7OZS: Hexameric 5S RNP from C. thermophilum

Structure of the hexameric 5S RNP from C. thermophilum. Determined by electron microscopy at 3.5 Å resolution. Released 12 Oct 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Thermochaetoides thermophila DSM 1495, Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Chains: 7
Atoms: 12,770
Mol. weight: 232.9 kDa
Released: 12 Oct 2022

Explore 7OZS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OZS contains 75 α-helices and 34 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.

Chain A: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
α-helix	30-39	10
β-strand	50-52	3	3
β-strand	54-55	2	4
β-strand	60-62	3	4
β-strand	65-67	3	3
β-strand	72-74	3	3
β-strand	78-79	2	4
α-helix	82-85	4
α-helix	95-112	18
β-strand	146	1	5
β-strand	148-150	3	3
α-helix	161-172	12
β-strand	175	1	5
β-strand	186	1	6
β-strand	193	1	6
α-helix	195-202	8
α-helix	205-216	12
α-helix	220-224	5
α-helix	227-231	5
α-helix	236-252	17
α-helix	268-275	8
α-helix	284-294	11
α-helix	295-299	5

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	14-22	9	1
α-helix	29-42	14
β-strand	47-48	2	1
β-strand	68-72	5	1
α-helix	75-87	13
β-strand	91-92	2	2
α-helix	94-96	3
β-strand	97	1	1
β-strand	103-107	5	1
β-strand	126-133	8	1
α-helix	137-140	4
α-helix	148-150	3
α-helix	157-167	11
β-strand	171-172	2	2

Chain C: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-19	8
α-helix	25-28	4
β-strand	30-34	5	7
α-helix	40-52	13
β-strand	57-59	3	7
α-helix	73-82	10
β-strand	86-91	6	7
β-strand	99-106	8	7
β-strand	109-118	10	7
α-helix	119	1
β-strand	124	1	7
α-helix	126-128	3
α-helix	132-135	4
α-helix	138-140	3
β-strand	141-146	6	7
α-helix	147-149	3
α-helix	156-168	13
β-strand	175-177	3	8
β-strand	183-189	7	7
α-helix	221-224	4
β-strand	225-235	11	7
α-helix	242	1
β-strand	243-261	19	7
α-helix	262-264	3
α-helix	265-271	7

Chain D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	7
β-strand	29-32	4	7
α-helix	35-36	2
α-helix	44-68	25
β-strand	71-72	2	8
β-strand	80-82	3	8
α-helix	84-86	3

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	21-23	3

Chain F: 36 helices, 0 β-strands

Element	Residues	Length
α-helix	36-43	8
α-helix	48-63	16
α-helix	68-73	6
α-helix	76-79	4
α-helix	80-84	5
α-helix	90-106	17
α-helix	109-117	9
α-helix	120-136	17
α-helix	147-168	22
α-helix	172-180	9
α-helix	182-194	13
α-helix	199-212	14
α-helix	217-224	8
α-helix	231-240	10
α-helix	246-259	14
α-helix	278-287	10
α-helix	302-328	27
α-helix	389-398	10
α-helix	412-416	5
α-helix	417-421	5
α-helix	422-429	8
α-helix	436-457	22
α-helix	462-464	3
α-helix	467-480	14
α-helix	481-485	5
α-helix	486-490	5
α-helix	496-513	18
α-helix	523-534	12
α-helix	551-553	3
α-helix	555-566	12
α-helix	573-588	16
α-helix	595-608	14
α-helix	615-616	2
α-helix	617-621	5
α-helix	626-643	18
α-helix	650-673	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putative ribosomal protein	B	protein	173	Thermochaetoides thermophila DSM 1495	G0SHQ2 (AlphaFold model)
60S ribosomal protein l5-like protein	A	protein	304	Thermochaetoides thermophila DSM 1495	G0SEG2 (AlphaFold model)
Ribosome biogenesis regulatory protein	D	protein	202	Thermochaetoides thermophila DSM 1495	G0SCH6 (AlphaFold model)
Ribosome production factor 2 homolog	C	protein	350	Thermochaetoides thermophila DSM 1495	G0SF80 (AlphaFold model)
5S rRNA	3	RNA	119	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
unknown	E	protein	23	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Syo1	F	protein	676	Thermochaetoides thermophila DSM 1495	G0S5S6

Sequence of entity 1 (B), FASTA

>7OZS_1 Putative ribosomal protein (chains B)
MSSEKAQNPMRELRIQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVYSKARYTVRQFGI
RRNEKIAVHVTVRGPKAEEILERGLKVKEYELRRRNFSETGNFGFGISEHIDLGIKYDPS
IGIYGMDFYCCMTRPGERVAKRRRCKSRIGASHRITREETIRWFKQRFDGIVR

