9F1C: 60S ribosomal protein L29

Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E. Determined by electron microscopy at 3.78 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.78 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Schistosoma japonicum
Chains: 90
Atoms: 236,684
Mol. weight: 4099.96 kDa
Ligands: IHP, ZN, SPM, SPD
Released: 21 Aug 2024

Explore 9F1C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F1C contains 679 α-helices and 603 β-strands across 83 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: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	39
β-strand	43-50	8	39
α-helix	51-52	2
β-strand	53	1	40
β-strand	56	1	40
α-helix	58-62	5
β-strand	66-70	5	39
α-helix	71-73	3
β-strand	82-92	11	39
β-strand	95-105	11	39
α-helix	107-113	7
β-strand	118	1	41
β-strand	120-128	9	39
β-strand	134-143	10	39
α-helix	144-146	3
β-strand	154	1	41
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	207-219	13	39
α-helix	225-232	8

Chain AA: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	126
β-strand	43-47	5	126
β-strand	54-55	2	127
β-strand	62-65	4	127
α-helix	71	1
β-strand	72-73	2	127
α-helix	74	1
β-strand	78-81	4	126

Chain Ab: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
α-helix	65-71	7
α-helix	78-84	7
α-helix	91-98	8
β-strand	103-115	13	80
β-strand	120-131	12	80
β-strand	136-144	9	80
α-helix	147-160	14
β-strand	162-164	3	80
β-strand	168	1	81
β-strand	179	1	81
β-strand	184-188	5	82
β-strand	191-197	7	82
β-strand	204-205	2	82
α-helix	208-217	10
β-strand	222-227	6	82
α-helix	233-249	17
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	142
β-strand	27-34	8	142
β-strand	41-47	7	142
β-strand	55-58	4	142
α-helix	65-67	3

Chain Ac: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	123
β-strand	45-52	8	123
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	123
α-helix	94-96	3
α-helix	98-111	14
α-helix	115-129	15
β-strand	133-141	9	124
β-strand	147-155	9	124
α-helix	164-167	4
β-strand	168-177	10	124
β-strand	180-189	10	124
α-helix	190-192	3
α-helix	203-204	2
β-strand	209-210	2	125
α-helix	211-214	4
β-strand	223-226	4	26

Chain AC: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	81-84	4
α-helix	88-93	6
α-helix	101-103	3
β-strand	106-108	3	159
β-strand	114-116	3	159
α-helix	119	1
β-strand	120	1	160
α-helix	121	1
β-strand	131	1	160
β-strand	132-134	3	161
β-strand	138-141	4	161
β-strand	146-149	4	161

Chain Ad: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	146
α-helix	16-18	3
β-strand	27-28	2	146
α-helix	30-32	3
α-helix	38-40	3
β-strand	42-43	2	147
α-helix	44-46	3
α-helix	47-51	5
α-helix	58-66	9
β-strand	71-72	2	148
β-strand	75-76	2	148
β-strand	83-84	2	147
β-strand	89-92	4	148
β-strand	97-100	4	148
β-strand	102-103	2	149
β-strand	109-110	2	149
β-strand	113	1	148
α-helix	118-120	3
β-strand	121-125	5	150
β-strand	126-131	6	151
α-helix	133-135	3
β-strand	137-141	5	151
β-strand	146-148	3	151
β-strand	159-163	5	150
β-strand	168-173	6	150
β-strand	180-183	4	152
β-strand	192-199	8	152
β-strand	207-211	5	152
β-strand	217-221	5	152
α-helix	222-224	3
β-strand	225-227	3	152
β-strand	229-230	2	153
β-strand	233-234	2	153
α-helix	248-262	15

