6QTB: Midasin,Midasin

Name: PDB 6QTB: Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum
Published: 2019-08-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum. Determined by X-ray diffraction at 1.89 Å resolution. Released 7 Aug 2019.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Chains: 4
Atoms: 5,794
Mol. weight: 86.14 kDa
Ligands: MG
Released: 7 Aug 2019

Explore 6QTB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QTB contains 37 α-helices and 30 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: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4703-4732	30
β-strand	4778-4787	10	1
β-strand	4789	1	2
α-helix	4790-4792	3
α-helix	4794-4796	3
α-helix	4800-4815	16
β-strand	4821-4828	8	1
β-strand	4832-4836	5	1
α-helix	4841-4842	2
α-helix	4846-4853	8
β-strand	4860	1	2
α-helix	4865-4883	19
β-strand	4892-4901	10	1
α-helix	4907-4922	16
β-strand	4925-4932	8	1
α-helix	4943-4945	3
β-strand	4947-4951	5	3
β-strand	4957-4961	5	3
α-helix	4962-4965	4
β-strand	4971-4974	4	1
α-helix	4977-4979	3
α-helix	4980-4987	8
α-helix	4988-4992	5

Chain B: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	14-20	7	3
α-helix	24-26	3
α-helix	27-29	3
α-helix	30-32	3
β-strand	34-38	5	3
α-helix	43-51	9
β-strand	63-67	5	3
β-strand	70-71	2	3
α-helix	76-82	7
α-helix	89-90	2
β-strand	91-97	7	3

Chain D: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4703-4732	30
β-strand	4779-4787	9	4
β-strand	4789	1	5
α-helix	4790-4792	3
α-helix	4794-4796	3
α-helix	4800-4818	19
β-strand	4821-4828	8	4
β-strand	4832-4836	5	4
α-helix	4841-4842	2
α-helix	4846-4853	8
β-strand	4860	1	5
α-helix	4865-4885	21
β-strand	4893-4901	9	4
α-helix	4907-4922	16
β-strand	4925-4932	8	4
α-helix	4935-4937	3
α-helix	4943-4945	3
β-strand	4947-4951	5	6
β-strand	4957-4961	5	6
α-helix	4962-4965	4
β-strand	4971-4974	4	4
α-helix	4977-4979	3
α-helix	4980-4994	15

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	14-20	7	6
α-helix	27-29	3
α-helix	30-32	3
β-strand	34-38	5	6
α-helix	43-51	9
β-strand	63-67	5	6
β-strand	70-71	2	6
α-helix	76-82	7
α-helix	89-90	2
β-strand	91-97	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Midasin,Midasin	A, D	protein	280	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SHE6
Ribosome biogenesis protein YTM1	B, E	protein	101	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SFB5 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6QTB_1 Midasin,Midasin (chains A, D)
MHISDEQLKRPLRDYGEALEMWSTFQTKTQALSQSLSSQLRLILTGSGIPSKRAYQILLC
VDDSSSMSDDNRSTAGNLALESLVMVARALTVLEAGQIGVMGFGTDVFVAHALTDPPFTS
QDAGARVLQQFTFRQDSTDMVLLLRRTIDHFREARLIQASSSRGGEDLWQLALILSDGLV
QSRDHARLRPLLREAMEQRVMVVFIVMDDARSRKGHSVLELKEARFGPDGVPVIHRYLDS
FPFPYYLIVHHLEDLPGALAALLRTWFAEVNSGSHHHHHH

Sequence of entity 2 (B, E), FASTA

>6QTB_2 Ribosome biogenesis protein YTM1 (chains B, E)
MKHHHHHHPMAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLD
TGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Crystal structures of Rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin-ligand-type complexes. Ahmed, Y.L., Thoms, M., Mitterer, V. et al. Nat Commun (2019) 10:3050-3050. DOI 10.1038/s41467-019-10922-6 · PubMed

Other PDB entries of the same protein (UniProt G0SHE6), best resolution first:

6QTA 1.89 Å, Crystal structure of Rea1-MIDAS/Rsa4-UBL complex from Chaetomium thermophilum
6QT8 2.33 Å, Crystal structure of Rea1-MIDAS domain from Chaetomium thermophilum

Browse structure collections

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