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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	TRANSCRIPTION FACTOR E2-ALPHA × 1 （P15923） RHOMBOTIN-2 × 1 （P25791） LIM DOMAIN-BINDING PROTEIN 1 × 1 （Q86U70） EBOX FORWARD × 1 EBOX REVERSE × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	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 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	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 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	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 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ypa__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ypa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ypa__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.06 Å
Rg (electron density)	26.40 Å
Total Rg	26.99 Å
Atom count	2894
Residues	318
Excluded volume	49968 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ypa__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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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6. 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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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

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TRANSCRIPTION FACTOR E2-ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RHOMBOTIN-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

LIM DOMAIN-BINDING PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ypa__assembly_1__model_1

2ypa__assembly_1__model_1 | I(q)

2ypa__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)