SAXSdb — 6k9f

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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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 345–431 Chain B； UniProt 345–431 Chain C； UniProt 345–431 Chain D； UniProt 345–431 Chain E； UniProt 345–431 Chain F； UniProt 345–431 Chain G； UniProt 345–431 Chain H； UniProt 345–431 Chain I； UniProt 345–431 Chain J； UniProt 345–431 Chain K； UniProt 345–431 Chain L； UniProt 345–431	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.70 Å R-free 0.302

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 6K9F	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
6XKJ Cryo-EM structure of CARD8-CARD filament Deposited 2020-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain B 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain C 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain D 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain E 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain F 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain G 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain H 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain I 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain J 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain K 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain L 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain M 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain N 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain O 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537) Chain P 451–537（87 aa） Fragment：CARD domain (UNP residues 451-537)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
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	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–91； UniProt 345–431 Author chain B； PDBConstruct 5–91； UniProt 345–431 Author chain C； PDBConstruct 5–91； UniProt 345–431 Author chain D； PDBConstruct 5–91； UniProt 345–431 Author chain E； PDBConstruct 5–91； UniProt 345–431 Author chain F； PDBConstruct 5–91； UniProt 345–431 Author chain G； PDBConstruct 5–91； UniProt 345–431 Author chain H； PDBConstruct 5–91； UniProt 345–431 Author chain I； PDBConstruct 5–91； UniProt 345–431 Author chain J； PDBConstruct 5–91； UniProt 345–431 Author chain K； PDBConstruct 5–91； UniProt 345–431 Author chain L； PDBConstruct 5–91； UniProt 345–431

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	6k9f
Deposition date deposition_date	2019-06-15
Structure title title	Structure of unknow protein 4
Keywords keywords	filament, SIGNALING PROTEIN; SIGNALING PROTEIN
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	33.43 Å
Radius of gyration Rg (electron density) rg_electron	32.63 Å
Forward intensity I(0) i0	245069000.00
Molecular weight molecular_weight	120820.0 kDa
Excluded volume excluded_volume	150150 Å³
Envelope volume envelope_volume	213790 Å³
Hydration-shell volume shell_volume	53431 Å³
Envelope diameter envelope_diameter	103.8 Å
Shell Rg shell_rg	40.59 Å
Envelope Rg envelope_rg	31.68 Å
Shape Rg shape_rg	32.67 Å
Total Rg total_rg	33.18 Å
Total atoms total_atoms	8484
Residues n_residues	1044
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	97.9 Å
Rg (real space) rg_real	33.19 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.4510e+08
I(0) uncertainty (real space) i0_real_error	3.0000e+06
Rg (reciprocal space) rg_reciprocal	33.34 Å
I(0) (reciprocal space) i0_reciprocal	245100000.0000
Solution quality estimate total_estimate	0.9007
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.8 Å
Skewness Skewness skewness	0.015
Kurtosis Kurtosis kurtosis	-0.483
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48980000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.935

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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	3.700 Å
Low-resolution limit resolution_low	92.400 Å
R factor r_factor	0.2547
R_work r_work	0.2530
R_free r_free	0.3017

Resolution resolution	3.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	98280

Description description	Caspase recruitment domain-containing protein 8
Molecular weight formula_weight	10445.8 kDa
Source method src_method	man
Copy count entity_count	12

Structure of unknow protein 4

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

Refinement Refinement

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)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	8484

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 BL21(DE3)

fit	/app/data/saxs_computation/k9/6k9f/6k9f.fit
pddf	/app/data/pr_computation/k9/6k9f/6k9f.pr.out
profile	/app/data/saxs_computation/k9/6k9f/6k9f.dat