SAXSdb — 7y3k

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

Sal-like 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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 855–930 Chain B； UniProt 855–930	Not recorded	DNA (16-mer) × 1 DNA (16-mer) × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M BIS-TRIS, pH 5.5, 0.2 M Sodium chloride, 25% polyethylene glycol 3350	Resolution 2.50 Å R-free 0.250

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 7Y3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 405–432（28 aa）	Not recorded	ZN ZINC ION × 2 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG MME 500, 8% PEG 20K, 210mM calcium acetate, 100mM tris pH 7.5	Resolution 3.58 Å R-free 0.267
7BQU Cereblon in complex with SALL4 and (S)-thalidomide Deposited 2020-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 410–432（23 aa）	Not recorded	EF2 S-Thalidomide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride	Resolution 1.90 Å R-free 0.236
7BQV Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide Deposited 2020-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 410–432（23 aa）	Not recorded	F4U 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG 4000, 0.1 M MES (pH 6.0), 0.2 M lithium sulfate	Resolution 1.80 Å R-free 0.223
7Y3I Structure of DNA bound SALL4 Deposited 2022-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain B 855–930（76 aa） Chain D 855–930（76 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M BIS-tris, pH 6.5, 25% w/v polyethylene glycol 3350	Resolution 2.45 Å R-free 0.242
7Y3I Structure of DNA bound SALL4 Deposited 2022-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 855–930（76 aa） Chain C 855–930（76 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M BIS-tris, pH 6.5, 25% w/v polyethylene glycol 3350	Resolution 2.45 Å R-free 0.242
7Y3M Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA Deposited 2022-06-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 378–453（76 aa） Chain B 378–453（76 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M HEPES, pH 6.5, 10% polyethylene glycol 6000, 5% (v/v) 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.72 Å R-free 0.268
7Y3M Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA Deposited 2022-06-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 378–453（76 aa） Chain F 378–453（76 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M HEPES, pH 6.5, 10% polyethylene glycol 6000, 5% (v/v) 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.72 Å R-free 0.268
7Y3M Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA Deposited 2022-06-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain I 378–453（76 aa） Chain J 378–453（76 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M HEPES, pH 6.5, 10% polyethylene glycol 6000, 5% (v/v) 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.72 Å R-free 0.268
8CUC Crystal structure analysis of SALL4 zinc finger domain in complex with DNA Deposited 2022-05-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain F 864–929（66 aa） Chain H 864–929（66 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG3350, 40 mM ammonium sulfate, Bis-Tris, pH 6.0	Resolution 2.09 Å R-free 0.231
8CUC Crystal structure analysis of SALL4 zinc finger domain in complex with DNA Deposited 2022-05-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain E 864–929（66 aa） Chain G 864–929（66 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG3350, 40 mM ammonium sulfate, Bis-Tris, pH 6.0	Resolution 2.09 Å R-free 0.231
8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 379–432（54 aa）	Not recorded	ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 2.95 Å R-free 0.272
8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 379–432（54 aa）	Not recorded	ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 2.95 Å R-free 0.272
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 379–432（54 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 2.90 Å R-free 0.273
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 379–432（54 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 2.90 Å R-free 0.273
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 370–454（85 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 3.10 Å R-free 0.346
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 370–454（85 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 3.10 Å R-free 0.346
9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 392–449（58 aa）	Not recorded	ZN ZINC ION × 2 QFC Mezigdomide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.	Resolution 2.70 Å
9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 392–449（58 aa）	Mutation：G416A	ZN ZINC ION × 2 QFC Mezigdomide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.	Resolution 2.70 Å

11 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SALL4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–79； UniProt 855–930 Author chain B； PDBConstruct 4–79； UniProt 855–930

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	7y3k
Deposition date deposition_date	2022-06-11
Structure title title	Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA
Keywords keywords	SALL4, zinc finger, AT-rich DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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	18.15 Å
Radius of gyration Rg (electron density) rg_electron	17.39 Å
Forward intensity I(0) i0	15475800.00
Molecular weight molecular_weight	21899.0 kDa
Excluded volume excluded_volume	24000 Å³
Envelope volume envelope_volume	30865 Å³
Hydration-shell volume shell_volume	15303 Å³
Envelope diameter envelope_diameter	60.9 Å
Shell Rg shell_rg	22.86 Å
Envelope Rg envelope_rg	17.44 Å
Shape Rg shape_rg	17.34 Å
Total Rg total_rg	18.16 Å
Total atoms total_atoms	1478
Residues n_residues	140
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	61.5 Å
Rg (real space) rg_real	18.08 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.5480e+07
I(0) uncertainty (real space) i0_real_error	1.9160e+05
Rg (reciprocal space) rg_reciprocal	18.09 Å
I(0) (reciprocal space) i0_reciprocal	15480000.0000
Solution quality estimate total_estimate	0.8824
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.328
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1679000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Sal-like protein 4
Molecular weight formula_weight	8709.0 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	1500

GHMMTPLLAAQPRRQAKQHGCTRCGKNFSSASALQIHERTHTGEKPFVCNICGRAFTTKGNLKVHYMTHGANNNSARRG

来源 Source

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

Entity 2 Entity 2 polymer

Description description	DNA (16-mer)
Molecular weight formula_weight	4896.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GGAAATATTATATTCC

Entity 3 Entity 3 polymer

Description description	DNA (16-mer)
Molecular weight formula_weight	4896.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

GGAATATAATATTTCC

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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8. Citations (2)

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Unit-cell length a length_a	43.364 Å
Unit-cell length b length_b	49.868 Å
Unit-cell length c length_c	105.406 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.501 Å
Low-resolution limit resolution_low	28.722 Å
R factor r_factor	0.2103
R_work r_work	0.2059
R_free r_free	0.2504

fit	/app/data/saxs_computation/y3/7y3k/7y3k.fit
pddf	/app/data/pr_computation/y3/7y3k/7y3k.pr.out
profile	/app/data/saxs_computation/y3/7y3k/7y3k.dat

Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA

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

Sal-like 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)