2LXC: Ubiquitin-like protein MDY2

Solution structure of the complex between the Sgt2 homodimerization domain and the Get5 UBL domain. Determined by solution NMR. Released 21 Nov 2012.

Method: Solution NMR
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 1,750
Mol. weight: 24.95 kDa
Released: 21 Nov 2012

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

Secondary structure: helices and β-sheets

2LXC contains 12 α-helices and 9 β-strands across 3 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	74-80	7	1
α-helix	85	1
β-strand	86-92	7	1
β-strand	97	1	2
α-helix	98-107	10
α-helix	114-116	3
β-strand	117-121	5	1
β-strand	124-125	2	1
β-strand	131	1	2
α-helix	132-135	4
β-strand	143-148	6	1

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-21	17
α-helix	27-43	17
α-helix	48-50	3
α-helix	51-54	4

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
α-helix	5-21	17
α-helix	27-44	18
α-helix	48-50	3
α-helix	51-54	4
β-strand	63	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein MDY2	A	protein	81	Saccharomyces cerevisiae	Q12285 (AlphaFold model)
Small glutamine-rich tetratricopeptide repeat-containing protein 2	B, C	protein	74	Saccharomyces cerevisiae	Q12118 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2LXC_1 Ubiquitin-like protein MDY2 (chains A)
MVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFL
SDLKVTPANSTITVMIKPNLE

Sequence of entity 2 (B, C), FASTA

>2LXC_2 Small glutamine-rich tetratricopeptide repeat-containing protein 2 (chains B, C)
SVDSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKS
EFKGQHLADILNSA

Primary citation

Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface. Chartron, J.W., Vandervelde, D.G., Clemons, W.M. Cell Rep (2012) 2:1620-1632. DOI 10.1016/j.celrep.2012.10.010 · PubMed

Other PDB entries of the same protein (UniProt Q12285 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VEJ 1.23 Å, Crystal structure of the Get5 carboxyl domain from S. cerevisiae
4A20 1.78 Å, Crystal structure of the Ubl domain of Mdy2 (Get5) at 1.78A
3ZDM 1.8 Å, Crystal structure of the Sgt2 N domain and the Get5 UBL domain complex
2WPV 1.99 Å, Crystal structure of S. cerevisiae Get4-Get5 complex
4GOC 2.4 Å, Crystal structure of the Get5 ubiquitin-like domain
3LKU 2.8 Å, Crystal structure of S. cerevisiae Get4 in complex with an N-terminal fragment of Get5
5BW8 2.8 Å, 2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae
9NS5 3.19 Å, Get3(D57N)-Get4/5 Complex (ATP-bound)
4PWX 5.4 Å, Crystal structure of an ATP-bound Get3-Get4-Get5 complex from S.cerevisiae
5BWK 6.0 Å, 6.0 A Crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae
2LNZ Solution structure of the Get5 carboxyl domain from S. cerevisiae
2LXA Solution structure of the Get5 ubiquitin-like domain

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