SAXSdb — 6x05

▼

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

Nucleoporin NUP133

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 55–481	Not recorded	VHH-SAN4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG 3,350, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5	Resolution 2.10 Å R-free 0.219

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 6X05	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KFO Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae Deposited 2009-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 881–1157（277 aa） Fragment：C-terminal domain, residues 881-1157	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG 3350, 200mM Potassium Thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.90 Å R-free 0.245
6X02 Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 Deposited 2020-05-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 521–1157（637 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% PEG 8,000, 30% ethylene glycol, 0.1M imidazole titrated with MES pH 6.5, 15mM sodium nitrate, 15mM sodium phosphate dibasic, 15mM ammonium sulfate	Resolution 6.38 Å R-free 0.324
6X03 Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9 Deposited 2020-05-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 521–1157（637 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；6% PEG 8,000, 30% ethylene glycol, 0.1M imidazole titrated with MES pH 6.5, 15mM sodium nitrate, 15mM sodium phosphate dibasic, 15mM ammonium sulfate	Resolution 7.30 Å R-free 0.353
6X04 Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5 Deposited 2020-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 55–481（427 aa） Chain C 55–481（427 aa） Chain E 55–481（427 aa） Chain G 55–481（427 aa） Chain I 55–481（427 aa） Chain K 55–481（427 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；15% PEG MME 2,000, 0.1M potassium chloride, 0.1M Tris/HCl pH 8	Resolution 2.68 Å R-free 0.261
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric	Chain g 1–1157（1157 aa） Chain r 1–1157（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain g 1–1157（1157 aa） Chain r 1–1157（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain g 1–1157（1157 aa） Chain r 1–1157（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric	Chain g 1–1157（1157 aa） Chain n 1–1157（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain g 1–1157（1157 aa） Chain n 1–1157（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain g 1–1157（1157 aa） Chain n 1–1157（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NU133_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–428； UniProt 55–481

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	6x05
Deposition date deposition_date	2020-05-15
Structure title title	Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN4
Keywords keywords	STRUCTURAL PROTEIN, Nucleoporin, Nanobody; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.56 Å
Radius of gyration Rg (electron density) rg_electron	27.85 Å
Forward intensity I(0) i0	49639300.00
Molecular weight molecular_weight	55472.0 kDa
Excluded volume excluded_volume	69645 Å³
Envelope volume envelope_volume	88794 Å³
Hydration-shell volume shell_volume	28455 Å³
Envelope diameter envelope_diameter	104.5 Å
Shell Rg shell_rg	32.93 Å
Envelope Rg envelope_rg	28.10 Å
Shape Rg shape_rg	27.83 Å
Total Rg total_rg	28.47 Å
Total atoms total_atoms	3912
Residues n_residues	500
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	100.4 Å
Rg (real space) rg_real	28.85 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	4.9640e+07
I(0) uncertainty (real space) i0_real_error	7.3550e+05
Rg (reciprocal space) rg_reciprocal	28.76 Å
I(0) (reciprocal space) i0_reciprocal	49640000.0000
Solution quality estimate total_estimate	0.8341
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.575
Kurtosis Kurtosis kurtosis	-0.160
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10800000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.786; Smooth: 0.950

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nucleoporin NUP133
Molecular weight formula_weight	48493.7 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	4158

GFDNSKVFTENNRYIVKTLQTDYSSGFSNDDELNGYIDMQIGYGLVNDHKKVYIWNIHSTQKDTPYITVPFRSDDNDEIAVAPRCILTFPATMDESPLALNPNDQDETGGLIIIKGSKAIYYEDINSINNLNFKLSEKFSHELELPINSSGGEKCDLMLNCEPAGIVLSTNMGRIFFITIRNSMGKPQLKLGKLLNKPFKLGIWSKIFNTNSSVVSLRNGPILGKGTRLVYITTNKGIFQTWQLSATNSHPTKLIDVNIYEAILESLQDLYPFAHGTLKIWDSHPLQDESSQLFLSSIYDSSCNETYYILSTIIFDSSSNSFTIFSTYRLNTFMESITDTKFKPKIFIPQMENANDTNEVTSILVMFPNAVVITQVNSKLDSSYSMRRKWEDIVSLRNDIDIIGSGYDSKSLYVLTKQMGVLQFFVKE

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	VHH-SAN4
Molecular weight formula_weight	13505.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

QLQLVESGGGSVQAGGSLTLSCTASESISKRIHGIGWFRQRRGEQREEIAYITTGGRPNLGDSVKDRFTISRDKSNGTVYLQMNSLKPEDTAVYYCHGRGRWWGTEGRLDYWGQGTQVTVSS

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6x05k_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6x05A01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

▶

8. Citations (1)

▶

Unit-cell length a length_a	93.381 Å
Unit-cell length b length_b	154.693 Å
Unit-cell length c length_c	41.423 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	59.570 Å
R factor r_factor	0.1765
R_work r_work	0.1742
R_free r_free	0.2188

fit	/app/data/saxs_computation/x0/6x05/6x05.fit
pddf	/app/data/pr_computation/x0/6x05/6x05.pr.out
profile	/app/data/saxs_computation/x0/6x05/6x05.dat

Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN4

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

Nucleoporin NUP133

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)