	137.4 Å
Rg (real space) rg_real	41.97 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	3.5970e+08
I(0) uncertainty (real space) i0_real_error	6.0910e+06
Rg (reciprocal space) rg_reciprocal	41.93 Å
I(0) (reciprocal space) i0_reciprocal	359700000.0000
Solution quality estimate total_estimate	0.8743
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.0 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	21960000.0000
Real-space data points n_real_points	39
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: 1.000; Smooth: 0.816

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Importin-4
Molecular weight formula_weight	44835.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A,B,C
Atom count atom_count	11162

GSAFFDEKEDTCAAVGEISVNTSVAFLPYMESVFEEVFKLLECPHLNVRKAAHEALGQFCCALHKACQSCPSEPNTAALQAALARVVPSYMQAVNRERERQVVMAVLEALTGVLRSCGTLTLKPPGRLAELCGVLKAVLQRKTACQDTDEEEEEEDDDQAEYDAMLLEHAGEAIPALAAAAGGDSFAPFFAGFLPLLVCKTKQGCTVAEKSFAVGTLAETIQGLGAASAQFVSRLLPVLLSTAQEADPEVRSNAIFGMGVLAEHGGHPAQEHFPKLLGLLFPLLARERHDRVRDNICGALARLLMASPTRKPEPQVLAALLHALPLKEDLEEWVTIGRLFSFLYQSSPDQVIDVAPELLRICSLILADNKIPPDTKAALLLLLTFLAKQHTDSFQAALGSLPVDKAQELQAVLGLS

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	histone H3
Molecular weight formula_weight	1949.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

ARTKQTARKSTGGKAPRK

来源 Source

来源生物 organism	Xenopus laevis
NCBI Class编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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8. Citations (2)

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Unit-cell length a length_a	65.021 Å
Unit-cell length b length_b	108.536 Å
Unit-cell length c length_c	124.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.223 Å
Low-resolution limit resolution_low	49.977 Å
R factor r_factor	0.2246
R_work r_work	0.2180
R_free r_free	0.2809

fit	/app/data/saxs_computation/xb/5xbk/5xbk.fit
pddf	/app/data/pr_computation/xb/5xbk/5xbk.pr.out
profile	/app/data/saxs_computation/xb/5xbk/5xbk.dat

Crystal structure of human Importin4

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

Importin-4

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)