SAXSdb — 6xkj

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

Caspase recruitment domain-containing protein 8

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 homooligomer Homooligomer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 451–537 Chain B； UniProt 451–537 Chain C； UniProt 451–537 Chain D； UniProt 451–537 Chain E； UniProt 451–537 Chain F； UniProt 451–537 Chain G； UniProt 451–537 Chain H； UniProt 451–537 Chain I； UniProt 451–537 Chain J； UniProt 451–537 Chain K； UniProt 451–537 Chain L； UniProt 451–537 Chain M； UniProt 451–537 Chain N； UniProt 451–537 Chain O； UniProt 451–537 Chain P； UniProt 451–537	Fragment：CARD domain (UNP residues 451-537)	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.54 Å

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 6XKJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IKM X-ray structure of CARD8 CARD domain Deposited 2012-12-26	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 345–431（87 aa） Fragment：MBP tagged human CARD8 CARD domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	IOD IODIDE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；16% PEG8000, 0.1 M NaI, 0.1 M NaAc, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.46 Å R-free 0.253
6K9F Structure of unknow protein 4 Deposited 2019-06-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 345–431（87 aa） Chain B 345–431（87 aa） Chain C 345–431（87 aa） Chain D 345–431（87 aa） Chain E 345–431（87 aa） Chain F 345–431（87 aa） Chain G 345–431（87 aa） Chain H 345–431（87 aa） Chain I 345–431（87 aa） Chain J 345–431（87 aa） Chain K 345–431（87 aa） Chain L 345–431（87 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å R-free 0.302
7JKQ Human DPP9-CARD8 complex Deposited 2020-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–537（537 aa） Chain C 1–537（537 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM HEPES, pH 7.5, 150 mM NaCl, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7JN7 Human DPP9-CARD8 complex Deposited 2020-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–537（537 aa） Chain C 1–537（537 aa）	Not recorded	GK2 [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

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

View Construct and Data Evidence

UniProt name	CARD8_HUMAN
Isoform	Q9Y2G2-5
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 451–537 Author chain B； PDBConstruct 1–87； UniProt 451–537 Author chain C； PDBConstruct 1–87； UniProt 451–537 Author chain D； PDBConstruct 1–87； UniProt 451–537 Author chain E； PDBConstruct 1–87； UniProt 451–537 Author chain F； PDBConstruct 1–87； UniProt 451–537 Author chain G； PDBConstruct 1–87； UniProt 451–537 Author chain H； PDBConstruct 1–87； UniProt 451–537 Author chain I； PDBConstruct 1–87； UniProt 451–537 Author chain J； PDBConstruct 1–87； UniProt 451–537 Author chain K； PDBConstruct 1–87； UniProt 451–537 Author chain L； PDBConstruct 1–87； UniProt 451–537 Author chain M； PDBConstruct 1–87； UniProt 451–537 Author chain N； PDBConstruct 1–87； UniProt 451–537 Author chain O； PDBConstruct 1–87； UniProt 451–537 Author chain P； PDBConstruct 1–87； UniProt 451–537

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	6xkj
Deposition date deposition_date	2020-06-26
Structure title title	Cryo-EM structure of CARD8-CARD filament
Keywords keywords	Filament, inflammasome, signaling, UPA, FIIND, CARD, NLRP1, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	35.43 Å
Radius of gyration Rg (electron density) rg_electron	34.77 Å
Forward intensity I(0) i0	404381000.00
Molecular weight molecular_weight	157460.0 kDa
Excluded volume excluded_volume	195600 Å³
Envelope volume envelope_volume	259750 Å³
Hydration-shell volume shell_volume	60749 Å³
Envelope diameter envelope_diameter	115.5 Å
Shell Rg shell_rg	42.75 Å
Envelope Rg envelope_rg	33.94 Å
Shape Rg shape_rg	34.81 Å
Total Rg total_rg	35.19 Å
Total atoms total_atoms	11056
Residues n_residues	1360
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	110.7 Å
Rg (real space) rg_real	35.23 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	4.0440e+08
I(0) uncertainty (real space) i0_real_error	6.1650e+06
Rg (reciprocal space) rg_reciprocal	35.36 Å
I(0) (reciprocal space) i0_reciprocal	404400000.0000
Solution quality estimate total_estimate	0.8875
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	83320000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.54 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	111333

Description description	Caspase recruitment domain-containing protein 8
Molecular weight formula_weight	10103.4 kDa
Source method src_method	man
Copy count entity_count	16

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A,B,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	11056

Cryo-EM structure of CARD8-CARD filament

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

Caspase recruitment domain-containing protein 8

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/xk/6xkj/6xkj.fit
pddf	/app/data/pr_computation/xk/6xkj/6xkj.pr.out
profile	/app/data/saxs_computation/xk/6xkj/6xkj.dat