9NL5: Large ribosomal subunit protein uL1

Name: PDB 9NL5: E. coli pre-elongation complex without an A-site tRNA with EQ2-EttA in Hydrolytic 1 conformation
Published: 2025-04-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E. coli pre-elongation complex without an A-site tRNA with EQ2-EttA in Hydrolytic 1 conformation. Determined by electron microscopy at 3.0 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Escherichia coli
Chains: 56
Atoms: 149,888
Mol. weight: 2226.83 kDa
Ligands: ATP, ZN, MG
Released: 2 Apr 2025

Explore 9NL5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NL5 contains 258 α-helices and 354 β-strands across 51 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 1: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	26-31	6
α-helix	32-35	4
β-strand	42	1	1
β-strand	45-46	2	2
β-strand	61-62	2	3
β-strand	75	1	4
β-strand	76	1	5
α-helix	83-89	7
β-strand	94	1	5
α-helix	104-107	4
β-strand	113	1	4
α-helix	140-142	3
α-helix	150-158	9
α-helix	160-161	2
β-strand	162-163	2	3
β-strand	165	1	2
β-strand	171-172	2	2
α-helix	182-198	17
β-strand	212-215	4	2
β-strand	216	1	1
β-strand	221-223	3	2

Chain 13: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	15-19	5	9
β-strand	24	1	10
α-helix	25-37	13
β-strand	45	1	11
β-strand	48	1	11
β-strand	53-57	5	9
α-helix	59-61	3
β-strand	63	1	10
α-helix	68-71	4
β-strand	73-77	5	12
β-strand	84-88	5	12
α-helix	89-95	7
α-helix	97-108	12
α-helix	110	1
α-helix	113-119	7
β-strand	122-124	3	9
α-helix	133-135	3
β-strand	138-139	2	9

Chain 14: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	18
β-strand	7-10	4	19
β-strand	12	1	20
β-strand	16-24	9	19
β-strand	33	1	18
β-strand	38-46	9	19
β-strand	57-64	8	19
β-strand	70	1	21
β-strand	76	1	21
β-strand	83-87	5	19
β-strand	94	1	19
β-strand	99	1	20
α-helix	105-107	3
α-helix	110-112	3
α-helix	113-118	6

Chain 15: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
α-helix	46-47	2
β-strand	52	1	27
β-strand	54	1	27
α-helix	55-56	2
α-helix	57-60	4
α-helix	62-63	2
α-helix	70-73	4
β-strand	74-77	4	28
α-helix	79-84	6
β-strand	89-90	2	29
α-helix	92-97	6
β-strand	107-110	4	28
β-strand	121-122	2	29
α-helix	129-136	8
β-strand	141-142	2	29

Chain 16: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	32
β-strand	39-42	4	33
α-helix	43-57	15
β-strand	62-65	4	32
β-strand	71-75	5	33
α-helix	76-77	2
α-helix	87	1
β-strand	88-96	9	33
β-strand	101-106	6	32
α-helix	110-121	12
β-strand	128-132	5	32

Chain 17: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-30	17
β-strand	33-37	5	41
α-helix	38-54	17
α-helix	60-68	9
α-helix	73-78	6
α-helix	83-86	4
β-strand	95-102	8	41
α-helix	108	1
β-strand	109-115	7	41

Chain 18: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-21	19
β-strand	25-30	6	42
β-strand	35-40	6	42
β-strand	47-52	6	42
α-helix	56-59	4
α-helix	68-85	18
β-strand	89	1	43
β-strand	91-93	3	42
α-helix	102-112	11
β-strand	116	1	43

Chain 19: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	24-33	10	21
β-strand	36-50	15	21
α-helix	53-55	3
β-strand	57-62	6	21
β-strand	69-74	6	21
β-strand	80-82	3	21
β-strand	85-87	3	21
β-strand	89	1	44
α-helix	97-101	5
α-helix	104-107	4
β-strand	111	1	44

