9QQA: Small ribosomal subunit protein eS27

Name: PDB 9QQA: Ternary complex of translating ribosome, NAC and NMT1
Published: 2025-07-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Ternary complex of translating ribosome, NAC and NMT1. Determined by electron microscopy at 2.8 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 86
Atoms: 226,637
Mol. weight: 3954.49 kDa
Ligands: ZN, SPM, SPD, MG
Released: 16 Jul 2025

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

Secondary structure: helices and β-sheets

9QQA contains 590 α-helices and 586 β-strands across 80 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 Aa: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	82
β-strand	43-50	8	82
α-helix	51-52	2
β-strand	53	1	83
β-strand	56	1	83
α-helix	58-61	4
β-strand	66-70	5	82
α-helix	71-73	3
β-strand	82-92	11	82
β-strand	95-105	11	82
α-helix	107-113	7
β-strand	118	1	84
β-strand	120-128	9	82
β-strand	134-143	10	82
β-strand	154	1	84
α-helix	158-177	20
α-helix	181-186	6
α-helix	192-200	9
β-strand	207-219	13	82
α-helix	225-231	7

Chain AA: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	7
β-strand	43-47	5	7
β-strand	54-55	2	8
β-strand	62-65	4	8
β-strand	72-73	2	8
β-strand	78-81	4	7

Chain Ab: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
α-helix	65-71	7
α-helix	79-83	5
α-helix	91-98	8
β-strand	103-115	13	89
β-strand	120-131	12	89
β-strand	136-144	9	89
α-helix	147-159	13
β-strand	163-164	2	89
β-strand	168	1	90
β-strand	179	1	90
β-strand	184-188	5	91
β-strand	191-196	6	91
β-strand	204-205	2	91
α-helix	208-216	9
β-strand	222-227	6	91
α-helix	233-245	13
α-helix	253-255	3
α-helix	258-259	2
α-helix	265-268	4
α-helix	270-275	6

Chain AB: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-21	12	19
β-strand	27-34	8	19
β-strand	41-47	7	19
β-strand	55-58	4	19
α-helix	65-67	3

Chain Ac: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-41	8	93
β-strand	46-52	7	93
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-89	6	93
α-helix	94-96	3
α-helix	98-110	13
α-helix	115-128	14
β-strand	133-141	9	94
β-strand	147-155	9	94
α-helix	164-167	4
β-strand	168-176	9	94
β-strand	181-189	9	94
α-helix	190-192	3
α-helix	203-204	2
β-strand	209-210	2	95
α-helix	211-214	4
β-strand	223-226	4	58

Chain AC: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	81-84	4
α-helix	88-93	6
α-helix	95-97	3
α-helix	101-103	3
β-strand	106-108	3	28
β-strand	114-116	3	28
α-helix	119	1
β-strand	120	1	29
α-helix	121	1
β-strand	131	1	29
β-strand	133-134	2	30
β-strand	138-141	4	30
β-strand	146-149	4	30

Chain Ad: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	98
α-helix	16-18	3
β-strand	27	1	98
α-helix	30-32	3
α-helix	38-40	3
β-strand	42-43	2	99
α-helix	44-46	3
α-helix	47-51	5
α-helix	58-65	8
β-strand	71-72	2	100
β-strand	75-76	2	100
β-strand	83-84	2	99
β-strand	89-92	4	100
β-strand	97-100	4	100
β-strand	102-103	2	101
β-strand	109-110	2	101
β-strand	113	1	100
α-helix	118-120	3
β-strand	121-125	5	102
β-strand	126-131	6	103
α-helix	133-135	3
β-strand	137-141	5	103
β-strand	146-148	3	103
β-strand	159-163	5	102
β-strand	169-173	5	102
β-strand	180-183	4	104
β-strand	192-199	8	104
β-strand	207-211	5	104
β-strand	217-221	5	104
α-helix	222-224	3
β-strand	225-227	3	104
β-strand	229-230	2	105
β-strand	233-234	2	105
α-helix	245-247	3
α-helix	248-261	14

Chain AD: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	85-89	5
α-helix	91-92	2
α-helix	94-97	4
α-helix	99-102	4
α-helix	105-115	11
α-helix	126-128	3