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

75 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
mRNA	AH	RNA	3	Oryctolagus cuniculus
60S ribosomal protein L29	Bb	protein	245	Oryctolagus cuniculus	G1SGR6 (AlphaFold model)
5S rRNA	B7	RNA	120	Oryctolagus cuniculus
P-site tRNA	AT	RNA	76	Oryctolagus cuniculus
Small ribosomal subunit protein uS13	Ar	protein	151	Oryctolagus cuniculus	G1TPG3 (AlphaFold model)
5.8S rRNA	B8	RNA	158	Oryctolagus cuniculus
60S ribosomal protein L22	BU	protein	128	Oryctolagus cuniculus	G1TSG1 (AlphaFold model)
40S ribosomal protein S19	As	protein	145	Oryctolagus cuniculus	G1TN62 (AlphaFold model)
Large ribosomal subunit protein uL2	BA	protein	257	Oryctolagus cuniculus	G1TT27
Ribosomal protein L23	BV	protein	140	Oryctolagus cuniculus	G1T6D1
Small ribosomal subunit protein uS10	At	protein	119	Oryctolagus cuniculus	G1SIZ2
Ribosomal protein L3	BB	protein	403	Oryctolagus cuniculus	G1TL06

78 more molecules are not listed.

Sequence of entity 1 (AH), FASTA

>9F1C_1 mRNA (chains AH)
NNN

Sequence of entity 2 (Bb), FASTA

>9F1C_2 60S ribosomal protein L29 (chains Bb)
MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQAN
NAKAMAARAEAIKALVKPKEVKPTIPKGVSRKLHRLAYIAHPKLGRRARARIARGLRLSR
PQTKAKAKTEPQIKGKVKAQIKAQAQAQIKSKGKGKAQAETKPKAQAETKPKAQAQAKPK
AQAQGKPKAQAQGKPKAQAQAKPKAQAQAKPKAQAQTKPKAQATPAAPVPAQAPPKGAQP
PAKAP

Sequence of entity 3 (B7), FASTA

>9F1C_3 5S rRNA (chains B7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 4 (AT), FASTA

>9F1C_4 P-site tRNA (chains AT)
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNCCA

Sequence of entity 5 (Ar), FASTA

>9F1C_5 Small ribosomal subunit protein uS13 (chains Ar)
SLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTE
DEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHR
GLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK

Sequence of entity 6 (B8), FASTA

>9F1C_6 5.8S rRNA (chains B8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUUG

Sequence of entity 7 (BU), FASTA

>9F1C_7 60S ribosomal protein L22 (chains BU)
MAPVKKLVAKGGKKKKQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGA
VTIERSKSKITVTSEVPFSKRYLKYLTKKYLKKNNLRDWLRVVANSKESYELRYFQINQD
EEEEEDED

Sequence of entity 8 (As), FASTA

>9F1C_8 40S ribosomal protein S19 (chains As)
MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAAST
ARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGG
RKLTPQGQRDLDRIAGQVAAANKKH

Sequence of entity 9 (BA), FASTA

>9F1C_9 Large ribosomal subunit protein uL2 (chains BA)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNXQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 10 (BV), FASTA

>9F1C_10 Ribosomal protein L23 (chains BV)
MSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDM
VMATVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGP
VAKECADLWPRIASNAGSIA

Sequence of entity 11 (At), FASTA

>9F1C_11 Small ribosomal subunit protein uS10 (chains At)
MAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKT
LRITTRKTPCGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA

Sequence of entity 12 (BB), FASTA

>9F1C_12 Ribosomal protein L3 (chains BB)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
ZN	Zinc ion	Zn	8
SPM	Spermine	C10 H26 N4	3
SPD	Spermidine	C7 H19 N3	30
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	420

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

Primary citation

NAC guides a ribosomal multienzyme complex for nascent protein processing. Lentzsch, A.M., Yudin, D., Gamerdinger, M. et al. Nature (2024) 633:718-724. DOI 10.1038/s41586-024-07846-7 · PubMed

Other PDB entries of the same protein (UniProt G1SGR6 (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…
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
7OBR 2.8 Å, RNC-SRP early complex

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