8QFC: UFL1 E3 ligase bound 60S ribosome

Name: PDB 8QFC: UFL1 E3 ligase bound 60S ribosome
Published: 2024-02-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

UFL1 E3 ligase bound 60S ribosome. Determined by electron microscopy at 3.2 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 10,968
Mol. weight: 217.81 kDa
Released: 21 Feb 2024

Explore 8QFC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QFC contains 74 α-helices and 43 β-strands across 5 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: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-18	12
α-helix	29-30	2
β-strand	31-38	8	1
β-strand	50-54	5	2
β-strand	65-68	4	3
α-helix	71-78	8
β-strand	84	1	3
α-helix	87-92	6
α-helix	97-106	10
β-strand	109-113	5	3
α-helix	114-117	4
α-helix	120-123	4
α-helix	135	1
β-strand	136-138	3	3
α-helix	144-151	8
β-strand	154-158	5	2
β-strand	164-171	8	1
α-helix	178-193	16
β-strand	201-207	7	1
β-strand	214-215	2	1

Chain B: 35 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	30-42	13
β-strand	48-49	2	4
β-strand	55-57	3	4
α-helix	59-72	14
β-strand	76-78	3	5
α-helix	79-86	8
α-helix	90-103	14
β-strand	107-109	3	5
β-strand	113-116	4	5
α-helix	117-134	18
β-strand	136-137	2	6
α-helix	139-146	8
α-helix	150-159	10
β-strand	161	1	7
β-strand	165	1	7
β-strand	168-169	2	6
β-strand	177-178	2	6
α-helix	180-194	15
β-strand	201-202	2	8
α-helix	203-210	8
α-helix	214-227	14
β-strand	232-235	4	8
β-strand	243-246	4	8
α-helix	247-264	18
β-strand	266-267	2	9
α-helix	271-274	4
α-helix	280-287	8
β-strand	293-295	3	9
β-strand	300-302	3	9
α-helix	305-319	15
β-strand	322-324	3	10
α-helix	326-328	3
α-helix	335-346	12
β-strand	356-358	3	10
β-strand	362-364	3	10
α-helix	366-387	22
α-helix	479-489	11
α-helix	495-523	29
α-helix	528-531	4
α-helix	532-536	5
α-helix	537-560	24
α-helix	563-573	11
α-helix	574-578	5
α-helix	579-593	15
α-helix	600-602	3
α-helix	605-612	8
α-helix	617-628	12
α-helix	629-631	3
α-helix	636-648	13
α-helix	658-678	21
α-helix	682-698	17
α-helix	709-716	8
α-helix	722-732	11
α-helix	774-785	12

Chain C: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	11
α-helix	13-15	3
α-helix	16-22	7
α-helix	30-46	17
α-helix	65-78	14
α-helix	92-105	14
α-helix	106-108	3
α-helix	109-120	12
α-helix	121-125	5
α-helix	126-167	42
α-helix	175-184	10
α-helix	189-198	10
α-helix	202-215	14
α-helix	225-232	8
α-helix	238-242	5
α-helix	347-372	26
α-helix	374-375	2
α-helix	377-382	6
α-helix	395-417	23
α-helix	420-424	5
α-helix	428-468	41
α-helix	470-493	24
β-strand	499-501	3	11

Chain D: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	121-187	67
β-strand	197-203	7	12
α-helix	209-226	18
β-strand	228-229	2	13
α-helix	233-238	6
α-helix	242-255	14
β-strand	260-263	4	13
β-strand	267-270	4	13
α-helix	273-286	14
β-strand	288-290	3	4
α-helix	291-301	11

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	12
β-strand	17-23	7	12
β-strand	28	1	14
α-helix	29-40	12
β-strand	50-51	2	12
β-strand	56	1	12
β-strand	62	1	14
α-helix	63-69	7
β-strand	73-76	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
60S ribosomal protein L10a	A	protein	217	Homo sapiens	P62906 (AlphaFold model)
E3 UFM1-protein ligase 1	B	protein	809	Homo sapiens	O94874 (AlphaFold model)
CDK5 regulatory subunit-associated protein 3	C	protein	511	Homo sapiens	Q96JB5 (AlphaFold model)
DDRGK domain-containing protein 1	D	protein	303	Homo sapiens	Q96HY6 (AlphaFold model)
Ubiquitin-fold modifier 1	E	protein	87	Homo sapiens	P61960