72 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
18S rRNA	A2	RNA	1870	Oryctolagus cuniculus
Small ribosomal subunit protein eS27	AA	protein	84	Oryctolagus cuniculus	G1TZ76 (AlphaFold model)
Small ribosomal subunit protein eS28	AB	protein	69	Oryctolagus cuniculus	G1TIB4 (AlphaFold model)
Ubiquitin-ribosomal protein eS31 fusion protein	AC	protein	156	Oryctolagus cuniculus	G1SK22 (AlphaFold model)
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein	AD	protein	133	Oryctolagus cuniculus	G1T8A2 (AlphaFold model)
eS26	AE	protein	115	Oryctolagus cuniculus	A0A2K5LQY6
Small ribosomal subunit protein RACK1	AF	protein	317	Oryctolagus cuniculus	G1SJB4
Small ribosomal subunit protein uS14	AG	protein	56	Oryctolagus cuniculus	G1U7M4
P site Phe tRNA	AT	RNA	76	Oryctolagus cuniculus
Small ribosomal subunit protein uS2	AZ	protein	295	Oryctolagus cuniculus	G1TLT8
40S ribosomal protein S3a	Aa	protein	264	Oryctolagus cuniculus	G1SS70
40S ribosomal protein S2	Ab	protein	293	Oryctolagus cuniculus	O18789

74 more molecules are not listed.

Sequence of entity 1 (A2), FASTA

>9QQA_1 18S rRNA (chains A2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCUCCCCCCGGCCCCGGCCGGGGGGGUGGGCGCCGGCGGCUUUGGUGACUCUAGA
UAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCU
AUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAG
GGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGC
GCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUC
UUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGA
GGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUG
CUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCG
AGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUG
UCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGC
CGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUU
CGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGG
UGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUC
AUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACC
AUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCC
GGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGA
AUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAA
ACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGU
GGGUGGUGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAA
CGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAA
CUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAU
GCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCC
UACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCA
AUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAA
GUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCC
CUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCG
AACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGA
AGGAUCAUUA

Sequence of entity 2 (AA), FASTA

>9QQA_2 Small ribosomal subunit protein eS27 (chains AA)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH

Sequence of entity 3 (AB), FASTA

>9QQA_3 Small ribosomal subunit protein eS28 (chains AB)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR

Sequence of entity 4 (AC), FASTA

>9QQA_4 Ubiquitin-ribosomal protein eS31 fusion protein (chains AC)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRE
CPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK

Sequence of entity 5 (AD), FASTA

>9QQA_5 Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein (chains AD)
MQLFVRAQELHTLEVTGRETVAQIKAHVASLEGIAPEDQVVLLAGTPLEDEATLGQCGVE
ALSTLEVAGRMLGGKVHGSLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVV
PTFGKKKGPNANS

Sequence of entity 6 (AE), FASTA

>9QQA_6 eS26 (chains AE)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 7 (AF), FASTA

>9QQA_7 Small ribosomal subunit protein RACK1 (chains AF)
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALR
GHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQI
VSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLA
NCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC
FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFA
GYTDNLVRVWQVTIGTR

Sequence of entity 8 (AG), FASTA

>9QQA_8 Small ribosomal subunit protein uS14 (chains AG)
MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 9 (AT), FASTA

>9QQA_9 P site Phe tRNA (chains AT)
GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCCGGUUCGAAA
CCGGGCGGAAACACCA

Sequence of entity 10 (AZ), FASTA

>9QQA_10 Small ribosomal subunit protein uS2 (chains AZ)
XSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Sequence of entity 11 (Aa), FASTA

>9QQA_11 40S ribosomal protein S3a (chains Aa)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 12 (Ab), FASTA

>9QQA_12 40S ribosomal protein S2 (chains Ab)
MADDAGAAGGPGGPGGPGMGGRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
LPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGAALKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
SPM	Spermine	C10 H26 N4	3
SPD	Spermidine	C7 H19 N3	30
MG	Magnesium ion	Mg	407

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

Primary citation

Mechanism of cotranslational protein N-myristoylation in human cells. Gamerdinger, M., Echeverria, B., Lentzsch, A.M. et al. Mol Cell (2025) 85:2749. DOI 10.1016/j.molcel.2025.06.015 · PubMed

Other PDB entries of the same protein (UniProt G1TZ76 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
7JQB 2.7 Å, SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
9BDL 2.8 Å, 80S ribosome with angiogenin

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