6YAM: 60s ribosomal protein l41

Name: PDB 6YAM: Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA
Published: 2020-04-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA. Determined by electron microscopy at 3.6 Å resolution. Released 8 Apr 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 50
Atoms: 118,536
Mol. weight: 1967.72 kDa
Ligands: GNP, MG, SF4
Released: 8 Apr 2020

Explore 6YAM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YAM contains 392 α-helices and 357 β-strands across 47 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 a: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	110
β-strand	13-15	3	110
β-strand	20-28	9	110
α-helix	37-48	12
β-strand	55-62	8	110
α-helix	63	1
β-strand	69-76	8	110
α-helix	79-85	7
α-helix	88-91	4
α-helix	108-114	7
α-helix	122-126	5

Chain A: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	44
β-strand	31-36	6	44
β-strand	43-47	5	44
β-strand	50	1	45
β-strand	52	1	45
β-strand	68-77	10	44
β-strand	82-86	5	44
α-helix	92-118	27
α-helix	126-130	5
α-helix	131-135	5
α-helix	136-143	8
α-helix	149-158	10
α-helix	172-183	12
α-helix	204-213	10
β-strand	226-229	4	46
β-strand	235-238	4	46
α-helix	248-263	16

Chain b: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	111
β-strand	29-31	3	111
β-strand	36-43	8	112
α-helix	50-54	5
β-strand	57	1	81
α-helix	63-65	3
β-strand	66-73	8	112
α-helix	75-80	6
α-helix	96-99	4

Chain B: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	56-60	5	49
α-helix	68-74	7
β-strand	95-103	9	49
β-strand	117-118	2	50
β-strand	128-129	2	50
β-strand	138-147	10	49
α-helix	152-154	3
α-helix	155-162	8
β-strand	167-173	7	49
α-helix	181-193	13
β-strand	198-204	7	49
α-helix	210-223	14
β-strand	234-236	3	49
α-helix	245-254	10
α-helix	258-260	3
α-helix	266-267	2
β-strand	268-273	6	51
β-strand	291-298	8	51
β-strand	301-302	2	52
β-strand	306-314	9	51
α-helix	315	1
β-strand	324-336	13	51
β-strand	339-340	2	51
β-strand	343-344	2	52
β-strand	348-354	7	51
α-helix	358-360	3
β-strand	369-372	4	51
β-strand	379-390	12	53
α-helix	407-411	5
β-strand	416-421	6	53
β-strand	424-434	11	53
β-strand	437-448	12	53
β-strand	454-459	6	53
β-strand	464-472	9	53

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	1
β-strand	45-47	3	1
α-helix	53-55	3
β-strand	66	1	2
β-strand	71	1	2

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	12-20	9
β-strand	25-26	2	4
β-strand	38-41	4	4
β-strand	47-49	3	4
α-helix	51-67	17
β-strand	74-78	5	5
α-helix	82-93	12
β-strand	97-100	4	5
β-strand	121-125	5	5
α-helix	131-137	7
β-strand	145-147	3	5
β-strand	159-160	2	5
α-helix	169-185	17

Chain d: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
β-strand	10-21	12	3
β-strand	27-33	7	3
β-strand	41-46	6	3
β-strand	55-58	4	3

Chain D: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	7
β-strand	32-34	3	8
β-strand	43-45	3	8
β-strand	48-50	3	7
α-helix	51-52	2
β-strand	53	1	9
β-strand	56	1	9
α-helix	59-61	3
β-strand	69	1	8
β-strand	84-91	8	8
β-strand	95-103	9	8
α-helix	108-112	5
β-strand	120-128	9	10
β-strand	134-142	9	10
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	210-215	6	10
α-helix	225-231	7

39 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
initiator methionylated tRNA	1	RNA	75	Oryctolagus cuniculus
60s ribosomal protein l41	l	protein	25	Oryctolagus cuniculus	A0A087WNH4 (AlphaFold model)
40S ribosomal protein uS2	C	protein	208	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
40S ribosomal protein eS1	D	protein	264	Oryctolagus cuniculus	G1TN72 (AlphaFold model)
40S ribosomal protein uS5	E	protein	226	Oryctolagus cuniculus
40S ribosomal protein uS3	F	protein	227	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
40S ribosomal protein eS4	G	protein	263	Oryctolagus cuniculus	G1TK17
40S ribosomal protein uS7	H	protein	191	Oryctolagus cuniculus	U3KMN4
40S ribosomal protein eS6	I	protein	237	Oryctolagus cuniculus	G1TM55
ribosomal protein eS7	J	protein	190	Oryctolagus cuniculus	G1SVB0
40S ribosomal protein eS8	K	protein	206	Oryctolagus cuniculus	G1TJW1
40S ribosomal protein uS4	L	protein	182	Oryctolagus cuniculus	B7NZS8

38 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>6YAM_1 initiator methionylated tRNA (chains 1)
AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAAC
CAUCCUCUGCUACCA

Sequence of entity 2 (l), FASTA

>6YAM_2 60s ribosomal protein l41 (chains l)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 3 (C), FASTA

>6YAM_3 40S ribosomal protein uS2 (chains C)
SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLA
ARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRL
LVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLARE
VLRMRGTISREHPWEVMPDLYFYRDPEE

Sequence of entity 4 (D), FASTA

>6YAM_4 40S ribosomal protein eS1 (chains D)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLHLFCVGFTKKCNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (E), FASTA

>6YAM_5 40S ribosomal protein uS5 (chains E)
GKAGDKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGAALKDKVLKIMPV
QKQTQAGQRTRFKAFVAIGDYNGHVGLGMKCSKEVATAIRGAIILAKLSIVPVRRGYWGN
KIGKPHTVRCKVTGRCGSVLVRLIPAPRGTGIISAPVPKKLLLMAGIDDCYTSAGGCTAT
LGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT

Sequence of entity 6 (F), FASTA

>6YAM_6 40S ribosomal protein uS3 (chains F)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 7 (G), FASTA

>6YAM_7 40S ribosomal protein eS4 (chains G)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 8 (H), FASTA

>6YAM_8 40S ribosomal protein uS7 (chains H)
TPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLT
NSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGT
VRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKK
DELERVAKSNR

Sequence of entity 9 (I), FASTA

>6YAM_9 40S ribosomal protein eS6 (chains I)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Sequence of entity 10 (J), FASTA

>6YAM_10 ribosomal protein eS7 (chains J)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQL

Sequence of entity 11 (K), FASTA

>6YAM_11 40S ribosomal protein eS8 (chains K)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVGVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 12 (L), FASTA

>6YAM_12 40S ribosomal protein uS4 (chains L)
WVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEK
DPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHA
RVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAG
AG

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MG	Magnesium ion	Mg	1
SF4	Iron/sulfur cluster	Fe4 S4	2

Primary citation

Structural Insights into the Mammalian Late-Stage Initiation Complexes. Simonetti, A., Guca, E., Bochler, A. et al. Cell Rep (2020) 31:107497-107497. DOI 10.1016/j.celrep.2020.03.061 · PubMed

Other PDB entries of the same protein (UniProt A0A087WNH4 (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…
8Q87 2.4 Å, Structure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1
8Q7Z 2.5 Å, Structure of the G. gallus 80S non-rotated ribosome
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…

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