3ZDM: Sgt2 N domain and the Get5 UBL domain complex

Crystal structure of the Sgt2 N domain and the Get5 UBL domain complex. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Oct 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 6
Atoms: 3,492
Mol. weight: 48.99 kDa
Released: 2 Oct 2013

Explore 3ZDM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZDM contains 25 α-helices and 14 β-strands across 6 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.

Chains A and D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	5-21	17
α-helix	27-44	18
α-helix	48-50	3
α-helix	51-56	6
α-helix	58-68	11

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-21	17
α-helix	27-44	18

Chains C and F: 5 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
α-helix	126-127	2
β-strand	131	1	2
α-helix	132-135	4
β-strand	143-148	6	1

Chain E: 3 helices, 0 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Small glutamine-rich tetratricopeptide repeat- containing protein 2	A, B, D, E	protein	72	SACCHAROMYCES CEREVISIAE	Q12118 (AlphaFold model)
Ubiquitin-like protein MDY2	C, F	protein	81	SACCHAROMYCES CEREVISIAE	Q12285 (AlphaFold model)

Sequence of entity 1 (A, B, D, E), FASTA

>3ZDM_1 SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2 (chains A, B, D, E)
MSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEF
KGQHLADILNSA

Sequence of entity 2 (C, F), FASTA

>3ZDM_2 UBIQUITIN-LIKE PROTEIN MDY2 (chains C, F)
NAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNL
FLSDLKVTPANSTITVMIKPN

Primary citation

Structure of the Sgt2 Dimerization Domain Complexed with the Get5 Ubl Domain Involved in the Targeting of Tail-Anchored Membrane Proteins to the Endoplasmic Reticulum. Tung, J.-Y., Li, Y.-C., Lin, T.-W. et al. Acta Crystallogr D Biol Crystallogr (2013) 69:2081. DOI 10.1107/S0907444913019379 · PubMed

Other PDB entries of the same protein (UniProt Q12118 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LYP 1.55 Å, Crystal structure of the Tpr Domain of Sgt2.
5LYN 2.0 Å, Structure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 peptide fragment
2LXB Solution structure of the Sgt2 homodimerization domain
2LXC Solution structure of the complex between the Sgt2 homodimerization domain and the Get5…
4ASV Solution structure of the N-terminal dimerisation domain of Sgt2
4ASW Structure of the complex between the N-terminal dimerisation domain of Sgt2 and the UBL…
9LLV Dimer Sgt2 from S.cerevisiae

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