9NDP: Stalled ribosome and nascent chain

Name: PDB 9NDP: Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC
Published: 2025-09-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC. Determined by electron microscopy at 2.82 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 2.82 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 87
Atoms: 218,587
Mol. weight: 3443.23 kDa
Ligands: COA, ZN, MG
Released: 10 Sept 2025

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

Secondary structure: helices and β-sheets

9NDP contains 554 α-helices and 598 β-strands across 81 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 0: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	88-92	5
α-helix	101-104	4
β-strand	106-108	3	1
β-strand	114-116	3	1
α-helix	119	1
β-strand	120	1	2
α-helix	121	1
β-strand	131	1	2
β-strand	133-134	2	3
β-strand	139-141	3	3
β-strand	146-148	3	3

Chain 6: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	17
α-helix	17	1
β-strand	18-22	5	18
β-strand	31-35	5	18
β-strand	42-44	3	18
β-strand	54-57	4	18
β-strand	66-71	6	19
β-strand	77-82	6	19
β-strand	87-91	5	19
β-strand	97-101	5	19
β-strand	108-113	6	20
β-strand	119-124	6	20
β-strand	129-133	5	20
β-strand	138-142	5	20
β-strand	154-156	3	21
β-strand	164-169	6	21
β-strand	173-178	6	21
β-strand	184-189	6	21
β-strand	195-200	6	22
β-strand	206-211	6	22
β-strand	215-220	6	22
β-strand	229-231	3	22
β-strand	236-241	6	23
β-strand	247-252	6	23
β-strand	255-260	6	23
β-strand	266-270	5	23
α-helix	282-285	4
β-strand	286-291	6	17
β-strand	297-302	6	17
β-strand	307-312	6	17

Chain 9: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	30-31	2	33
α-helix	33-35	3
β-strand	38-39	2	33
α-helix	40-50	11
β-strand	53	1	34

Chain a: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-10	4
α-helix	42-48	7
β-strand	72-74	3	35
α-helix	75-81	7
α-helix	84-92	9
β-strand	98	1	120
β-strand	100-102	3	36
α-helix	103-106	4
β-strand	110-112	3	35
β-strand	122-126	5	36
β-strand	128-129	2	35
α-helix	131-140	10
β-strand	142-146	5	36

Chain A: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-12	7
α-helix	30-32	3
α-helix	34-38	5
β-strand	40-49	10	37
α-helix	50-51	2
β-strand	58-64	7	37
β-strand	71-77	7	37
β-strand	79	1	38
β-strand	83	1	39
β-strand	87-91	5	37
β-strand	101-103	3	37
α-helix	104-106	3
α-helix	108	1
β-strand	112-114	3	37
β-strand	116	1	40
β-strand	126	1	40
β-strand	134-140	7	37
α-helix	142-144	3
β-strand	145-149	5	37
β-strand	155-159	5	37
β-strand	163-166	4	37
β-strand	169	1	38
α-helix	174-176	3
α-helix	182-192	11
β-strand	224-225	2	41
β-strand	237-238	2	41

Chain AA: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	84-88	5
α-helix	90-91	2
α-helix	93-96	4
α-helix	98-101	4
α-helix	104-111	8
α-helix	112-116	5
α-helix	125-127	3

Chain b: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-24	3
α-helix	37-48	12
α-helix	49-51	3
α-helix	55-75	21
α-helix	91-100	10
α-helix	106-116	11

Chain B: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	51
β-strand	45-54	10	52
β-strand	56-60	5	53
β-strand	70-73	4	53
β-strand	76-80	5	52
α-helix	82-83	2
β-strand	84-95	12	54
β-strand	98-106	9	54
α-helix	112-117	6
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-165	7	54
α-helix	177-179	3
β-strand	180-184	5	54
β-strand	185-186	2	51
α-helix	190-199	10
β-strand	204-205	2	54
α-helix	207-209	3
β-strand	216-222	7	52
α-helix	223-224	2
β-strand	225-229	5	55
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-273	4	55
β-strand	276-288	13	52
β-strand	292-293	2	56
β-strand	298-299	2	56
β-strand	320	1	57
β-strand	324	1	57
β-strand	330-334	5	52
β-strand	344-349	6	52
β-strand	365-368	4	53
α-helix	382-389	8

73 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
Ribosomal protein S27a	0	protein	156	Oryctolagus cuniculus	G1SK22 (AlphaFold model)
mRNA	4	RNA	6	Homo sapiens
RACK1	6	protein	317	Oryctolagus cuniculus	G1SJB4 (AlphaFold model)
5S rRNA	7	RNA	120	Oryctolagus cuniculus
eS29	9	protein	56	Oryctolagus cuniculus	G1U7M4 (AlphaFold model)
Ribosomal protein L8	A	protein	257	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
Ribosomal protein L3	B	protein	403	Oryctolagus cuniculus	G1TL06
60S ribosomal protein L4	C	protein	413	Oryctolagus cuniculus	G1SVW5
Large ribosomal subunit protein uL18	D	protein	297	Oryctolagus cuniculus	P19949
Large ribosomal subunit protein uL30	F	protein	249	Oryctolagus cuniculus	A0AAG1W3S3
60S ribosomal protein L7a	G	protein	319	Oryctolagus cuniculus	G1STW0
60S ribosomal protein L9	H	protein	192	Oryctolagus cuniculus	G1SWI6

75 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9NDP_1 Ribosomal protein S27a (chains 0)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRE
CPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK

Sequence of entity 2 (4), FASTA

>9NDP_2 mRNA (chains 4)
UUAAUG

Sequence of entity 3 (6), FASTA

>9NDP_3 RACK1 (chains 6)
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALR
GHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQI
VSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLA
NCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC
FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFA
GYTDNLVRVWQVTIGTR

Sequence of entity 4 (7), FASTA

>9NDP_4 5S rRNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 5 (9), FASTA

>9NDP_5 eS29 (chains 9)
MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 6 (A), FASTA

>9NDP_6 Ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 7 (B), FASTA

>9NDP_7 Ribosomal protein L3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 8 (C), FASTA

>9NDP_8 60S ribosomal protein L4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKKKPVVGRKAAAAKKPAADKKAADKRAGPEDKKPAA

Sequence of entity 9 (D), FASTA

>9NDP_9 Large ribosomal subunit protein uL18 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 10 (F), FASTA

>9NDP_10 Large ribosomal subunit protein uL30 (chains F)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSL
GKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQ
INRLIRRMN

Sequence of entity 11 (G), FASTA

>9NDP_11 60S ribosomal protein L7a (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG

Sequence of entity 12 (H), FASTA

>9NDP_12 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Ligands and cofactors

ID	Name	Formula	Copies
COA	Coenzyme a	C21 H36 N7 O16 P3 S	1
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	296

Primary citation

NAC couples protein synthesis with nascent polypeptide myristoylation on the ribosome. Zdancewicz, S., Maldosevic, E., Malezyna, K. et al. EMBO J (2025) 44:6320-6342. DOI 10.1038/s44318-025-00548-4 · PubMed

Other PDB entries of the same protein (UniProt G1SK22 (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…
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…
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
9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
9Q7Q 2.86 Å, ABCE1-eRF1-rnc-AMD1C
11HG 2.9 Å, Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveled
11JJ 2.9 Å, Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveled

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