43 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large ribosomal subunit protein uL1	1	protein	220	Escherichia coli	P0A7L0 (AlphaFold model)
Large ribosomal subunit protein uL13	13	protein	142	Escherichia coli	P0AA10 (AlphaFold model)
50S ribosomal protein L14	14	protein	122	Escherichia coli	P0ADY3 (AlphaFold model)
50S ribosomal protein L15	15	protein	143	Escherichia coli	P02413 (AlphaFold model)
50S ribosomal protein L16	16	protein	136	Escherichia coli	P0ADY7
Large ribosomal subunit protein bL17	17	protein	120	Escherichia coli	P0AG44
Large ribosomal subunit protein uL18	18	protein	116	Escherichia coli	P0C018
50S ribosomal protein L19	19	protein	114	Escherichia coli	P0A7K6
50S ribosomal protein L2	2	protein	271	Escherichia coli	P60422
Large ribosomal subunit protein bL20	20	protein	117	Escherichia coli	P0A7L3
Large ribosomal subunit protein bL21	21	protein	103	Escherichia coli	P0AG48
Large ribosomal subunit protein uL22	22	protein	110	Escherichia coli	P61175

44 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>9NL5_1 Large ribosomal subunit protein uL1 (chains 1)
KRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVL
PHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAMRVVG
QLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDADKL
KENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVD

Sequence of entity 2 (13), FASTA

>9NL5_2 Large ribosomal subunit protein uL13 (chains 13)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 3 (14), FASTA

>9NL5_3 50S ribosomal protein L14 (chains 14)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV

Sequence of entity 4 (15), FASTA

>9NL5_4 50S ribosomal protein L15 (chains 15)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 5 (16), FASTA

>9NL5_5 50S ribosomal protein L16 (chains 16)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Sequence of entity 6 (17), FASTA

>9NL5_6 Large ribosomal subunit protein bL17 (chains 17)
MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV
ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE

Sequence of entity 7 (18), FASTA

>9NL5_7 Large ribosomal subunit protein uL18 (chains 18)
DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQ
LKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF

Sequence of entity 8 (19), FASTA

>9NL5_8 50S ribosomal protein L19 (chains 19)
SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTV
RKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN

Sequence of entity 9 (2), FASTA

>9NL5_9 50S ribosomal protein L2 (chains 2)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS

Sequence of entity 10 (20), FASTA

>9NL5_10 Large ribosomal subunit protein bL20 (chains 20)
ARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLW
IARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA

Sequence of entity 11 (21), FASTA

>9NL5_11 Large ribosomal subunit protein bL21 (chains 21)
MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIK
AEVVAHGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGISA

Sequence of entity 12 (22), FASTA

>9NL5_12 Large ribosomal subunit protein uL22 (chains 22)
METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEH
NDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	125

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

Primary citation

Cryo-EM studies of the four E. coli paralogs establish ABCF proteins as master plumbers of the peptidyl-transferase center of the ribosome. Singh, S., Gentry, R.C., Fu, Z. et al. bioRxiv (2023). DOI 10.1101/2023.06.15.543498

Other PDB entries of the same protein (UniProt P0A7L0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SLG 2.16 Å, Doxycycline Bound E. coli Ribosome with Rearranged Peptidyl Transferase Centre
7UG7 2.58 Å, 70S ribosome complex in an intermediate state of translocation bound to EF-G(GDP)…
9SS6 2.6 Å, 70S ribosome from RimM-KO
9SS4 2.7 Å, pre-50S ribosomal subunit in rimM-KO with RsfS (-H68)
7ST2 2.9 Å, Post translocation, non-rotated 70S ribosome with EF-G dissociated (Structure VII)
7TOS 2.9 Å, E. coli 70S ribosomes bound with the ALS/FTD-associated dipeptide repeat protein PR20
9TKR 2.9 Å, E. coli 70S elongation competent complex (70S EC)
6WD0 3.0 Å, Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate…
6WDE 3.0 Å, Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate…
9TKP 3.0 Å, 70S Initiation Complex with extended IF2 bound (70S IC-I)
8PKL 3.09 Å, Escherichia coli paused disome complex (leading 70S non-rotated closed PRE state)
6ENU 3.1 Å, Polyproline-stalled ribosome in the presence of elongation-factor P (EF-P)

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