9XTC: PDB entry 9XTC

Name: PDB 9XTC: E.coli delta lepA 30S ribosomal subunit class C, body domain
Published: 2026-04-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E.coli delta lepA 30S ribosomal subunit class C, body domain. Determined by electron microscopy at 2.1 Å resolution. Released 8 Apr 2026.

Method: Electron microscopy
Resolution: 2.1 Å
Organism: Escherichia coli
Chains: 13
Atoms: 39,857
Mol. weight: 670.13 kDa
Ligands: MG
Released: 8 Apr 2026

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

Secondary structure: helices and β-sheets

9XTC contains 65 α-helices and 64 β-strands across 12 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 B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	17	1	16
α-helix	25-30	6
β-strand	31-35	5	16
β-strand	38-41	4	16
α-helix	42	1
α-helix	43-62	20
β-strand	67-70	4	17
α-helix	74-76	3
α-helix	77-86	10
β-strand	90-92	3	17
α-helix	104-122	19
α-helix	124-126	3
α-helix	131-148	18
β-strand	160-163	4	17
α-helix	170-179	10
β-strand	183-187	5	17
β-strand	198-201	4	17
α-helix	207-226	20

Chain D: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	28-31	4
α-helix	37	1
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-95	10
β-strand	97	1	3
α-helix	98-104	7
α-helix	111-119	9
β-strand	123-125	3	4
β-strand	128-129	2	4
α-helix	135	1
β-strand	136	1	3
α-helix	137-138	2
β-strand	141-145	5	4
α-helix	147-149	3
α-helix	154-164	11
α-helix	166-168	3
β-strand	171-174	4	4
β-strand	179-182	4	4
α-helix	185-187	3
α-helix	188-190	3
α-helix	197-205	9

Chain E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12-24	13	5
β-strand	29-40	12	5
β-strand	45-53	9	5
α-helix	56-69	14
β-strand	72-73	2	5
β-strand	85-89	5	6
β-strand	92-98	7	6
β-strand	105-106	2	6
α-helix	109-118	10
β-strand	123-129	7	6
α-helix	133-146	14
α-helix	150-157	8

Chain F: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	4-10	7	2
α-helix	12-14	3
α-helix	17-32	16
β-strand	35-36	2	1
β-strand	41-45	5	2
β-strand	57-61	5	2
β-strand	64-66	3	1
α-helix	68-79	12
β-strand	86-91	6	2

Chain H: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	7
α-helix	31-42	12
β-strand	48-52	5	7
β-strand	58-62	5	7
β-strand	65-66	2	8
β-strand	69-70	2	8
β-strand	75-77	3	9
β-strand	80	1	10
β-strand	83	1	10
β-strand	86-87	2	9
α-helix	89-91	3
α-helix	96-98	3
β-strand	101-106	6	9
β-strand	109-112	4	9
α-helix	113-118	6
β-strand	123-129	7	9

Chain K: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-24	8	11
β-strand	29-34	6	11
β-strand	40-45	6	11
α-helix	46-48	3
α-helix	59-73	15
α-helix	74-76	3
β-strand	80-86	7	11
α-helix	90-92	3
α-helix	94-101	8
β-strand	105-111	7	11
α-helix	121-123	3

Chain L: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	14-19	6
α-helix	22-24	3
β-strand	29-40	12	12
β-strand	50-57	8	12
β-strand	62-66	5	12
β-strand	79-84	6	12
β-strand	95-97	3	12
α-helix	104-107	4
α-helix	114-116	3
α-helix	120-122	3

Chain O: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	5-15	11
α-helix	25-45	21
α-helix	50-73	24
α-helix	75-85	11

4 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
RNA (1176-mer)	A	RNA	1542	Escherichia coli
Small ribosomal subunit protein bS6, non-modified isoform	F	protein	100	Escherichia coli	P02358 (AlphaFold model)
30S ribosomal protein S15	O	protein	89	Escherichia coli	P0ADZ4 (AlphaFold model)
30S ribosomal protein S4	D	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	E	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S8	H	protein	130	Escherichia coli	P0A7W7
Small ribosomal subunit protein uS11	K	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	L	protein	124	Escherichia coli	P0A7S3
30S ribosomal protein S16	P	protein	82	Escherichia coli	P0A7T3
30S ribosomal protein S17	Q	protein	84	Escherichia coli	P0AG63
30S ribosomal protein S18	R	protein	75	Escherichia coli	P0A7T7
30S ribosomal protein S20	T	protein	87	Escherichia coli	P0A7U7

1 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9XTC_1 RNA (1176-MER) (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Sequence of entity 2 (F), FASTA

>9XTC_2 Small ribosomal subunit protein bS6, non-modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEAS

Sequence of entity 3 (O), FASTA

>9XTC_3 30S ribosomal protein S15 (chains O)
MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMV
SQRRKLLDYLKRKDVARYTQLIERLGLRR

Sequence of entity 4 (D), FASTA

>9XTC_4 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (E), FASTA

>9XTC_5 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (H), FASTA

>9XTC_6 30S ribosomal protein S8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 7 (K), FASTA

>9XTC_7 Small ribosomal subunit protein uS11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 8 (L), FASTA

>9XTC_8 30S ribosomal protein S12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Sequence of entity 9 (P), FASTA

>9XTC_9 30S ribosomal protein S16 (chains P)
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHW
VGQGATISDRVAALIKEVNKAA

Sequence of entity 10 (Q), FASTA

>9XTC_10 30S ribosomal protein S17 (chains Q)
MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVE
IRECRPLSKTKSWTLVRVVEKAVL

Sequence of entity 11 (R), FASTA

>9XTC_11 30S ribosomal protein S18 (chains R)
MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIK
RARYLSLLPYTDRHQ

Sequence of entity 12 (T), FASTA

>9XTC_12 30S ribosomal protein S20 (chains T)
MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDR
QAAKGLIHKNKAARHKANLTAQINKLA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	39

Primary citation

The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly. Kravchenko, O., Maksimova, E., Baymukhametov, T. et al. Int J Mol Sci (2026) 27. DOI 10.3390/ijms27010489 · PubMed

Other PDB entries of the same protein (UniProt P02358 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
8CGU 1.89 Å, Gentamicin bound to the 30S body
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA
7K00 1.98 Å, Structure of the Bacterial Ribosome at 2 Angstrom Resolution
8QOA 2.0 Å, Structure of SecM-stalled Escherichia coli 70S ribosome

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