9F1B: Large ribosomal subunit protein uL22

Mammalian ternary complex of a translating 80S ribosome, NAC and NatA/E. Determined by electron microscopy at 3.01 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Schistosoma japonicum
Chains: 89
Atoms: 234,232
Mol. weight: 4100.33 kDa
Ligands: MG, IHP, SPD, SPM
Released: 21 Aug 2024

Explore 9F1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F1B contains 669 α-helices and 584 β-strands across 82 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	78
β-strand	43-50	8	78
α-helix	51-52	2
β-strand	53	1	79
β-strand	56	1	79
α-helix	58-62	5
β-strand	66-70	5	78
α-helix	71-73	3
β-strand	82-92	11	78
β-strand	95-105	11	78
α-helix	107-113	7
β-strand	118	1	80
β-strand	120-128	9	78
β-strand	134-143	10	78
α-helix	144-146	3
β-strand	154	1	80
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	207-219	13	78
α-helix	225-232	8

Chain AA: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	103
β-strand	43-47	5	103
β-strand	55	1	104
β-strand	62	1	104
β-strand	64-65	2	105
α-helix	71	1
β-strand	72-73	2	105
α-helix	74	1
β-strand	78-81	4	103

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	103-116	14	111
β-strand	119-131	13	111
β-strand	136-144	9	111
α-helix	147-160	14
β-strand	162-164	3	111
β-strand	168	1	112
β-strand	179	1	112
β-strand	184-188	5	113
β-strand	191-196	6	113
β-strand	204-205	2	113
α-helix	208-216	9
β-strand	222-227	6	113
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	9
β-strand	27-34	8	9
β-strand	41-47	7	9
β-strand	55-58	4	9
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	137
β-strand	45-52	8	137
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	137
α-helix	94-96	3
α-helix	98-111	14
α-helix	115-128	14
β-strand	133-141	9	138
β-strand	147-155	9	138
α-helix	164-167	4
β-strand	168-177	10	138
β-strand	180-189	10	138
α-helix	190-192	3
α-helix	203-204	2
β-strand	209-210	2	10
α-helix	211-214	4
β-strand	223-226	4	24

Chain AC: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	81-84	4
α-helix	88-93	6
α-helix	101-104	4
β-strand	106-108	3	142
β-strand	114-116	3	142
α-helix	119	1
β-strand	120	1	143
α-helix	121	1
β-strand	131	1	143
β-strand	133-134	2	144
β-strand	138-141	4	144
β-strand	146-149	4	144

Chain Ad: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	159
α-helix	16-18	3
β-strand	27-28	2	159
α-helix	30-32	3
α-helix	38-40	3
β-strand	42-43	2	160
α-helix	44-45	2
α-helix	46-51	6
α-helix	58-66	9
β-strand	71-72	2	161
β-strand	75-76	2	161
β-strand	83-84	2	160
β-strand	89-92	4	161
β-strand	97-100	4	161
β-strand	102-103	2	162
β-strand	109-110	2	162
β-strand	113-114	2	161
α-helix	118-120	3
β-strand	121-125	5	163
β-strand	126-131	6	164
α-helix	133-135	3
β-strand	137-141	5	164
β-strand	146-148	3	164
β-strand	159-163	5	163
β-strand	168-173	6	163
β-strand	180-183	4	165
β-strand	192-199	8	165
β-strand	207-211	5	165
β-strand	217-221	5	165
α-helix	222-224	3
β-strand	225-230	6	165
β-strand	233-234	2	165
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

74 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 uL22	BP	protein	184	Oryctolagus cuniculus	G1SCJ6 (AlphaFold model)
40S ribosomal protein eS17	Aq	protein	135	Oryctolagus cuniculus	G1TU13 (AlphaFold model)
Large ribosomal subunit protein eL42	Bo	protein	106	Oryctolagus cuniculus	A0AAA9WX15 (AlphaFold model)
P-site tRNA	AT	RNA	76	Oryctolagus cuniculus
Small ribosomal subunit protein uS13	Ar	protein	151	Oryctolagus cuniculus	G1TPG3 (AlphaFold model)
Transcription factor BTF3	Cu	protein	162	Homo sapiens	P20290
Large ribosomal subunit protein eL13	BL	protein	211	Oryctolagus cuniculus	G1TKB3
Ribosomal_L23eN domain-containing protein	BX	protein	156	Oryctolagus cuniculus	G1SE76
60S ribosomal protein L37a	Bp	protein	92	Oryctolagus cuniculus	G1SY53
Large ribosomal subunit protein eL18	BQ	protein	188	Oryctolagus cuniculus
40S ribosomal protein S19	As	protein	145	Oryctolagus cuniculus	G1TN62
Large ribosomal subunit protein eL28	Br	protein	136	Oryctolagus cuniculus	G1U7L1

77 more molecules are not listed.

Sequence of entity 1 (BP), FASTA

>9F1B_1 Large ribosomal subunit protein uL22 (chains BP)
MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPF
RRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVN
KAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKL
MARE

Sequence of entity 2 (Aq), FASTA

>9F1B_2 40S ribosomal protein eS17 (chains Aq)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGAV

Sequence of entity 3 (Bo), FASTA

>9F1B_3 Large ribosomal subunit protein eL42 (chains Bo)
MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKA
KTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF

Sequence of entity 4 (AT), FASTA

>9F1B_4 P-site tRNA (chains AT)
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNCCA

Sequence of entity 5 (Ar), FASTA

>9F1B_5 Small ribosomal subunit protein uS13 (chains Ar)
SLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTE
DEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHR
GLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK

Sequence of entity 6 (Cu), FASTA

>9F1B_6 Transcription factor BTF3 (chains Cu)
MKETIMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIE
EVNMFTNQGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGADSLTSLRR
LAEALPKQSVDGKAPLATGEDDDDEVPDLVENFDEASKNEAN

Sequence of entity 7 (BL), FASTA

>9F1B_7 Large ribosomal subunit protein eL13 (chains BL)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 8 (BX), FASTA

>9F1B_8 Ribosomal_L23eN domain-containing protein (chains BX)
MAPKAKKEAPAPPKVEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKY
PRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDID
VAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII

Sequence of entity 9 (Bp), FASTA

>9F1B_9 60S ribosomal protein L37a (chains Bp)
MAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSC
MKTVAGGAWTYNTTSAVTVKSAIRRLKELKDQ

Sequence of entity 10 (BQ), FASTA

>9F1B_10 Large ribosomal subunit protein eL18 (chains BQ)
MGVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPP
LSLSRMIRKMKLPGRENKTAVVVGTVTDDVRVQEVPKLKVCALRVTSRARSRILKAGGKI
LTFDQLALDSPKGRGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGR
RASRGYKN

Sequence of entity 11 (As), FASTA

>9F1B_11 40S ribosomal protein S19 (chains As)
MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAAST
ARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGG
RKLTPQGQRDLDRIAGQVAAANKKH

Sequence of entity 12 (Br), FASTA

>9F1B_12 Large ribosomal subunit protein eL28 (chains Br)
SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVV
VVMKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQ
KPVMVKRKRTRPTKSS

Ligands and cofactors

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

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 G1SCJ6 (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…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail

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