6YAN: 60s ribosomal protein l41

Name: PDB 6YAN: Mammalian 48S late-stage translation initiation complex with histone 4 mRNA
Published: 2020-04-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Mammalian 48S late-stage translation initiation complex with histone 4 mRNA. Determined by electron microscopy at 3.48 Å resolution. Released 8 Apr 2020.

Method: Electron microscopy
Resolution: 3.48 Å
Organisms: Oryctolagus cuniculus, Mus musculus
Chains: 39
Atoms: 84,251
Mol. weight: 1273.88 kDa
Released: 8 Apr 2020

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

Secondary structure: helices and β-sheets

6YAN contains 178 α-helices and 265 β-strands across 36 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	80
β-strand	13-15	3	80
β-strand	20-29	10	80
α-helix	37-45	9
β-strand	55-62	8	80
α-helix	63	1
β-strand	67-76	10	80
α-helix	79-85	7
α-helix	88-91	4
α-helix	106-114	9
α-helix	123-126	4

Chain A: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	19-24	6	42
β-strand	31-36	6	42
β-strand	43-47	5	42
β-strand	68-77	10	42
β-strand	82-86	5	42
α-helix	92-114	23
α-helix	126-139	14
α-helix	150-158	9
α-helix	172-183	12
α-helix	204-213	10
β-strand	226-231	6	43
β-strand	234-238	5	43
α-helix	248-263	16

Chain b: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	81
β-strand	29-31	3	81
β-strand	36-43	8	82
α-helix	50-54	5
β-strand	66-73	8	82
α-helix	75-80	6
α-helix	96-99	4

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	56-60	5	48
α-helix	68-74	7
β-strand	80	1	48
β-strand	96-103	8	48
β-strand	117-118	2	49
β-strand	128-129	2	49
α-helix	137	1
β-strand	138-147	10	48
α-helix	152-154	3
α-helix	155-162	8
β-strand	167-172	6	48
α-helix	181-193	13
β-strand	199-202	4	48
α-helix	210-223	14
β-strand	234-236	3	48
α-helix	245-254	10
β-strand	268-275	8	50
β-strand	291-298	8	50
α-helix	301-302	2
β-strand	306-314	9	50
β-strand	324-335	12	50
β-strand	336	1	51
β-strand	339	1	51
β-strand	349-354	6	50
α-helix	358-361	4
β-strand	369-372	4	50
β-strand	379-390	12	52
α-helix	406-411	6
β-strand	416-421	6	52
β-strand	424-434	11	52
β-strand	437-448	12	52
β-strand	454-459	6	52
β-strand	464-472	9	52

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	83
β-strand	44-47	4	83
β-strand	64-65	2	84
α-helix	71	1
β-strand	72-73	2	84

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
β-strand	38-41	4	2
β-strand	47-49	3	2
α-helix	51-66	16
β-strand	74-78	5	3
α-helix	82-93	12
β-strand	97-100	4	3
β-strand	121-125	5	3
α-helix	131-137	7
β-strand	145-147	3	3
β-strand	159-160	2	3
α-helix	170-186	17
α-helix	200-202	3

Chain d: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	12-21	10	1
β-strand	27-33	7	1
β-strand	41-46	6	1
β-strand	55-56	2	1
β-strand	65	1	1

Chain D: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	5
β-strand	33-34	2	6
β-strand	43-45	3	6
β-strand	48-50	3	5
α-helix	51-52	2
α-helix	59-61	3
β-strand	69-70	2	6
α-helix	72-75	4
β-strand	83-91	9	6
β-strand	96-103	8	6
α-helix	108-113	6
β-strand	120-128	9	7
β-strand	134-142	9	7
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	210-215	6	7
β-strand	219	1	7
α-helix	225-231	7

28 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
60s ribosomal protein l41	l	protein	25	Oryctolagus cuniculus	A0A087WNH4 (AlphaFold model)
40S ribosomal protein SA	C	protein	208	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
ribosomal protein eS1	D	protein	215	Oryctolagus cuniculus	G1TN72 (AlphaFold model)
40S ribosomal protein uS5	E	protein	226	Oryctolagus cuniculus
Ribosomal protein S3	F	protein	227	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
40S ribosomal protein S4	G	protein	263	Oryctolagus cuniculus	G1TK17
Ribosomal protein S5	H	protein	191	Oryctolagus cuniculus	G1TFM5
40S ribosomal protein S6	I	protein	237	Oryctolagus cuniculus	A0A5K1UJS7
ribosomal protein eS7	J	protein	190	Oryctolagus cuniculus	G1SVB0
40S ribosomal protein S8	K	protein	206	Oryctolagus cuniculus	G1TJW1
Ribosomal protein S9 (Predicted)	L	protein	182	Oryctolagus cuniculus	B7NZS8
40S ribosomal protein eS10	M	protein	98	Oryctolagus cuniculus	G1T168

27 more molecules are not listed.

Sequence of entity 1 (l), FASTA

>6YAN_1 60s ribosomal protein l41 (chains l)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 2 (C), FASTA

>6YAN_2 40S ribosomal protein SA (chains C)
SGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLA
ARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRL
LVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLARE
VLRMRGTISREHPWEVMPDLYFYRDPEE

Sequence of entity 3 (D), FASTA

>6YAN_3 ribosomal protein eS1 (chains D)
KKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDE
VAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLHLF
CVGFTKKCNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIE
KACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHG

Sequence of entity 4 (E), FASTA

>6YAN_4 40S ribosomal protein uS5 (chains E)
GKAGDKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGAALKDKVLKIMPV
QKQTQAGQRTRFKAFVAIGDYNGHVGLGMKCSKEVATAIRGAIILAKLSIVPVRRGYWGN
KIGKPHTVRCKVTGRCGSVLVRLIPAPRGTGIISAPVPKKLLLMAGIDDCYTSAGGCTAT
LGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT

Sequence of entity 5 (F), FASTA

>6YAN_5 Ribosomal protein S3 (chains F)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 6 (G), FASTA

>6YAN_6 40S ribosomal protein S4 (chains G)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (H), FASTA

>6YAN_7 Ribosomal protein S5 (chains H)
TPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLT
NSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGT
VRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKK
DELERVAKSNR

Sequence of entity 8 (I), FASTA

>6YAN_8 40S ribosomal protein S6 (chains I)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Sequence of entity 9 (J), FASTA

>6YAN_9 ribosomal protein eS7 (chains J)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQL

Sequence of entity 10 (K), FASTA

>6YAN_10 40S ribosomal protein S8 (chains K)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVGVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 11 (L), FASTA

>6YAN_11 Ribosomal protein S9 (Predicted) (chains L)
WVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEK
DPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHA
RVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAG
AG

Sequence of entity 12 (M), FASTA

>6YAN_12 40S ribosomal protein eS10 (chains M)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSR

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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