SAXSdb — 6x07

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

Nucleoporin NIC96

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 186–839	Not recorded	VHH-SAN12 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；8% PEG 8,000 and 0.1M tri-sodium citrate pH 5	Resolution 2.10 Å R-free 0.245

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 6X07	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QX5 Structure of nucleoporin Nic96 Deposited 2007-08-10	Different construct 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 186–839（654 aa） Fragment：residues 186-839	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Potassium Thiocyanate, 1mM Cetyltrimethylammonium bromide, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.285
2QX5 Structure of nucleoporin Nic96 Deposited 2007-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 186–839（654 aa） Fragment：residues 186-839	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；289 K；18% PEG 3350, 0.1M Bis Tris propane, 0.2M Potassium Thiocyanate, 1mM Cetyltrimethylammonium bromide, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.285
2RFO Crystral Structure of the nucleoporin Nic96 Deposited 2007-10-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 189–839（651 aa） Fragment：UNP residues 189-839	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3-10% PEG3350, 0.1M BisTris pH6.5, 0.05M lithium sulfate, 3% 1,6-hexandiole, 0.01mM DTE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.285
2RFO Crystral Structure of the nucleoporin Nic96 Deposited 2007-10-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 189–839（651 aa） Fragment：UNP residues 189-839	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3-10% PEG3350, 0.1M BisTris pH6.5, 0.05M lithium sulfate, 3% 1,6-hexandiole, 0.01mM DTE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.285
7N85 Inner ring spoke 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 × 240 PDB declaration: 240-meric	Chain Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å
7N85 Inner ring spoke 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 × 30 PDB declaration: 30-meric	Chain Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å
7N85 Inner ring spoke 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 × 30 PDB declaration: 30-meric	Chain Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 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 Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 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 Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 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 Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 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
7WOO Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–839（839 aa） Chain Z 1–839（839 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
7WOT Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore complex Deposited 2022-01-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–839（839 aa） Chain M 1–839（839 aa） Chain N 1–839（839 aa） Chain Z 1–839（839 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
8TJ5 Inner spoke ring of the yeast NPC Deposited 2023-07-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 46 PDB declaration: 46-meric	Chain Q 1–839（839 aa） Chain R 1–839（839 aa） Chain S 1–839（839 aa） Chain T 1–839（839 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NIC96_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–669； UniProt 186–839

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	6x07
Deposition date deposition_date	2020-05-15
Structure title title	Nic96 from S. cerevisiae bound by VHH-SAN12
Keywords keywords	Nucleoporin, nanobody, STRUCTURAL PROTEIN; STRUCTURAL 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	42.32 Å
Radius of gyration Rg (electron density) rg_electron	43.20 Å
Forward intensity I(0) i0	95393200.00
Molecular weight molecular_weight	79973.0 kDa
Excluded volume excluded_volume	100400 Å³
Envelope volume envelope_volume	137010 Å³
Hydration-shell volume shell_volume	30655 Å³
Envelope diameter envelope_diameter	148.4 Å
Shell Rg shell_rg	40.22 Å
Envelope Rg envelope_rg	43.02 Å
Shape Rg shape_rg	43.17 Å
Total Rg total_rg	43.14 Å
Total atoms total_atoms	5642
Residues n_residues	730
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	140.1 Å
Rg (real space) rg_real	42.96 Å
Rg uncertainty (real space) rg_real_error	1.94 Å
I(0) (real space) i0_real	9.5390e+07
I(0) uncertainty (real space) i0_real_error	1.9870e+06
Rg (reciprocal space) rg_reciprocal	42.33 Å
I(0) (reciprocal space) i0_reciprocal	95330000.0000
Solution quality estimate total_estimate	0.6988
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.587
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5458000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.553; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.350; Smooth: 0.071

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nucleoporin NIC96
Molecular weight formula_weight	76575.1 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	5802

GPGSEFELGAPAGRQGNKGNNILNSNESRLNVNENNILREKFENYARIVFQFNNSRQANGNFDIANEFISILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNEGLATNVNKIKSFIDTKLKKADKSWKISNLTVINGVPIWALIFYLLRAGLIKEALQVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLAVYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYGPSRFSNYYLQTLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLFKIDSSTRLTKKPKRDIRFANILANYTKSFRYSDPRVAVEYLVLITLNEGPTDVELCHEALRELVLETKEFTVLLGKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNMIHILNESKYQSSTKGQQIDSLKNVARQCMIYAGMIQYRMPRETYSTLINIDVSL

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-SAN12
Molecular weight formula_weight	14426.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQVQLVETGGGLVQAGGSLRLSCATSGFNFRLRTMGWYRQAPGKERELVASITSGGSTDYADSVKGRFTISRDNAKNTISLEMNSLKPDDTAVYYCNIWAPTTAAITNWGQGTQVTVSSLPETGGLEHHHHHH

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	128

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6x07b_
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.1.1.1 — V set domains (antibody variable domain-like)

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8. Citations (1)

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Unit-cell length a length_a	48.126 Å
Unit-cell length b length_b	79.653 Å
Unit-cell length c length_c	283.515 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	60.910 Å
R factor r_factor	0.2277
R_work r_work	0.2271
R_free r_free	0.2452

fit	/app/data/saxs_computation/x0/6x07/6x07.fit
pddf	/app/data/pr_computation/x0/6x07/6x07.pr.out
profile	/app/data/saxs_computation/x0/6x07/6x07.dat

Nic96 from S. cerevisiae bound by VHH-SAN12

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

Nucleoporin NIC96

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) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)