SAXSdb — 8ozb

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

Nucleoporin NUP35

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 173–248 Chain F； UniProt 173–248	Not recorded	Nup35 nanobody × 1 Nup35 nanobody × 1	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

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 8OZB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4LIR Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution Deposited 2013-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 151–266（116 aa） Fragment：UNP residues 151-266 Chain B 151–266（116 aa） Fragment：UNP residues 151-266	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, 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
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

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

View Construct and Data Evidence

UniProt name	NUP35_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–76； UniProt 173–248 Author chain F； PDBConstruct 1–76； UniProt 173–248

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	8ozb
Deposition date deposition_date	2023-05-08
Structure title title	Crystal structure of Nup35-Nb complex
Keywords keywords	Nuclear pore complex Nanobody, 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	26.59 Å
Radius of gyration Rg (electron density) rg_electron	26.05 Å
Forward intensity I(0) i0	31102700.00
Molecular weight molecular_weight	42327.0 kDa
Excluded volume excluded_volume	52707 Å³
Envelope volume envelope_volume	63839 Å³
Hydration-shell volume shell_volume	22140 Å³
Envelope diameter envelope_diameter	97.8 Å
Shell Rg shell_rg	31.07 Å
Envelope Rg envelope_rg	26.13 Å
Shape Rg shape_rg	26.00 Å
Total Rg total_rg	26.77 Å
Total atoms total_atoms	2976
Residues n_residues	385
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	92.4 Å
Rg (real space) rg_real	26.83 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	3.1100e+07
I(0) uncertainty (real space) i0_real_error	5.3690e+05
Rg (reciprocal space) rg_reciprocal	26.76 Å
I(0) (reciprocal space) i0_reciprocal	31100000.0000
Solution quality estimate total_estimate	0.8132
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.505
Kurtosis Kurtosis kurtosis	-0.445
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11870000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.681; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.567; Smooth: 0.959

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nup35 nanobody
Molecular weight formula_weight	12582.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3045

QLVESGGGLVQAGGSLRLSCVGTGNISSAYTMAWYRQAAGKEREVVAGILNGGSTHYADSVKGRFTISRDNAKNTVYLQMNSLQPEDTGVYCCHVVIESTRFVYDHYWGQGTRVTV

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nup35 nanobody
Molecular weight formula_weight	12669.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QLVESGGGLVQAGGSLRLSCVGTGNISSAYTMAWYRQAAGKEREVVAGILNGGSTHYADSVKGRFTISRDNAKNTVYLQMNSLQPEDTGVYCCHVVIESTRFVYDHYWGQGTRVTVS

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nucleoporin NUP35
Molecular weight formula_weight	8590.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

DSWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKSV

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

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8. Citations (1)

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Unit-cell length a length_a	49.120 Å
Unit-cell length b length_b	77.220 Å
Unit-cell length c length_c	127.470 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 2 2 21
Space-group number int_tables_number	17
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2431
R_work r_work	0.2417
R_free r_free	0.2674

fit	/app/data/saxs_computation/oz/8ozb/8ozb.fit
pddf	/app/data/pr_computation/oz/8ozb/8ozb.pr.out
profile	/app/data/saxs_computation/oz/8ozb/8ozb.dat

Crystal structure of Nup35-Nb complex

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

Nucleoporin NUP35

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)