SAXSdb — 4ncv

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

Fibritin

OrganismNot specified

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 458–484 Chain B； UniProt 458–484 Chain C； UniProt 458–484	Fragment：C-terminus fragment (UNP residues 458-484) 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；293 K；1.4 M Na/K-phosphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.163

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 4NCV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NCU Foldon domain wild type Deposited 2013-10-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 458–484（27 aa） Fragment：C-terminus fragment (UNP residues 458-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% PEG 200, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.11 Å R-free 0.141
4NCW foldon domain wild type C-conjugate Deposited 2013-10-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 458–484（27 aa） Fragment：C-terminus fragment (UNP residues 458-484) Chain B 458–484（27 aa） Fragment：C-terminus fragment (UNP residues 458-484) Chain C 458–484（27 aa） Fragment：C-terminus fragment (UNP residues 458-484)	Not recorded	2KN N,N',N''-triethylbenzene-1,3,5-tricarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M Ammoniumsulfate, 30% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.30 Å R-free 0.193
4ZYP Crystal Structure of Motavizumab and Quaternary-Specific RSV-Neutralizing Human Antibody AM14 in Complex with Prefusion RSV F Glycoprotein Deposited 2015-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 458–484（27 aa） Chain B 458–484（27 aa） Chain C 458–484（27 aa）	Mutation：S155C, S190F, V207L, S290C, I379V, M447V Mutation：S155C, S190F, V207L, S290C, I379V, M447V Mutation：S155C, S190F, V207L, S290C, I379V, M447V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；5.645mg/mL EndoH digested DS-Cav1 + AM14 Fab + Motavizumab Fab, 11.4% PEG8000, 1.71% MPD, 0.1M Imidazole pH 6.5	Resolution 5.50 Å R-free 0.277
5C0R Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed with the Broadly Neutralizing Antibody C179 Deposited 2015-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 458–485（28 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；15% (w/v) PEG 1500, 5% (v/v) MPD, 200 mM ammonium chloride, 100 mM Tris, pH 8.5	Resolution 3.19 Å R-free 0.251
5C0S Crystal structure of a generation 4 influenza hemagglutinin stabilized stem in complex with the broadly neutralizing antibody CR6261 Deposited 2015-06-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 458–485（28 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7% (w/v) PEG 4000, 4.5% (v/v) isopropanol, 100 mM imidazole, pH 6.5	Resolution 4.30 Å R-free 0.310
6CRV SARS Spike Glycoprotein, Stabilized variant, C3 symmetry Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6CRW SARS Spike Glycoprotein, Stabilized variant, single upwards S1 CTD conformation Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6CRX SARS Spike Glycoprotein, Stabilized variant, two S1 CTDs in the upwards conformation Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V968P Mutation：K968P, V968P Mutation：K968P, V968P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6CRZ SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, C3 symmetry Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V968P Mutation：K968P, V968P Mutation：K968P, V968P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6CS0 SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, one S1 CTD in an upwards conformation Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V968P Mutation：K968P, V968P Mutation：K968P, V968P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6CS1 SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, two S1 CTDs in an upwards conformation Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6CS2 SARS Spike Glycoprotein - human ACE2 complex, Stabilized variant, all ACE2-bound particles Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 457–484（28 aa） Chain B 457–484（28 aa） Chain C 457–484（28 aa）	Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D9IEJ2_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–28； UniProt 458–484 Author chain B； PDBConstruct 2–28； UniProt 458–484 Author chain C； PDBConstruct 2–28； UniProt 458–484

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	4ncv
Deposition date deposition_date	2013-10-25
Structure title title	Foldon domain wild type N-conjugate
Keywords keywords	trimeric scaffold, chemical ligation, folding, trazido-functionalized trimesic acid scaffold, VIRAL PROTEIN; VIRAL 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	13.06 Å
Radius of gyration Rg (electron density) rg_electron	11.45 Å
Forward intensity I(0) i0	1754210.00
Molecular weight molecular_weight	9328.0 kDa
Excluded volume excluded_volume	11811 Å³
Envelope volume envelope_volume	12516 Å³
Hydration-shell volume shell_volume	9352 Å³
Envelope diameter envelope_diameter	36.5 Å
Shell Rg shell_rg	17.10 Å
Envelope Rg envelope_rg	11.73 Å
Shape Rg shape_rg	11.42 Å
Total Rg total_rg	12.98 Å
Total atoms total_atoms	663
Residues n_residues	81
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	39.5 Å
Rg (real space) rg_real	12.94 Å
Rg uncertainty (real space) rg_real_error	0.16 Å
I(0) (real space) i0_real	1.7540e+06
I(0) uncertainty (real space) i0_real_error	1.8150e+04
Rg (reciprocal space) rg_reciprocal	12.95 Å
I(0) (reciprocal space) i0_reciprocal	1754000.0000
Solution quality estimate total_estimate	0.8926
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.5 Å
Skewness Skewness skewness	0.021
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	418900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.954

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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	27.970 Å
Unit-cell length b length_b	47.930 Å
Unit-cell length c length_c	27.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1349
R_work r_work	0.1335
R_free r_free	0.1632

Description description	Fibritin
Molecular weight formula_weight	3110.5 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	789

Foldon domain wild type N-conjugate

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

Fibritin

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

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

fit	/app/data/saxs_computation/nc/4ncv/4ncv.fit
pddf	/app/data/pr_computation/nc/4ncv/4ncv.pr.out
profile	/app/data/saxs_computation/nc/4ncv/4ncv.dat