SAXSdb — 2ypa

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

T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1

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 Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 180–253	Fragment：BHLH, RESIDUES 180-253	TRANSCRIPTION FACTOR E2-ALPHA × 1 （P15923） RHOMBOTIN-2 × 1 （P25791） LIM DOMAIN-BINDING PROTEIN 1 × 1 （Q86U70） EBOX FORWARD × 1 EBOX REVERSE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.80 Å R-free 0.269

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 2YPA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YPB Structure of the SCL:E47 complex bound to DNA Deposited 2012-10-30	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 180–253（74 aa） Fragment：BHLH, RESIDUES 5-78	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.87 Å R-free 0.288

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TAL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–91； UniProt 180–253

TRANSCRIPTION FACTOR E2-ALPHA

HOMO SAPIENS

UniProt P15923

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 Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain B； UniProt 535–613	Fragment：RESIDUES 535-613	T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1 × 1 （P17542） RHOMBOTIN-2 × 1 （P25791） LIM DOMAIN-BINDING PROTEIN 1 × 1 （Q86U70） EBOX FORWARD × 1 EBOX REVERSE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.80 Å R-free 0.269

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 2YPA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MH0 Solution NMR structure of the p300 Taz2:ETAD1 complex Deposited 2013-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–37（37 aa） Fragment：Activation domain 1 (ETAD1), E2A residues 1-37	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.4 mM [U-99% 13C; U-99% 15N] ETAD1, 2 mM Taz2, 20 mM MES, 1 mM sodium azide, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3078 uM ETAD1, 1038 uM [U-99% 13C; U-99% 15N] Taz2, 20 mM MES, 1 mM sodium azide, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YPB Structure of the SCL:E47 complex bound to DNA Deposited 2012-10-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 535–613（79 aa） Fragment：RESIDUES 535-613	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.87 Å R-free 0.288
3U5V Crystal structure of Max-E47 Deposited 2011-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 560–610（51 aa） Fragment：SEE REMARK 999	Not recorded	NO3 NITRATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% glycerol, 3.2-3.5 M sodium nitrate, 0.1 M sodium acetate anhydrous, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.235
6MGN mouse Id1 (51-104) - human hE47 (348-399) complex Deposited 2018-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 558–609（52 aa） Fragment：unp residues 558-609	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M potassium phosphate (pH 6.0), 0.25 M NaCl, 22.5% PEG8000.	Resolution 1.90 Å R-free 0.217

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

View Construct and Data Evidence

UniProt name	TFE2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–82； UniProt 535–613

RHOMBOTIN-2

HOMO SAPIENS

UniProt P25791

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 Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain C； UniProt 25–156	Fragment：LIM, RESIDUES 25-156	T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1 × 1 （P17542） TRANSCRIPTION FACTOR E2-ALPHA × 1 （P15923） LIM DOMAIN-BINDING PROTEIN 1 × 1 （Q86U70） EBOX FORWARD × 1 EBOX REVERSE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.80 Å R-free 0.269

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 2YPA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XJY Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；25% PEG 1500 AND 100 MM SPG, BUFFER PH 4.0	Resolution 2.40 Å R-free 0.229
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 26–156（131 aa） Fragment：RESIDUES 26-156	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
4KFZ Crystal structure of LMO2 and anti-LMO2 VH complex Deposited 2013-04-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 9–158（150 aa） Fragment：UNP residues 9-158	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258
4KFZ Crystal structure of LMO2 and anti-LMO2 VH complex Deposited 2013-04-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 9–158（150 aa） Fragment：UNP residues 9-158	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258
4KFZ Crystal structure of LMO2 and anti-LMO2 VH complex Deposited 2013-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 9–158（150 aa） Fragment：UNP residues 9-158	Not recorded	ZN ZINC ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258
4KFZ Crystal structure of LMO2 and anti-LMO2 VH complex Deposited 2013-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 9–158（150 aa） Fragment：UNP residues 9-158	Not recorded	ZN ZINC ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100mM MES monohydrate pH 6.0, 0.8 M ammonium sulfate, and additive 1, 6 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.80 Å R-free 0.258

3 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBTN2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 14–145； UniProt 25–156

LIM DOMAIN-BINDING PROTEIN 1

HOMO SAPIENS

UniProt Q86U70

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 Heteromer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain D； UniProt 336–375	Fragment：LID, RESIDUES 336-375	T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1 × 1 （P17542） TRANSCRIPTION FACTOR E2-ALPHA × 1 （P15923） RHOMBOTIN-2 × 1 （P25791） EBOX FORWARD × 1 EBOX REVERSE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.80 Å R-free 0.269

