5EM2: Erb1-Ytm1 complex

Name: PDB 5EM2: Crystal structure of the Erb1-Ytm1 complex
Published: 2015-12-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of the Erb1-Ytm1 complex. Determined by X-ray diffraction at 2.67 Å resolution. Released 23 Dec 2015.

Method: X-ray diffraction
Resolution: 2.67 Å
Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Chains: 4
Atoms: 12,754
Mol. weight: 193.71 kDa
Ligands: MG
Released: 23 Dec 2015

Explore 5EM2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EM2 contains 32 α-helices and 134 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: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	435-438	4
β-strand	445-450	6	1
β-strand	456-461	6	2
β-strand	467-472	6	2
β-strand	476-481	6	2
β-strand	486-492	7	2
β-strand	499-504	6	3
β-strand	513-517	5	3
β-strand	520-524	5	3
α-helix	533-544	12
β-strand	568-570	3	3
α-helix	574-578	5
β-strand	581-586	6	3
β-strand	593-596	4	4
β-strand	602-606	5	4
α-helix	611-613	3
β-strand	615-619	5	4
β-strand	624-626	3	4
β-strand	638-641	4	5
β-strand	647-651	5	5
β-strand	656-660	5	5
β-strand	665-670	6	5
β-strand	677-682	6	6
β-strand	688-693	6	6
β-strand	698-702	5	6
β-strand	711-713	3	6
β-strand	720-725	6	7
β-strand	732-737	6	7
β-strand	742-748	7	7
β-strand	758-765	8	7
α-helix	768-770	3
β-strand	771	1	8
β-strand	774	1	8
β-strand	776-781	6	1
β-strand	788-792	5	1
β-strand	796-800	5	1

Chain B: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	9
α-helix	30-32	3
β-strand	34-38	5	9
α-helix	43-50	8
β-strand	63-67	5	9
β-strand	70-71	2	9
α-helix	76-82	7
β-strand	91-97	7	9
α-helix	98-99	2
β-strand	103-109	7	10
β-strand	114-120	7	11
α-helix	125-131	7
β-strand	145-150	6	11
β-strand	155-158	4	11
β-strand	164-167	4	11
α-helix	171-173	3
β-strand	180-185	6	12
β-strand	190-195	6	12
β-strand	200-209	10	12
β-strand	212-221	10	12
β-strand	228-234	7	13
β-strand	239-244	6	13
β-strand	248-253	6	13
α-helix	259-262	4
α-helix	264-266	3
β-strand	285-287	3	12
β-strand	291-294	4	13
β-strand	300-305	6	14
β-strand	312-317	6	14
β-strand	321-326	6	14
β-strand	331-337	7	14
β-strand	342-348	7	15
β-strand	357-362	6	15
β-strand	367-370	4	15
β-strand	382-384	3	15
β-strand	391-396	6	16
β-strand	403-408	6	16
β-strand	413-417	5	16
β-strand	422-423	2	15
β-strand	433-435	3	15
β-strand	439-441	3	16
α-helix	444-447	4
α-helix	454-455	2
α-helix	456-458	3
β-strand	463-469	7	10
β-strand	472-477	6	10
β-strand	481-486	6	10

Chain C: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	435-438	4
β-strand	445-449	5	17
β-strand	456-461	6	18
β-strand	467-472	6	18
β-strand	476-481	6	18
β-strand	486-492	7	18
β-strand	499-504	6	19
β-strand	513-517	5	19
β-strand	520-524	5	19
α-helix	533-544	12
β-strand	568-570	3	19
α-helix	574-578	5
β-strand	581-586	6	19
β-strand	593-596	4	20
β-strand	602-606	5	20
α-helix	611-613	3
β-strand	615-619	5	20
β-strand	624-626	3	20
β-strand	638-641	4	21
β-strand	647-651	5	21
β-strand	656-660	5	21
β-strand	665-670	6	21
β-strand	677-682	6	22
β-strand	688-693	6	22
β-strand	698-702	5	22
β-strand	709-713	5	22
β-strand	720-725	6	23
β-strand	732-737	6	23
β-strand	742-748	7	23
β-strand	758-765	8	23
α-helix	768-770	3
β-strand	771	1	24
β-strand	774	1	24
β-strand	776-781	6	17
β-strand	788-792	5	17
β-strand	797-800	4	17

