1RUT: PDB entry 1RUT

Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain. Determined by X-ray diffraction at 1.3 Å resolution. Released 12 Oct 2004.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Mus musculus
Chains: 1
Atoms: 1,448
Mol. weight: 20.46 kDa
Ligands: ZN
Released: 12 Oct 2004

Explore 1RUT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RUT contains 9 α-helices and 22 β-strands across 1 chain. 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 X: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	20-21	2
β-strand	22	1	1
β-strand	23	1	2
β-strand	29	1	1
β-strand	34-38	5	2
β-strand	41-43	3	2
α-helix	45-47	3
β-strand	49	1	3
β-strand	56	1	3
α-helix	57-60	4
β-strand	63-67	5	4
β-strand	70-72	3	4
α-helix	74-81	8
β-strand	85-86	2	5
β-strand	93-94	2	5
β-strand	99-100	2	6
β-strand	101-103	3	7
β-strand	106-108	3	7
α-helix	110-112	3
β-strand	114	1	8
α-helix	120	1
β-strand	121	1	8
α-helix	122	1
β-strand	127-131	5	9
β-strand	134-137	4	9
α-helix	138-140	3
β-strand	302-303	2	9
α-helix	304-307	4
β-strand	308-309	2	6
β-strand	319-321	3	4
β-strand	323-326	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fusion protein of Lmo4 protein and LIM domain-binding protein 1	X	protein	188	Mus musculus	P70662 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>1RUT_1 Fusion protein of Lmo4 protein and LIM domain-binding protein 1 (chains X)
GSLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRN
DYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSL
FCEHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFD
AANGIDDE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex. Deane, J.E., Ryan, D.P., Sunde, M. et al. EMBO J (2004) 23:3589-3598. DOI 10.1038/sj.emboj.7600376 · PubMed

Other PDB entries of the same protein (UniProt P70662 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PTL 2.5 Å, Structure of the self-association domain of the chromatin looping factor LDB1
4JCJ 3.0 Å, Crystal structure of Isl1 LIM domains with Ldb1 LIM-interaction domain
1J2O Structure of FLIN2, a complex containing the N-terminal LIM domain of LMO2 and ldb1-LID
1M3V FLIN4: Fusion of the LIM binding domain of Ldb1 and the N-terminal LIM domain of LMO4
2JTN NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex
2L6Y haddock model of GATA1NF:Lmo2LIM2-Ldb1LID
2L6Z haddock model of GATA1NF:Lmo2LIM2-Ldb1LID with FOG
2LXD Backbone 1H, 13C, and 15N Chemical Shift Assignments for LMO2(LIM2)-Ldb1(LID)

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