5CYK: Ytm1

Structure of Ytm1 bound to the C-terminal domain of Erb1-R486E. Determined by X-ray diffraction at 3.0 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Chaetomium thermophilum
Chains: 2
Atoms: 6,182
Mol. weight: 96.27 kDa
Released: 28 Oct 2015

Explore 5CYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CYK contains 13 α-helices and 68 β-strands across 2 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: 9 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	16-20	5	1
α-helix	31-33	3
α-helix	43-50	8
β-strand	63-67	5	1
β-strand	70-71	2	1
α-helix	76-82	7
β-strand	90-97	8	1
α-helix	98-99	2
β-strand	103-109	7	2
β-strand	114-120	7	3
α-helix	125-132	8
β-strand	145-150	6	3
β-strand	155-158	4	3
β-strand	164-167	4	3
β-strand	170	1	4
α-helix	172-174	3
β-strand	176	1	4
β-strand	180-185	6	5
β-strand	190-195	6	5
β-strand	199-207	9	5
β-strand	213-222	10	5
β-strand	228-234	7	6
β-strand	239-244	6	6
β-strand	249-253	5	6
β-strand	285-287	3	5
β-strand	293	1	6
β-strand	300-305	6	7
β-strand	312-317	6	7
β-strand	321-326	6	7
β-strand	334-337	4	7
β-strand	342-348	7	8
β-strand	357-362	6	8
β-strand	367-370	4	8
β-strand	382-384	3	8
β-strand	391-396	6	9
β-strand	403-408	6	9
β-strand	413-417	5	9
β-strand	422	1	8
α-helix	423-425	3
β-strand	434-435	2	8
β-strand	437-441	5	9
α-helix	444-447	4
α-helix	454-455	2
β-strand	463-467	5	2
β-strand	474-477	4	2
β-strand	481-486	6	2

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	436-438	3
β-strand	445-449	5	10
β-strand	456-461	6	11
β-strand	467-472	6	11
β-strand	476-481	6	11
β-strand	487-492	6	11
β-strand	499-504	6	12
β-strand	513-517	5	12
β-strand	520-524	5	12
α-helix	533-544	12
β-strand	567-570	4	12
α-helix	574-578	5
β-strand	581-587	7	12
β-strand	593-596	4	13
β-strand	602-606	5	13
β-strand	615-619	5	13
β-strand	624-626	3	13
β-strand	636-641	6	14
β-strand	647-652	6	14
β-strand	656-660	5	14
β-strand	666-670	5	14
β-strand	677-682	6	15
β-strand	688-693	6	15
β-strand	697-702	6	15
β-strand	711-714	4	15
β-strand	720-725	6	16
β-strand	732-737	6	16
β-strand	742-748	7	16
α-helix	756-757	2
β-strand	758-765	8	16
β-strand	771	1	17
β-strand	774	1	17
β-strand	776-781	6	10
β-strand	788-792	5	10
β-strand	797-800	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome biogenesis protein YTM1	A	protein	495	Chaetomium thermophilum	G0SFB5 (AlphaFold model)
Ribosome biogenesis protein ERB1	B	protein	389	Chaetomium thermophilum	G0SCK6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5CYK_1 Ribosome biogenesis protein YTM1 (chains A)
MDAPMEDAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLDTGS
IPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRSLIPPVYEASFEHDDWVSAVDVL
SATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNASGSVIATSPSGSHGGHTASI
KAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLELYGHTGSVDWLDVDGHSKHI
LTASADGAIGFWSASKASAPEPDASLLPGAHVSKRRKATSSVSTAQRGPLGLWSIHTAPA
TAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHPLLSLSALTRAGTTSPLLAA
GTSARHITMVDPRASSATTSVMTLRGHANKVVSLSPSPENEYSLVSGSHDGTCRVWDLRS
VRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGCKVFSVVWDKLGIFSGGEDK
KVQVNRGRNIVTEQK

Sequence of entity 2 (B), FASTA

>5CYK_2 Ribosome biogenesis protein ERB1 (chains B)
MAHHHHHHSAALEVLFQGPGPSPDELKPFPTVQQTIFRGHEGRVRSVAIDPTGVALATGG
DDGTVRVWELLTGEQVWSVKLNGDEAVNTVRWRPTKDTFILAAAAGEDIFLMIPTHPSVT
PALDQASRDILNAGFGHATNGKQQANLPPGKEPPGKWARPGTRLEDEGVLLRITVRSTIK
AISWHRRGDHFATVSPSGQRSSVAIHTLSKHLTQIPFRKLNGLAQTASFHPLRPLFFVAT
QRSIRCYDLQKLELVKIVQPGAKWISSFDVHPGGDNLVVGSYDKRLLWHDLDLSNRPYKT
MRFHTEAIRAVRFHKGGLPLFADASDDGSLQIFHGKVPNDQLENPTIVPVKMLKGHKVVN
KLGVLDIDWHPREPWCVSAGADGTARLWM

Primary citation

The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two beta-propellers during the assembly of large ribosomal subunits in eukaryotes. Wegrecki, M., Rodriguez-Galan, O., de la Cruz, J. et al. Nucleic Acids Res (2015) 43:11017-11030. DOI 10.1093/nar/gkv1043 · PubMed

Other PDB entries of the same protein (UniProt G0SFB5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QTB 1.89 Å, Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum
5CXB 2.1 Å, Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 2 space group
8PV2 2.63 Å, Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1
5EM2 2.67 Å, Crystal structure of the Erb1-Ytm1 complex
8I9Z 2.7 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4
8IA0 2.7 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6
8I9X 2.8 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1
5CXC 3.1 Å, Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group
8I9Y 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2

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