Sequence of entity 1 (A), FASTA

>8QFC_1 60S ribosomal protein L10a (chains A)
MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPR
PKFSVCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQI
PRILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELV
YNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY

Sequence of entity 2 (B), FASTA

>8QFC_2 E3 UFM1-protein ligase 1 (chains B)
MGHHHHHHENLYFQGMADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQL
EVVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEK
HVQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRII
SGHIDLDNRGVIFTEAFVARHKARIRGLFSAITRPTAVNSLISKYGFQEQLLYSVLEELV
NSGRLRGTVVGGRQDKAVFVPDIYSRTQSTWVDSFFRQNGYLEFDALSRLGIPDAVSYIK
KRYKTTQLLFLKAACVGQGLVDQVEASVEEAISSGTWVDIAPLLPTSLSVEDAAILLQQV
MRAFSKQASTVVFSDTVVVSEKFINDCTELFRELMHQKAEKEMKNNPVHLITEEDLKQIS
TLESVSTSKKDKKDERRRKATEGSGSMRGGGGGNAREYKIKKVKKKGRKDDDSDDESQSS
HTGKKKPEISFMFQDEIEDFLRKHIQDAPEEFISELAEYLIKPLNKTYLEVVRSVFMSST
TSASGTGRKRTIKDLQEEVSNLYNNIRLFEKGMKFFADDTQAALTKHLLKSVCTDITNLI
FNFLASDLMMAVDDPAAITSEIRKKILSKLSEETKVALTKLHNSLNEKSIEDFISCLDSA
AEACDIMVKRGDKKRERQILFQHRQALAEQLKVTEDPALILHLTSVLLFQFSTHSMLHAP
GRCVPQIIAFLNSKIPEDQHALLVKYQGLVVKQLVSQSKKTGQGDYPLNNELDKEQEDVA
STTRKELQELSSSIKDLVLKSRKSSVTEE

Sequence of entity 3 (C), FASTA

>8QFC_3 CDK5 regulatory subunit-associated protein 3 (chains C)
GPLVDMEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIA
QLLSGSYIHYFHCLRILDLLKGTEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELS
SLLVRNVNYEIPSLKKQIAKCQQLQQEYSRKEEECQAGAAEMREQFYHSCKQYGITGENV
RGELLALVKDLPSQLAEIGAAAQQSLGEAIDVYQASVGFVCESPTEQVLPMLRFVQKRGN
STVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISAEAAGIDWG
IFPESDSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETRNQFLD
ELMELEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKMVTMVSVLEDLIGKLTSL
QLQHLFMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLL
LEKTKELQKLIEADISKRYSGRPVNLMGTSL

Sequence of entity 4 (D), FASTA

>8QFC_4 DDRGK domain-containing protein 1 (chains D)
MWSHPQFEKLEVLFQGPASAGQEPLHNEELAGAGRVAQPGPLEPEEPRAGGRPRRRRDLG
SRLQAQRRAQRVAWAEADENEEEAVILAQEEEGVEKPAETHLSGKIGAKKLRKLEEKQAR
KAQREAEEAEREERKRLESQREAEWKKEEERLRLEEEQKEEEERKAREEQAQREHEEYLK
LKEAFVVEEEGVGETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQD
LLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGRESPAQ
APA

Sequence of entity 5 (E), FASTA

>8QFC_5 Ubiquitin-fold modifier 1 (chains E)
GPGSMSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIG
INPAQTAGNVFLKHGSELRIIPRDRVG

Primary citation

The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Makhlouf, L., Peter, J.J., Magnussen, H.M. et al. Nature (2024) 627:437-444. DOI 10.1038/s41586-024-07093-w · PubMed

Other PDB entries of the same protein (UniProt P62906 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
8G5Y 2.29 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)
9RPV 2.35 Å, Structure of the ZAK-bound human disome
8K2C 2.4 Å, Cryo-EM structure of the human 80S ribosome with Tigecycline
8XSX 2.4 Å, Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2
8FKV 2.47 Å, Human nucleolar pre-60S ribosomal subunit (State D1)
8FKW 2.5 Å, Human nucleolar pre-60S ribosomal subunit (State D2)
8FL3 2.53 Å, Human nuclear pre-60S ribosomal subunit (State I2)
8G60 2.54 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)
8IFE 2.57 Å, Arbekacin-added human 80S ribosome
8FKX 2.59 Å, Human nucleolar pre-60S ribosomal subunit (State E)
8IFD 2.59 Å, Dibekacin-added human 80S ribosome

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