2YPA: SCL:E47:LMO2:LDB1 complex

Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA. Determined by X-ray diffraction at 2.8 Å resolution. Released 31 Jul 2013.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 2,894
Mol. weight: 49.62 kDa
Ligands: ZN
Released: 31 Jul 2013

Explore 2YPA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YPA contains 7 α-helices and 18 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	184-211	28
α-helix	225-245	21

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	540-577	38
α-helix	585-608	24

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	1
β-strand	48-50	3	1
β-strand	56	1	2
β-strand	63	1	2
β-strand	71-74	4	3
β-strand	77-79	3	3
α-helix	81-88	8
α-helix	89-91	3
β-strand	92-93	2	4
β-strand	100-101	2	4
β-strand	106-110	5	5
β-strand	113-116	4	5
β-strand	121	1	6
β-strand	128	1	6
β-strand	134-138	5	7
β-strand	141-144	4	7
α-helix	148-153	6

Chain D: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	301-303	3	7
β-strand	308-309	2	5
β-strand	319-320	2	3
β-strand	323-326	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell acute lymphocytic leukemia protein 1	A	protein	91	HOMO SAPIENS	P17542 (AlphaFold model)
Transcription factor E2-alpha	B	protein	82	HOMO SAPIENS	P15923 (AlphaFold model)
Rhombotin-2	C	protein	145	HOMO SAPIENS	P25791 (AlphaFold model)
Lim domain-binding protein 1	D	protein	51	HOMO SAPIENS	Q86U70 (AlphaFold model)
Ebox forward	E	DNA	11	HOMO SAPIENS
Ebox reverse	F	DNA	11	HOMO SAPIENS

Sequence of entity 1 (A), FASTA

>2YPA_1 T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1 (chains A)
MGSSHHHHHHSQDPEISDGPHTKVVRRIFTNSRERWRQQNVNGAFAELRKLIPTHPPDKK
LSKNEILRLAMKYINFLAKLLNDQEEEGTQR

Sequence of entity 2 (B), FASTA

>2YPA_2 TRANSCRIPTION FACTOR E2-ALPHA (chains B)
MADLSLEEKDLRDRERRMANNARERVRVRDINEAFRELGRMCQMHLKSDKAQTKLLILQQ
AVQVILGLEQQVRERNLNPKAA

Sequence of entity 3 (C), FASTA

>2YPA_3 RHOMBOTIN-2 (chains C)
MGSSHHHHHHSQDPSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRL
YYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCV
GDRYLLINSDIVCEQDIYEWTKING

Sequence of entity 4 (D), FASTA

>2YPA_4 LIM DOMAIN-BINDING PROTEIN 1 (chains D)
GGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAANGIDDE

Sequence of entity 5 (E), FASTA

>2YPA_5 EBOX FORWARD (chains E)
ACCATCTGTTC

Sequence of entity 6 (F), FASTA

>2YPA_6 EBOX REVERSE (chains F)
GAACAGATGGT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets. El Omari, K., Hoosdally, S.J., Tuladhar, K. et al. Cell Rep (2013) 4:135. DOI 10.1016/J.CELREP.2013.06.008 · PubMed

Other PDB entries of the same protein (UniProt P17542 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2YPB 2.87 Å, Structure of the SCL:E47 complex bound to DNA

Browse structure collections

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