5CXB: Ytm1

Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 2 space group. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Nov 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Chaetomium thermophilum
Chains: 2
Atoms: 6,625
Mol. weight: 96.5 kDa
Released: 4 Nov 2015

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

Secondary structure: helices and β-sheets

5CXB contains 24 α-helices and 67 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: 18 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	1
α-helix	24-26	3
α-helix	27-29	3
α-helix	30-33	4
β-strand	34-38	5	1
α-helix	43-51	9
β-strand	63-67	5	1
β-strand	70-71	2	1
α-helix	76-82	7
α-helix	89	1
β-strand	90-97	8	1
α-helix	98-101	4
β-strand	103-109	7	2
β-strand	114-120	7	3
α-helix	125-131	7
α-helix	137-140	4
β-strand	145-150	6	3
β-strand	155-159	5	3
β-strand	164-167	4	3
α-helix	171-173	3
β-strand	180-187	8	4
β-strand	190-195	6	4
β-strand	199-207	9	4
β-strand	213-222	10	4
β-strand	228-234	7	5
β-strand	239-244	6	5
β-strand	249-253	5	5
α-helix	259-262	4
α-helix	264-266	3
β-strand	285-287	3	4
β-strand	291-293	3	5
β-strand	300-305	6	6
β-strand	312-317	6	6
β-strand	321-326	6	6
β-strand	332-337	6	6
β-strand	342-348	7	7
α-helix	349	1
β-strand	357-362	6	7
β-strand	367-370	4	7
β-strand	382-384	3	7
β-strand	391-396	6	8
β-strand	403-408	6	8
β-strand	413-417	5	8
β-strand	422-423	2	7
α-helix	424-425	2
α-helix	426-428	3
β-strand	433-435	3	7
β-strand	437-441	5	8
α-helix	444-447	4
α-helix	454-455	2
α-helix	456-458	3
β-strand	463-469	7	2
β-strand	472-477	6	2
β-strand	481-486	6	2

Chain B: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	435-438	4
β-strand	445-449	5	9
β-strand	456-461	6	10
β-strand	467-472	6	10
β-strand	476-481	6	10
β-strand	487-492	6	10
β-strand	499-504	6	11
β-strand	513-517	5	11
β-strand	520-524	5	11
α-helix	533-544	12
β-strand	568-570	3	11
α-helix	574-578	5
β-strand	581-586	6	11
β-strand	593-596	4	12
β-strand	602-606	5	12
α-helix	608-610	3
β-strand	615-619	5	12
β-strand	624-626	3	12
β-strand	636-641	6	13
β-strand	647-652	6	13
β-strand	656-660	5	13
β-strand	668-670	3	13
β-strand	677-682	6	14
β-strand	688-693	6	14
β-strand	698-702	5	14
β-strand	711-713	3	14
β-strand	720-725	6	15
β-strand	732-737	6	15
β-strand	741-748	8	15
α-helix	756-757	2
β-strand	758-766	9	15
α-helix	768-770	3
β-strand	771	1	16
β-strand	774	1	16
β-strand	776-781	6	9
β-strand	788-792	5	9
β-strand	797-800	4	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome biogenesis protein YTM1	A	protein	514	Chaetomium thermophilum	G0SFB5 (AlphaFold model)
Ribosome biogenesis protein ERB1	B	protein	369	Chaetomium thermophilum	G0SCK6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5CXB_1 Ribosome biogenesis protein YTM1 (chains A)
MAHHHHHHSSGLEVLFQGPMDAPMEDAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADI
RRYGLSRILNSESMLDTGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRSLIP
PVYEASFEHDDWVSAVDVLSATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNAS
GSVIATSPSGSHGGHTASIKAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLEL
YGHTGSVDWLDVDGHSKHILTASADGAIGFWSASKASAPEPDASLLPGAHVSKRRKATSS
VSTAQRGPLGLWSIHTAPATAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHP
LLSLSALTRAGTTSPLLAAGTSARHITMVDPRASSATTSVMTLRGHANKVVSLSPSPENE
YSLVSGSHDGTCRVWDLRSVRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGC
KVFSVVWDKLGIFSGGEDKKVQVNRGRNIVTEQK

Sequence of entity 2 (B), FASTA

>5CXB_2 Ribosome biogenesis protein ERB1 (chains B)
PSPDELKPFPTVQQTIFRGHEGRVRSVAIDPTGVALATGGDDGTVRVWELLTGRQVWSVK
LNGDEAVNTVRWRPTKDTFILAAAAGEDIFLMIPTHPSVTPALDQASRDILNAGFGHATN
GKQQANLPPGKEPPGKWARPGTRLEDEGVLLRITVRSTIKAISWHRRGDHFATVSPSGQR
SSVAIHTLSKHLTQIPFRKLNGLAQTASFHPLRPLFFVATQRSIRCYDLQKLELVKIVQP
GAKWISSFDVHPGGDNLVVGSYDKRLLWHDLDLSNRPYKTMRFHTEAIRAVRFHKGGLPL
FADASDDGSLQIFHGKVPNDQLENPTIVPVKMLKGHKVVNKLGVLDIDWHPREPWCVSAG
ADGTARLWM

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
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
5CYK 3.0 Å, Structure of Ytm1 bound to the C-terminal domain of Erb1-R486E
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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