SAXSdb — 6ei6

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

Coiled-coil and C2 domain-containing protein 1-like

Drosophila melanogaster

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 550–816	Not recorded	SO4 SULFATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.1 M Bis-Tris pH 6.5, 15-25% PEG 3500 Mme, 200 mM ammonium sulfate	Resolution 2.46 Å R-free 0.247
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 550–816	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.1 M Bis-Tris pH 6.5, 15-25% PEG 3500 Mme, 200 mM ammonium sulfate	Resolution 2.46 Å R-free 0.247

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 6EI6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VO5 Crystal structure of Lgd-Shrub complex, single chain fusion Deposited 2017-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 359–423（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；18% PEG 3350 0.1 M sodium citrate pH 5.5 Cryopreserved using 20% glycerol, 25% PEG 3350, 0.1 M sodium citrate 5.4	Resolution 2.00 Å R-free 0.269
5VO5 Crystal structure of Lgd-Shrub complex, single chain fusion Deposited 2017-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 359–423（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；18% PEG 3350 0.1 M sodium citrate pH 5.5 Cryopreserved using 20% glycerol, 25% PEG 3350, 0.1 M sodium citrate 5.4	Resolution 2.00 Å R-free 0.269
7ZSD cryo-EM structure of omicron spike in complex with de novo designed binder, local Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 359–423（65 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
7ZSS cryo-EM structure of D614 spike in complex with de novo designed binder Deposited 2022-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 359–423（65 aa） Chain P 359–423（65 aa） Chain h 359–423（65 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å

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

View Construct and Data Evidence

UniProt name	C2D1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–270； UniProt 550–816 Author chain B； PDBConstruct 4–270； UniProt 550–816

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	6ei6
Deposition date deposition_date	2017-09-18
Structure title title	CC2D1B coordinates ESRCT-III activity during the mitotic reformation of the nuclear envelope
Keywords keywords	ESCRT protein regulator, nuclear envelope reformation, polymerization, CYTOSOLIC PROTEIN; CYTOSOLIC 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	36.24 Å
Radius of gyration Rg (electron density) rg_electron	36.32 Å
Forward intensity I(0) i0	55369700.00
Molecular weight molecular_weight	57269.0 kDa
Excluded volume excluded_volume	70938 Å³
Envelope volume envelope_volume	102390 Å³
Hydration-shell volume shell_volume	25565 Å³
Envelope diameter envelope_diameter	131.0 Å
Shell Rg shell_rg	39.18 Å
Envelope Rg envelope_rg	35.57 Å
Shape Rg shape_rg	36.37 Å
Total Rg total_rg	36.36 Å
Total atoms total_atoms	4005
Residues n_residues	484
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	125.8 Å
Rg (real space) rg_real	36.68 Å
Rg uncertainty (real space) rg_real_error	1.82 Å
I(0) (real space) i0_real	5.5370e+07
I(0) uncertainty (real space) i0_real_error	1.1010e+06
Rg (reciprocal space) rg_reciprocal	36.41 Å
I(0) (reciprocal space) i0_reciprocal	55360000.0000
Solution quality estimate total_estimate	0.7614
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.7 Å
Skewness Skewness skewness	0.451
Kurtosis Kurtosis kurtosis	-0.649
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3802000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.603; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.346; Smooth: 0.739

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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	Coiled-coil and C2 domain-containing protein 1-like
Molecular weight formula_weight	31241.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4169

GAMLSTLPVPPSQRDNLEASFAIVSAEECDPTDDICEIGVRMEEQLAKQLMMCKNTRDHHKAMGDVAGMNRFENLALTVQKDLDLVRYSKRKNEPLPKFHYEKRSFNIVHCNTDLTDSELEIVVVRGISYNVANPKDVDTYVRVEFPLLNDESFKTKTNVIRDTSSPDYDERFKVDIQRTNRQFQRIFKRHGVKFEIYSRGGFLRSDTLIGTVNVKLQPLETKCEIHDTYDLMDGRKQVGGKLEVKIRVRNPILTKQMEHITEKWLVLDA

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	164

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8. Citations (1)

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Unit-cell length a length_a	87.410 Å
Unit-cell length b length_b	54.050 Å
Unit-cell length c length_c	97.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.461 Å
Low-resolution limit resolution_low	59.594 Å
R factor r_factor	0.2072
R_work r_work	0.2050
R_free r_free	0.2475

fit	/app/data/saxs_computation/ei/6ei6/6ei6.fit
pddf	/app/data/pr_computation/ei/6ei6/6ei6.pr.out
profile	/app/data/saxs_computation/ei/6ei6/6ei6.dat

CC2D1B coordinates ESRCT-III activity during the mitotic reformation of the nuclear envelope

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

Coiled-coil and C2 domain-containing protein 1-like

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