7QGG: 40S ribosomal protein SA

Name: PDB 7QGG: Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state
Published: 2022-10-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state. Determined by electron microscopy at 2.86 Å resolution. Released 26 Oct 2022.

Method: Electron microscopy
Resolution: 2.86 Å
Organism: Rattus norvegicus
Chains: 84
Atoms: 218,574
Mol. weight: 3778.14 kDa
Ligands: MG, ZN
Released: 26 Oct 2022

Explore 7QGG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QGG contains 490 α-helices and 546 β-strands across 76 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	9-13	5	65
β-strand	22-29	8	65
β-strand	40-48	9	65
α-helix	49-52	4
α-helix	60-64	5
β-strand	69-76	8	65
α-helix	77-79	3
β-strand	80-86	7	65
α-helix	98-100	3
α-helix	104-122	19
α-helix	133-135	3

Chain A: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	30-32	3
α-helix	34-38	5
β-strand	40-50	11	60
β-strand	57-64	8	60
β-strand	71-77	7	60
β-strand	79	1	61
β-strand	83	1	62
β-strand	87-91	5	60
β-strand	101-103	3	60
α-helix	104-106	3
α-helix	108	1
β-strand	112-114	3	60
β-strand	116	1	63
β-strand	126	1	63
β-strand	134-137	4	60
β-strand	145-149	5	60
β-strand	155-159	5	60
β-strand	163-166	4	60
β-strand	169	1	61
α-helix	174-176	3
α-helix	182-190	9
α-helix	198-200	3
α-helix	201-203	3
β-strand	224-225	2	64
α-helix	229-230	2
β-strand	237-238	2	64

Chain b: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-10	4
α-helix	42-45	4
β-strand	72-73	2	71
α-helix	75-77	3
α-helix	79-81	3
α-helix	84-90	7
β-strand	97-98	2	137
β-strand	100-102	3	72
α-helix	103-106	4
β-strand	110-111	2	71
β-strand	123-126	4	72
β-strand	128-129	2	71
α-helix	131-140	10
β-strand	143-146	4	72

Chain B: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	32-35	4
β-strand	43	1	67
β-strand	45-59	15	68
β-strand	71-80	10	68
β-strand	84-95	12	69
β-strand	98-106	9	69
α-helix	112-115	4
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-165	7	69
β-strand	180-184	5	69
β-strand	185	1	67
α-helix	190-199	10
β-strand	204-205	2	69
α-helix	207-209	3
β-strand	216-222	7	68
α-helix	223-225	3
β-strand	227-229	3	70
α-helix	231-234	4
α-helix	237-240	4
β-strand	270-272	3	70
β-strand	276-287	12	68
β-strand	330-334	5	68
β-strand	344-349	6	68
β-strand	365-368	4	68
α-helix	382-389	8

Chain c: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	37-49	13
α-helix	59-68	10
α-helix	92-99	8
α-helix	106-115	10

Chain C: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	75
β-strand	17-23	7	75
α-helix	24-25	2
α-helix	26-29	4
α-helix	31-32	2
α-helix	34-44	11
α-helix	45-48	4
α-helix	49-52	4
β-strand	64-66	3	76
β-strand	77-79	3	76
β-strand	90	1	76
α-helix	117-130	14
α-helix	134-138	5
β-strand	152-154	3	75
α-helix	158-160	3
α-helix	164-173	10
α-helix	177-185	9
β-strand	188-189	2	77
α-helix	190-191	2
α-helix	193-195	3
β-strand	201-202	2	77
β-strand	208-211	4	75
α-helix	217-221	5
β-strand	228-231	4	75
α-helix	237-240	4
α-helix	242-244	3
β-strand	250-253	4	75
α-helix	254-258	5
α-helix	260-264	5
α-helix	279-282	4
α-helix	289-293	5
α-helix	296-300	5
α-helix	302-306	5
α-helix	324-328	5
α-helix	332-364	33

Chain Cz: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4
β-strand	31-35	5	36
β-strand	50-54	5	37
β-strand	65-68	4	38
α-helix	78-80	3
β-strand	84-85	2	38
α-helix	87-89	3
α-helix	91-93	3
β-strand	109-111	3	38
α-helix	128-131	4
α-helix	145-151	7
β-strand	154-158	5	37
β-strand	159	1	39
β-strand	165	1	39
β-strand	167-171	5	36
α-helix	176-192	17
β-strand	205-208	4	36

Chain d: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	20-23	4
β-strand	26-29	4	79
α-helix	31-40	10
β-strand	45-49	5	79
α-helix	54-67	14
β-strand	70-74	5	79
α-helix	78-84	7
β-strand	93-98	6	79

68 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
RNA (1872-mer)	S2	RNA	1872	Rattus norvegicus
40S ribosomal protein SA	SA	protein	295	Rattus norvegicus	P38983 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	264	Rattus norvegicus	P49242 (AlphaFold model)
40S ribosomal protein S3	SD	protein	243	Rattus norvegicus	P62909 (AlphaFold model)
40S ribosomal protein S4, X isoform	SE	protein	263	Rattus norvegicus	P62703 (AlphaFold model)
40S ribosomal protein S5	SF	protein	204	Rattus norvegicus	B0BN81
40S ribosomal protein S7	SH	protein	194	Rattus norvegicus	P62083
40S ribosomal protein S8	SI	protein	208	Rattus norvegicus	P62243
40S ribosomal protein S10	SK	protein	165	Rattus norvegicus	P63326
40S ribosomal protein S11	SL	protein	158	Rattus norvegicus	A0A8B8VW69
40S ribosomal protein S15	SP	protein	145	Rattus norvegicus	A0A2K6QL61
Rps16 protein	SQ	protein	146	Rattus norvegicus	Q5XFV9

72 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>7QGG_1 RNA (1872-MER) (chains S2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCCUUCCCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAAC
CCGGUCAGCCCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUUGGUGACUCUA
GAUAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCC
CUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUC
AGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAG
GCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGAC
UCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUG
GAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGU
UGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGG
CGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAG
UGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGA
GCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUU
UUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGA
GGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUU
UCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGA
CCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUU
CCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGG
AAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCC
GUGGGUGGUGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAU
AACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCC
AACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUG
AUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUAC
CCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUG
CAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUU
AAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGG
CCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGU
CGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCG
GAAGGAUCAUUA

Sequence of entity 2 (SA), FASTA

>7QGG_2 40S ribosomal protein SA (chains SA)
MSGGLDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
AQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTEWS

Sequence of entity 3 (SB), FASTA

>7QGG_3 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGGSSGK
TTGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (SD), FASTA

>7QGG_4 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 5 (SE), FASTA

>7QGG_5 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 6 (SF), FASTA

>7QGG_6 40S ribosomal protein S5 (chains SF)
MTEWETATPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 7 (SH), FASTA

>7QGG_7 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 8 (SI), FASTA

>7QGG_8 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 9 (SK), FASTA

>7QGG_9 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 10 (SL), FASTA

>7QGG_10 40S ribosomal protein S11 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 11 (SP), FASTA

>7QGG_11 40S ribosomal protein S15 (chains SP)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK

Sequence of entity 12 (SQ), FASTA

>7QGG_12 Rps16 protein (chains SQ)
MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGK
ERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLL
VADPRRCESKKFGGPGARARYQKSYR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	33
ZN	Zinc ion	Zn	6

Primary citation

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state. Kipper, K., Mansour, A., Pulk, A. J Mol Biol (2022) 434:167801-167801. DOI 10.1016/j.jmb.2022.167801 · PubMed

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