SAXSdb — 4lir

▼

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

Nucleoporin NUP53

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 151–266 Chain B； UniProt 151–266	Fragment：UNP residues 151-266 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；277 K；20.0% MPD, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.46 Å R-free 0.206

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 4LIR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MW1 Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53 residues 84-150) Deposited 2021-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 84–150（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 17% (w/v) PEG 20000	Resolution 3.40 Å R-free 0.276
7MW1 Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53 residues 84-150) Deposited 2021-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 84–150（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.075 M TRIS pH 8.5, 17% (w/v) PEG 20000	Resolution 3.40 Å R-free 0.276
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 F0 1–326（326 aa） Chain F1 1–326（326 aa） Chain F2 1–326（326 aa） Chain F3 1–326（326 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 F0 1–326（326 aa） Chain F1 1–326（326 aa） Chain F2 1–326（326 aa） Chain F3 1–326（326 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
8OZB Crystal structure of Nup35-Nb complex Deposited 2023-05-08	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 E 173–248（76 aa） Chain F 173–248（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M HEPES (pH 6.5); 25% v/v PEG400; 0.05 M NaCl, 0.01 M MgCl2.	Resolution 2.09 Å R-free 0.267

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUP53_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–117； UniProt 151–266 Author chain B； PDBConstruct 2–117； UniProt 151–266

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4lir
Deposition date deposition_date	2013-07-03
Structure title title	Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution
Keywords keywords	;PF05172 family, Nup53/35/40-type RNA recognition motif, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, TRANSPORT PROTEIN, NUCLEAR PROTEIN, Partnership for T-Cell Biology, TCELL ;; TRANSPORT PROTEIN, NUCLEAR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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	16.05 Å
Forward intensity I(0) i0	6601840.00
Molecular weight molecular_weight	18359.0 kDa
Excluded volume excluded_volume	22724 Å³
Envelope volume envelope_volume	25846 Å³
Hydration-shell volume shell_volume	13786 Å³
Envelope diameter envelope_diameter	54.8 Å
Shell Rg shell_rg	21.63 Å
Envelope Rg envelope_rg	16.42 Å
Shape Rg shape_rg	16.06 Å
Total Rg total_rg	17.02 Å
Total atoms total_atoms	1264
Residues n_residues	156
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	54.6 Å
Rg (real space) rg_real	17.06 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	6.6020e+06
I(0) uncertainty (real space) i0_real_error	7.7900e+04
Rg (reciprocal space) rg_reciprocal	17.06 Å
I(0) (reciprocal space) i0_reciprocal	6602000.0000
Solution quality estimate total_estimate	0.8179
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.453
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2196000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4lira_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d4lirb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

CATH v4.4 (2 domains)

Domain ID domain_id	4lirA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	4lirB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	70.590 Å
Unit-cell length b length_b	70.590 Å
Unit-cell length c length_c	160.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.460 Å
Low-resolution limit resolution_low	28.558 Å
R factor r_factor	0.1915
R_work r_work	0.1908
R_free r_free	0.2058

Description description	Nucleoporin NUP53
Molecular weight formula_weight	13136.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1286

Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution

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

Nucleoporin NUP53

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

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

fit	/app/data/saxs_computation/li/4lir/4lir.fit
pddf	/app/data/pr_computation/li/4lir/4lir.pr.out
profile	/app/data/saxs_computation/li/4lir/4lir.dat