SAXSdb — 4jq5

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

Nucleoporin p58/p45

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 341–425 Chain B； UniProt 341–425 Chain C； UniProt 341–425 Chain D； UniProt 341–425	Fragment：UNP residues 341-425	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.19 Å R-free 0.293
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 341–425 Chain F； UniProt 341–425 Chain G； UniProt 341–425 Chain H； UniProt 341–425	Fragment：UNP residues 341-425	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.19 Å R-free 0.293
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain I； UniProt 341–425 Chain J； UniProt 341–425 Chain K； UniProt 341–425 Chain L； UniProt 341–425	Fragment：UNP residues 341-425	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；10% glycerol, 28% dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.19 Å R-free 0.293

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 4JQ5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JO7 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 stoichiometry Deposited 2013-03-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 341–428（88 aa） Fragment：UNP residues 341-428 Chain C 341–428（88 aa） Fragment：UNP residues 341-428	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 1.75 Å R-free 0.214
4JO7 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex with 2:2 stoichiometry Deposited 2013-03-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 341–428（88 aa） Fragment：UNP residues 341-428 Chain G 341–428（88 aa） Fragment：UNP residues 341-428	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M MES, pH 6.5, 6.7% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 1.75 Å R-free 0.214
4JO9 Crystal structure of the human Nup49CCS2+3* Nup57CCS3* complex 1:2 stoichiometry Deposited 2013-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 341–426（86 aa） Fragment：UNP residues 341-426	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 3.8；294 K；0.1 M sodium citrate, pH 3.8, 0.07 M calcium chloride, VAPOR DIFFUSION, temperature 294.0K	Resolution 2.50 Å R-free 0.294
5IJN Composite structure of the inner ring of the human nuclear pore complex (32 copies of Nup205) Deposited 2016-03-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric	Chain G 1–599（599 aa） Chain M 1–599（599 aa） Chain S 1–599（599 aa） Chain Y 1–599（599 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 21.40 Å
5IJO Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) Deposited 2016-03-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 208 PDB declaration: 208-meric	Chain G 1–599（599 aa） Chain M 1–599（599 aa） Chain S 1–599（599 aa） Chain Y 1–599（599 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 21.40 Å
7PER Model of the inner ring of the human nuclear pore complex Deposited 2021-08-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric	Chain G 1–599（599 aa） Chain M 1–599（599 aa） Chain S 1–599（599 aa） Chain Y 1–599（599 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.	Resolution 35.00 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric	Chain I0 1–599（599 aa） Chain I1 1–599（599 aa） Chain I2 1–599（599 aa） Chain I3 1–599（599 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric	Chain I0 1–599（599 aa） Chain I1 1–599（599 aa） Chain I2 1–599（599 aa） Chain I3 1–599（599 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.00 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUPL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–86； UniProt 341–425 Author chain B； PDBConstruct 2–86； UniProt 341–425 Author chain C； PDBConstruct 2–86； UniProt 341–425 Author chain D； PDBConstruct 2–86； UniProt 341–425 Author chain E； PDBConstruct 2–86； UniProt 341–425 Author chain F； PDBConstruct 2–86； UniProt 341–425 Author chain G； PDBConstruct 2–86； UniProt 341–425 Author chain H； PDBConstruct 2–86； UniProt 341–425 Author chain I； PDBConstruct 2–86； UniProt 341–425 Author chain J； PDBConstruct 2–86； UniProt 341–425 Author chain K； PDBConstruct 2–86； UniProt 341–425 Author chain L； PDBConstruct 2–86； UniProt 341–425

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	4jq5
Deposition date deposition_date	2013-03-20
Structure title title	Crystal structure of the human Nup49CCS2+3* coiled-coil segment
Keywords keywords	Nucleocytoplasmic transport, 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	41.53 Å
Radius of gyration Rg (electron density) rg_electron	42.12 Å
Forward intensity I(0) i0	214848000.00
Molecular weight molecular_weight	120890.0 kDa
Excluded volume excluded_volume	152090 Å³
Envelope volume envelope_volume	224400 Å³
Hydration-shell volume shell_volume	46797 Å³
Envelope diameter envelope_diameter	170.5 Å
Shell Rg shell_rg	44.04 Å
Envelope Rg envelope_rg	42.35 Å
Shape Rg shape_rg	42.10 Å
Total Rg total_rg	42.31 Å
Total atoms total_atoms	17026
Residues n_residues	1027
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	155.7 Å
Rg (real space) rg_real	41.83 Å
Rg uncertainty (real space) rg_real_error	1.97 Å
I(0) (real space) i0_real	2.1480e+08
I(0) uncertainty (real space) i0_real_error	4.1210e+06
Rg (reciprocal space) rg_reciprocal	41.54 Å
I(0) (reciprocal space) i0_reciprocal	214800000.0000
Solution quality estimate total_estimate	0.8048
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.9 Å
Skewness Skewness skewness	0.485
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	32760000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.597; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.709; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4jq5A00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5B00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5C00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5D00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5E00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5F00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5G00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5H00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5I00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5J00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5K00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

Domain ID domain_id	4jq5L00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

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8. Citations (1)

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Unit-cell length a length_a	63.820 Å
Unit-cell length b length_b	77.097 Å
Unit-cell length c length_c	77.197 Å
Unit-cell angle α angle_alpha	120.04 °
Unit-cell angle β angle_beta	90.12 °
Unit-cell angle γ angle_gamma	89.96 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.195 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2852
R_work r_work	0.2849
R_free r_free	0.2929

Description description	Nucleoporin p58/p45
Molecular weight formula_weight	10138.5 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	17026

Crystal structure of the human Nup49CCS2+3* coiled-coil segment

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

Nucleoporin p58/p45

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/jq/4jq5/4jq5.fit
pddf	/app/data/pr_computation/jq/4jq5/4jq5.pr.out
profile	/app/data/saxs_computation/jq/4jq5/4jq5.dat