Sequence of entity 2 (A), FASTA

>7OZS_2 60S ribosomal protein l5-like protein (chains A)
MAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAKNKYNAPKYRLVVRFTNRDI
ITQMVTSEINGDKIFAAAYSHELRAYGINHGLTNWAAAYATGLLLARRVLAKLGLDKTFT
GVEEPNGEYTLTEAAETEDGERRPFKAILDVGLARTSTGARVFGVMKGASDGGIFIPHSE
NRFPGYDIETEELDTEVLKKYIYGGHVAEYMETLADDDEERYKSQFVKYIEDDVEADSLE
ELYAEAHKQIRADPFRKYVSDAPKKSKEEWKAESLKYKKAKLSREERKARVEAKIKQLLA
EQDE

Sequence of entity 3 (D), FASTA

>7OZS_3 Ribosome biogenesis regulatory protein (chains D)
MSTDTSKPARLPVTVEKPTPYTFDLGLLLANDPNPVNVPKTTDTQVLEQHLASVARDGAQ
VLINQLLTTTTITATKDGVLLTLPPPTTPLPREKPVPQPKPETKWQAFARRRGIKPKTRE
QRRNLQYNPTTGQWERKWGYKGANKRGETDPIIEVSAAKEAMRPEGTSVRGDKRREIRAR
VKKNQKQMLRNQRIAAEKMGKK

Sequence of entity 4 (C), FASTA

>7OZS_4 Ribosome production factor 2 homolog (chains C)
MLRQIKPRNARSKRALEKRAPKIVENPKTCLFLRGTTCSQITQDAMNDLYAMRQVHAKRF
HKKNAIHPFEDATSLCFFSEKNDCSLMVFGSSNKKRPHTLTFVRMFDYKVLDMLEFYLDP
DTYRSISQFKTSKIPIGMRPMMVFAGTAFESPVPNAFTMAKSMLIDFFRGEPSDKIDVEG
LRFVVVVTADEPTSSTSTNNDGENPAPLPGMTDPRSIDPSQKPILRLRVYGIRTKRSGTR
LPRVEVEEHGPRMDFRLGRMREPDPAMLKEAMKKAKTPQEERTKKNISMDLLGDKIGRIH
MGKTDLSKLQTRKMKGLKRGRDEDEGGEDDRTDVVEAGSGEKKKKKKVKG

Sequence of entity 5 (3), FASTA

>7OZS_5 5S rRNA (chains 3)
ACGUACGACCAUACCCAGUGGAAAGCACGGCAUCCCGUCCGCUCUGCCCUAGUUAAGCCA
CUGAGGGCCCGGUUAGUAGUUGGGUCGGUGACGACCAGCGAAUCCCGGGUGUUGUACGU

Sequence of entity 6 (E), FASTA

>7OZS_6 unknown (chains E)
XXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 7 (F), FASTA

>7OZS_7 Syo1 (chains F)
MGKTRRNRVRNRTDPIAKPVKPPTDPELAKLREDKILPVLKDLKSPDAKSRTTAAGAIAN
IVQDAKCRKLLLREQVVHIVLTETLTDNNIDSRAAGWEILKVLAQEEEADFCVHLYRLDV
LTAIEHAAKAVLETLTTSEPPFSKLLKAQQRLVWDITGSLLVLIGLLALARDEIHEAVAT
KQTILRLLFRLISADIAPQDIYEEAISCLTTLSEDNLKVGQAITDDQETHVYDVLLKLAT
GTDPRAVMACGVLHNVFTSLQWMDHSPGKDGACDAILIPTLTRALEHVVPGGAKFNGDAR
YANITLLALVTLASIGTDFQETLVKGNQGSRESPISAADEEWNGFDDADGDAMDVDQKSS
SGEDQEEDYEEIDVKEDDEDDDDDSITSEMQADMERVVGADGTDDGDLEDLPTLRELIQT
AVPQLIRLSNLPIDSDESLTIQSHALSALNNISWTISCLEFANGENANIHNAWYPTAKKI
WRKTILPILEADSADLKLATQVTSLAWAVARVLHGETPTDGNPHRKFISLYHSSKQQAGG
NSNSIEEPEDPFQGLGVKCIGVVGSLAHDPAPIEVNREVGVFLVTLLRQSNNVPPAEIVE
ALNQLFDIYGDEELACDKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRTQPELRTRADEAL
LNLGRFVQYKKKHAPK

Primary citation

Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways. Castillo Duque de Estrada, N.M., Thoms, M., Flemming, D. et al. Nat Struct Mol Biol (2023). DOI 10.1038/s41594-023-01006-7 · PubMed

Other PDB entries of the same protein (UniProt G0SHQ2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PV7 2.12 Å, Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite…
8PVL 2.19 Å, Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite…
9I78 2.2 Å, Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon
9I1W 2.38 Å, High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium…
8PVK 2.55 Å, Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite…
8PV1 2.56 Å, Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite…
8PV2 2.63 Å, Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1
8PV3 2.8 Å, Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite…
8PV5 2.86 Å, Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite…
7OLC 2.9 Å, Thermophilic eukaryotic 80S ribosome at idle POST state
8PV4 2.9 Å, Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite…
8PV8 2.91 Å, Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without…

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