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 2YPA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XJY Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 334–368（35 aa） Fragment：RESIDUES 334-368	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；25% PEG 1500 AND 100 MM SPG, BUFFER PH 4.0	Resolution 2.40 Å R-free 0.229
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 334–368（35 aa） Fragment：RESIDUES 334-368	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 334–368（35 aa） Fragment：RESIDUES 334-368	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 334–368（35 aa） Fragment：RESIDUES 334-368	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 334–368（35 aa） Fragment：RESIDUES 334-368	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
2XJZ Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form Deposited 2010-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 334–368（35 aa） Fragment：RESIDUES 334-368	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；1.6 M NACL, 100 MM MES PH5 AND 1 MM DTT	Resolution 2.80 Å R-free 0.244
6TYD Structure of human LDB1 in complex with SSBP2 Deposited 2019-08-08	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 V 20–249（230 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；100 mM lithium sulfate monohydrate, 100 mM sodium citrate tribasic dihydrate pH 5.6, 1% v/v PEG400, 10mM DTT	Resolution 2.80 Å R-free 0.281
7OB5 Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide Deposited 2021-04-21	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 P 401–411（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.095 M Hepes pH 7.1, 28% PEG 400, 0.19 M CaCl2 and 5 % Glycerol	Resolution 1.80 Å R-free 0.171
7OB8 Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide and stabilizer Fusicoccin-A Deposited 2021-04-21	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 401–411（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FSC FUSICOCCIN × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.095 M Hepes pH 7.1, 28%PEG 400, 0.19 M CaCl2 and 5 % Glycerol	Resolution 1.80 Å R-free 0.199
8HIB The crystal structure of Pygo2-LDB1-SSBP2 triple complex Deposited 2022-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain V 20–249（230 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100 mM Li2SO4, 100 mM sodium citrate tribasic dihydrate pH 5.6, 1% v/v PEG400, and 10 mM DTT	Resolution 2.45 Å R-free 0.246
8SSU ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA Deposited 2023-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: trimeric	Chain A 195–258（64 aa） Fragment：Zinc finger domains 3-11 of CTCF, Residues 195-258 of LDB1	Not recorded	EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane/pH 6.4, 20% w/v Polyethylene glycol 3,350	Resolution 2.89 Å R-free 0.240
9F5B Identification of zinc ions in LMO4. Deposited 2024-04-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 336–375（40 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25 M Sodium Malonate pH 7, 20 % v/w PEG 3350	Resolution 1.80 Å R-free 0.234

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LDB1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 12–51； UniProt 336–375

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	2ypa
Deposition date deposition_date	2012-10-30
Structure title title	Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA
Keywords keywords	IMMUNE SYSTEM, HEMATOPOIESIS, LEUKEMIA; IMMUNE SYSTEM
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	27.06 Å
Radius of gyration Rg (electron density) rg_electron	26.40 Å
Forward intensity I(0) i0	38666900.00
Molecular weight molecular_weight	41971.0 kDa
Excluded volume excluded_volume	49968 Å³
Envelope volume envelope_volume	70025 Å³
Hydration-shell volume shell_volume	23155 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	32.23 Å
Envelope Rg envelope_rg	26.68 Å
Shape Rg shape_rg	26.40 Å
Total Rg total_rg	26.99 Å
Total atoms total_atoms	2894
Residues n_residues	318
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	88.2 Å
Rg (real space) rg_real	27.03 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	3.8670e+07
I(0) uncertainty (real space) i0_real_error	5.9240e+05
Rg (reciprocal space) rg_reciprocal	27.04 Å
I(0) (reciprocal space) i0_reciprocal	38670000.0000
Solution quality estimate total_estimate	0.8909
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.154
Kurtosis Kurtosis kurtosis	-0.719
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4005000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1
Molecular weight formula_weight	10721.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2894

MGSSHHHHHHSQDPEISDGPHTKVVRRIFTNSRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLLNDQEEEGTQR

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	TRANSCRIPTION FACTOR E2-ALPHA
Molecular weight formula_weight	9674.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADLSLEEKDLRDRERRMANNARERVRVRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLNPKAA

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 3 Entity 3 polymer

Description description	RHOMBOTIN-2
Molecular weight formula_weight	17007.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSQDPSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING

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 4 Entity 4 polymer

Description description	LIM DOMAIN-BINDING PROTEIN 1
Molecular weight formula_weight	5244.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAANGIDDE

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 5 Entity 5 polymer

Description description	EBOX FORWARD
Molecular weight formula_weight	3284.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

ACCATCTGTTC

Entity 6 Entity 6 polymer

Description description	EBOX REVERSE
Molecular weight formula_weight	3422.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GAACAGATGGT

Entity 7 Entity 7 non-polymer

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

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2ypaA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	2ypaB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	2ypaC01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

Domain ID domain_id	2ypaC02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

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8. Citations (1)

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Unit-cell length a length_a	102.966 Å
Unit-cell length b length_b	141.044 Å
Unit-cell length c length_c	148.793 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	16

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.150 Å
R factor r_factor	0.2261
R_work r_work	0.2240
R_free r_free	0.2695

fit	/app/data/saxs_computation/yp/2ypa/2ypa.fit
pddf	/app/data/pr_computation/yp/2ypa/2ypa.pr.out
profile	/app/data/saxs_computation/yp/2ypa/2ypa.dat

Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA

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

T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

TRANSCRIPTION FACTOR E2-ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

RHOMBOTIN-2

State in the Current Structure

Other States of the Same Protein in the Database

LIM DOMAIN-BINDING PROTEIN 1

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)