Chain D: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	14-20	7	25
α-helix	30-32	3
β-strand	34-38	5	25
α-helix	43-50	8
β-strand	63-67	5	25
β-strand	70-71	2	25
α-helix	76-83	8
β-strand	91-97	7	25
α-helix	98-99	2
β-strand	103-109	7	26
β-strand	114-120	7	27
α-helix	125-131	7
β-strand	145-150	6	27
β-strand	155-158	4	27
β-strand	164-167	4	27
α-helix	171-173	3
β-strand	180-185	6	28
β-strand	190-195	6	28
β-strand	200-209	10	28
β-strand	212-221	10	28
β-strand	228-234	7	29
β-strand	239-244	6	29
β-strand	249-253	5	29
α-helix	259-262	4
α-helix	264-266	3
β-strand	286-287	2	28
β-strand	291-293	3	29
β-strand	300-305	6	30
β-strand	312-317	6	30
β-strand	321-326	6	30
β-strand	331-337	7	30
β-strand	342-348	7	31
β-strand	357-362	6	31
β-strand	367-370	4	31
β-strand	382-384	3	31
β-strand	391-396	6	32
β-strand	403-408	6	32
β-strand	413-417	5	32
β-strand	422-423	2	31
β-strand	433-435	3	31
β-strand	439-441	3	32
α-helix	444-447	4
α-helix	454-455	2
α-helix	456-458	3
β-strand	463-469	7	26
β-strand	472-477	6	26
β-strand	481-486	6	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome biogenesis protein ERB1	A, C	protein	388	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SCK6 (AlphaFold model)
Ribosome biogenesis protein YTM1	B, D	protein	499	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SFB5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5EM2_1 Ribosome biogenesis protein ERB1 (chains A, C)
MAHHHHHHMIDPNSLLPKLPSPDELKPFPTVQQTIFRGHEGRVRSVAIDPTGVALATGGD
DGTVRVWELLTGRQVWSVKLNGDEAVNTVRWRPTKDTFILAAAAGEDIFLMIPTHPSVTP
ALDQASRDILNAGFGHATNGKQQANLPPGKEPPGKWARPGTRLEDEGVLLRITVRSTIKA
ISWHRRGDHFATVSPSGQRSSVAIHTLSKHLTQIPFRKLNGLAQTASFHPLRPLFFVATQ
RSIRCYDLQKLELVKIVQPGAKWISSFDVHPGGDNLVVGSYDKRLLWHDLDLSNRPYKTM
RFHTEAIRAVRFHKGGLPLFADASDDGSLQIFHGKVPNDQLENPTIVPVKMLKGHKVVNK
LGVLDIDWHPREPWCVSAGADGTARLWM

Sequence of entity 2 (B, D), FASTA

>5EM2_2 Ribosome biogenesis protein YTM1 (chains B, D)
GGAHMDAPMEDAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESML
DTGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRSLIPPVYEASFEHDDWVSA
VDVLSATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNASGSVIATSPSGSHGGH
TASIKAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLELYGHTGSVDWLDVDGH
SKHILTASADGAIGFWSASKASAPEPDASLLPGAHVSKRRKATSSVSTAQRGPLGLWSIH
TAPATAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHPLLSLSALTRAGTTSP
LLAAGTSARHITMVDPRASSATTSVMTLRGHANKVVSLSPSPENEYSLVSGSHDGTCRVW
DLRSVRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGCKVFSVVWDKLGIFSG
GEDKKVQVNRGRNIVTEQK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

Concerted removal of the Erb1-Ytm1 complex in ribosome biogenesis relies on an elaborate interface. Thoms, M., Ahmed, Y.L., Maddi, K. et al. Nucleic Acids Res (2016) 44:926-939. DOI 10.1093/nar/gkv1365 · PubMed

Other PDB entries of the same protein (UniProt G0SCK6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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
8I9P 3.0 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16
5CXC 3.1 Å, Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group
8I9R 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP
8I9V 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2
8I9W 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3
8I9Y 3.1 Å, Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2

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