› 2ypa

X-ray diffraction
2.8Å resolution

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

Released:
DOI: 10.2210/pdb2ypa/pdb
PDB entry 2ypa coloured by chain, front view.
PDB entry 2ypa coloured by chain, side view.
PDB entry 2ypa coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for LMO2-driven recruitment of the SCL:E47bHLH heterodimer to hematopoietic-specific transcriptional targets.
El Omari K, Hoosdally SJ, Tuladhar K, Karia D, Hall-Ponselé E, Platonova O, Vyas P, Patient R, Porcher C, Mancini EJ
Cell Rep 4 135-47 (2013)
PMID: 23831025

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-115951 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
T-cell acute lymphocytic leukemia protein 1 Chain: A
Molecule details ›
Chain: A
Length: 91 amino acids
Theoretical weight: 10.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17542 (Residues: 180-253; Coverage: 22%)
Gene names: BHLHA17, SCL, TAL1, TCL5
Sequence domains: Helix-loop-helix DNA-binding domain
Structure domains: Helix-loop-helix DNA-binding domain
Transcription factor E2-alpha Chain: B
Molecule details ›
Chain: B
Length: 82 amino acids
Theoretical weight: 9.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P15923 (Residues: 538-616; Coverage: 12%)
Gene names: BHLHB21, E2A, ITF1, TCF3
Sequence domains: Helix-loop-helix DNA-binding domain
Structure domains: Helix-loop-helix DNA-binding domain
Rhombotin-2 Chain: C
Molecule details ›
Chain: C
Length: 145 amino acids
Theoretical weight: 17.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P25791 (Residues: 25-156; Coverage: 84%)
Gene names: LMO2, RBTN2, RBTNL1, RHOM2, TTG2
Sequence domains: LIM domain
Structure domains: Cysteine Rich Protein
LIM domain-binding protein 1 Chain: D
Molecule details ›
Chain: D
Length: 51 amino acids
Theoretical weight: 5.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86U70 (Residues: 336-375; Coverage: 10%)
Gene names: CLIM2, LDB1
Sequence domains: LIM interaction domain (LID)
EBOX FORWARD Chain: E
Molecule details ›
Chain: E
Length: 11 nucleotides
Theoretical weight: 3.28 KDa
EBOX REVERSE Chain: F
Molecule details ›
Chain: F
Length: 11 nucleotides
Theoretical weight: 3.42 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: F222
Unit cell:
a: 102.966Å b: 141.044Å c: 148.793Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.269
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Mechanisms and proteins involved in long-distance interactions.
Maksimenko et al. (2014)
12 more

8 mentions without citation

Structural basis for LMO2-driven recruitment of the SCL:E47bHLH heterodimer to hematopoietic-specific transcriptional targets.
El Omari et al. (2013)
7 more