SAXSdb — 4jnv

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

Nucleoporin p54

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 453–491 Chain B； UniProt 453–491 Chain C； UniProt 453–491 Chain D； UniProt 453–491	Fragment：UNP residues 453-491 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；294 K；0.1 M sodium acetate, pH 5.3, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.85 Å R-free 0.277

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 4JNV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JNU Crystal structure of the human Nup57CCS3* coiled-coil segment, space group P21 Deposited 2013-03-15	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 453–491（39 aa） Fragment：UNP residues 453-491 Chain B 453–491（39 aa） Fragment：UNP residues 453-491 Chain C 453–491（39 aa） Fragment：UNP residues 453-491 Chain D 453–491（39 aa） Fragment：UNP residues 453-491	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；294 K；0.1 M sodium acetate, pH 5.3, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.45 Å R-free 0.218
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 B 453–491（39 aa） Fragment：UNP residues 453-491 Chain D 453–491（39 aa） Fragment：UNP residues 453-491	Not recorded	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 F 453–491（39 aa） Fragment：UNP residues 453-491 Chain H 453–491（39 aa） Fragment：UNP residues 453-491	Not recorded	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 A 453–491（39 aa） Fragment：UNP residues 453-491 Chain C 453–491（39 aa） Fragment：UNP residues 453-491	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 mutation/modification 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 F 1–507（507 aa） Chain L 1–507（507 aa） Chain R 1–507（507 aa） Chain X 1–507（507 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 mutation/modification 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 F 1–507（507 aa） Chain L 1–507（507 aa） Chain R 1–507（507 aa） Chain X 1–507（507 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 mutation/modification 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 F 1–507（507 aa） Chain L 1–507（507 aa） Chain R 1–507（507 aa） Chain X 1–507（507 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 mutation/modification 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 H0 1–507（507 aa） Chain H1 1–507（507 aa） Chain H2 1–507（507 aa） Chain H3 1–507（507 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 mutation/modification 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 H0 1–507（507 aa） Chain H1 1–507（507 aa） Chain H2 1–507（507 aa） Chain H3 1–507（507 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

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUP54_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–40； UniProt 453–491 Author chain B； PDBConstruct 2–40； UniProt 453–491 Author chain C； PDBConstruct 2–40； UniProt 453–491 Author chain D； PDBConstruct 2–40； UniProt 453–491

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	4jnv
Deposition date deposition_date	2013-03-15
Structure title title	Crystal structure of the human Nup57CCS3* coiled-coil segment, space group C2
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	17.08 Å
Radius of gyration Rg (electron density) rg_electron	16.56 Å
Forward intensity I(0) i0	4359530.00
Molecular weight molecular_weight	15215.0 kDa
Excluded volume excluded_volume	19200 Å³
Envelope volume envelope_volume	22520 Å³
Hydration-shell volume shell_volume	12345 Å³
Envelope diameter envelope_diameter	59.5 Å
Shell Rg shell_rg	21.31 Å
Envelope Rg envelope_rg	17.08 Å
Shape Rg shape_rg	16.57 Å
Total Rg total_rg	17.44 Å
Total atoms total_atoms	2180
Residues n_residues	126
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	61.9 Å
Rg (real space) rg_real	17.16 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	4.3600e+06
I(0) uncertainty (real space) i0_real_error	5.5880e+04
Rg (reciprocal space) rg_reciprocal	17.15 Å
I(0) (reciprocal space) i0_reciprocal	4360000.0000
Solution quality estimate total_estimate	0.7986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.540
Kurtosis Kurtosis kurtosis	-0.012
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2110000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.507; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.857; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	70.506 Å
Unit-cell length b length_b	36.623 Å
Unit-cell length c length_c	63.179 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	19.814 Å
R factor r_factor	0.2410
R_work r_work	0.2370
R_free r_free	0.2769

Description description	Nucleoporin p54
Molecular weight formula_weight	4794.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2234

Crystal structure of the human Nup57CCS3* coiled-coil segment, space group C2

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

Nucleoporin p54

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 water

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

fit	/app/data/saxs_computation/jn/4jnv/4jnv.fit
pddf	/app/data/pr_computation/jn/4jnv/4jnv.pr.out
profile	/app/data/saxs_computation/jn/4jnv/4jnv.dat