SAXSdb — 9dtg

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

Isoform 2 of Kelch repeat and BTB domain-containing protein 4

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–534 Chain B； UniProt 1–534	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.83 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 9DTG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EQX Solution structure of the BACK domain of Kelch repeat and BTB domain-containing protein 4 Deposited 2007-03-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 142–239（98 aa） Fragment：BACK domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.15mM 13C-15N PROTEIN; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
8VOJ The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and IP6 Deposited 2024-01-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–534（534 aa） Chain B 1–534（534 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
8VPQ The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML Deposited 2024-01-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–534（534 aa） Chain B 1–534（534 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8VRT The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant Deposited 2024-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 17–534（518 aa） Chain B 17–534（518 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
9DTQ The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant Deposited 2024-10-01	Different construct 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 17–534（518 aa） Chain E 17–534（518 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9GGL Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171 Deposited 2024-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–534（518 aa） Chain C 17–534（518 aa）	Not recorded	ZN ZINC ION × 1 A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9GGM Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex Deposited 2024-08-13	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 A 17–534（518 aa） Chain C 17–534（518 aa）	Mutation：Indel mutation R313PRR Mutation：Indel mutation R313PRR	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9GGN Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171 Deposited 2024-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 17–534（518 aa） Chain C 17–534（518 aa）	Not recorded	A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9I2C Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue UM171 Deposited 2025-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 17–534（518 aa） Chain C 17–534（518 aa）	Not recorded	A1ACV (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KBTB4_HUMAN
Isoform	Q9NVX7-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–534； UniProt 1–534 Author chain B； PDBConstruct 1–534； UniProt 1–534

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	9dtg
Deposition date deposition_date	2024-09-30
Structure title title	The cryo-EM structure of apo KBTBD4
Keywords keywords	molecular glue, targeted protein degradation, E3 ligase, transcription and tranlation, LIGASE; LIGASE
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	42.57 Å
Radius of gyration Rg (electron density) rg_electron	42.06 Å
Forward intensity I(0) i0	199394000.00
Molecular weight molecular_weight	114690.0 kDa
Excluded volume excluded_volume	143120 Å³
Envelope volume envelope_volume	215690 Å³
Hydration-shell volume shell_volume	42026 Å³
Envelope diameter envelope_diameter	134.8 Å
Shell Rg shell_rg	48.52 Å
Envelope Rg envelope_rg	40.93 Å
Shape Rg shape_rg	42.07 Å
Total Rg total_rg	42.38 Å
Total atoms total_atoms	8069
Residues n_residues	1023
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	135.7 Å
Rg (real space) rg_real	42.66 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	1.9940e+08
I(0) uncertainty (real space) i0_real_error	3.4910e+06
Rg (reciprocal space) rg_reciprocal	42.57 Å
I(0) (reciprocal space) i0_reciprocal	199400000.0000
Solution quality estimate total_estimate	0.8502
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.235
Kurtosis Kurtosis kurtosis	-0.778
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21520000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.412

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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	3.83 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	550442

Description description	Isoform 2 of Kelch repeat and BTB domain-containing protein 4
Molecular weight formula_weight	59971.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8069

The cryo-EM structure of apo KBTBD4

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

Isoform 2 of Kelch repeat and BTB domain-containing protein 4

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	Trichoplusia ni

fit	/app/data/saxs_computation/dt/9dtg/9dtg.fit
pddf	/app/data/pr_computation/dt/9dtg/9dtg.pr.out
profile	/app/data/saxs_computation/dt/9dtg/9dtg.dat