8R6F: Wheat 40S ribosomal subunit, body domain

CryoEM structure of wheat 40S ribosomal subunit, body domain. Determined by electron microscopy at 2.34 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 2.34 Å
Organism: Triticum aestivum
Chains: 21
Atoms: 49,016
Mol. weight: 966.15 kDa
Ligands: ZN, MG
Released: 27 Dec 2023

Explore 8R6F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R6F contains 135 α-helices and 147 β-strands across 20 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: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	27
β-strand	29-31	3	27
β-strand	36-43	8	28
α-helix	49-55	7
β-strand	57	1	10
α-helix	63-65	3
β-strand	66-73	8	28
α-helix	75-80	6
α-helix	89-92	4
α-helix	96-98	3

Chain b: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	14-17	4
α-helix	22-24	3
β-strand	34-35	2	13
β-strand	38	1	14
β-strand	48-49	2	13
β-strand	57	1	15
β-strand	64	1	15
β-strand	66-67	2	16
β-strand	74-75	2	16
α-helix	76	1
β-strand	80	1	14
β-strand	83	1	13

Chain B: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	19
β-strand	32-33	2	20
β-strand	44	1	20
β-strand	47-49	3	19
α-helix	50-51	2
α-helix	57-60	4
β-strand	64-65	2	21
β-strand	68-69	2	21
α-helix	70-74	5
α-helix	77-79	3
β-strand	82-88	7	21
β-strand	92	1	22
β-strand	95	1	22
β-strand	96-97	2	20
β-strand	98-105	8	21
α-helix	107-113	7
β-strand	118	1	23
β-strand	120-128	9	21
β-strand	134-143	10	21
β-strand	154	1	23
α-helix	158-178	21
α-helix	181-188	8
α-helix	192-201	10
β-strand	207-219	13	21
α-helix	225-230	6

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	50-57	8
α-helix	64-68	5
α-helix	76-82	7
β-strand	87-99	13	31
β-strand	104-115	12	31
β-strand	120-128	9	31
α-helix	131-144	14
β-strand	147-148	2	31
β-strand	152	1	32
β-strand	163	1	32
β-strand	168-172	5	33
β-strand	175-181	7	33
β-strand	188-189	2	33
α-helix	192-201	10
β-strand	206-211	6	33
α-helix	217-229	13
α-helix	237-239	3
α-helix	242-243	2
α-helix	246-248	3
α-helix	249-252	4

Chain e: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	13-17	5
α-helix	19-20	2
α-helix	22-24	3
α-helix	27-30	4
α-helix	33-44	12

Chain E: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	4
α-helix	11-13	3
α-helix	16-18	3
β-strand	27-28	2	4
α-helix	29-32	4
α-helix	38-40	3
β-strand	42-43	2	5
α-helix	44-45	2
α-helix	46-51	6
α-helix	58-66	9
β-strand	71-72	2	6
β-strand	75-76	2	6
β-strand	83-84	2	5
β-strand	89-92	4	6
β-strand	97-103	7	6
β-strand	109-114	6	6
α-helix	118-120	3
β-strand	121-125	5	7
β-strand	126-131	6	8
α-helix	133-135	3
β-strand	137-141	5	8
β-strand	146-148	3	8
β-strand	159-163	5	7
β-strand	168-173	6	7
β-strand	180-183	4	9
β-strand	192-199	8	9
α-helix	205-206	2
β-strand	207-212	6	9
β-strand	217-221	5	9
α-helix	222-224	3
β-strand	225-227	3	9
α-helix	248-260	13

Chain G: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	34
β-strand	12-17	6	34
α-helix	21-25	5
β-strand	31	1	35
β-strand	35-37	3	34
β-strand	49-57	9	34
α-helix	61	1
β-strand	62	1	34
β-strand	63	1	36
β-strand	72-78	7	36
β-strand	81	1	37
β-strand	84	1	37
α-helix	89-90	2
β-strand	94-100	7	36
β-strand	103	1	35
β-strand	108-117	10	34
α-helix	131-133	3
β-strand	139	1	38
α-helix	140-147	8
α-helix	156-159	4
α-helix	160-162	3
β-strand	164-167	4	39
β-strand	173-176	4	39
α-helix	178-180	3
β-strand	181	1	38
α-helix	186-228	43

Chain h: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	96-98	3	42
α-helix	100-108	9
β-strand	116-118	3	42

12 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
40S ribosomal protein S24	Y	protein	137	Triticum aestivum	A0A3B6RHV8 (AlphaFold model)
40S ribosomal protein S23	X	protein	142	Triticum aestivum	W5FV77 (AlphaFold model)
40S ribosomal protein S4	E	protein	265	Triticum aestivum	A0A1D5SLI4 (AlphaFold model)
30S ribosomal protein S11, chloroplastic	O	protein	151	Triticum aestivum	A0A3B6SS17 (AlphaFold model)
Small ribosomal subunit protein uS8c	W	protein	130	Triticum aestivum	E2F3W4
40S ribosomal protein S27	b	protein	86	Triticum aestivum	A0A341UET3
40S ribosomal protein S30	e	protein	62	Triticum aestivum	A0A3B6S9M7
Small ribosomal subunit protein uS2	k	protein	308	Triticum aestivum	W5E2W7
Small ribosomal subunit protein eS1	B	protein	263	Triticum aestivum	A0A3B6IU74
Genome assembly, chromosome: II	V	protein	81	Triticum aestivum	A0A0C4BJ86
40S ribosomal protein S26	a	protein	139	Triticum aestivum	A0A3B6KQB8
30S ribosomal protein S4, chloroplastic	J	protein	195	Triticum aestivum	W5FPA7

9 more molecules are not listed.

Sequence of entity 1 (Y), FASTA

>8R6F_1 40S ribosomal protein S24 (chains Y)
MADAKTTTAVTLRTRKFMTNRLLARKQFVLEVIHPGRANVSKAELKERLAKVYEVKDPNC
IFVFKFRTHFGGGKSSGFGLIYDNLESAKKFEPKYRLIRNGLATKVEKSRKQIKERKNRT
KKIRGVKKTKAGDAKKK

Sequence of entity 2 (X), FASTA

>8R6F_2 40S ribosomal protein S23 (chains X)
MGKTRGMGAGRKLKTHRRNQRWADKAYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQ
PNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDEVLIAGFGRKGHAVGDIPGVRFK
VVKVSGVSLLALFKEKKEKPRS

Sequence of entity 3 (E), FASTA

>8R6F_3 40S ribosomal protein S4 (chains E)
MARGLKKHLKRLNAPSHWMLDKLGGAFAPKPSSGPHKARECLPLILILRNRLKYALTYRE
VQSILMQRHIMVDGKVRTDKTYPAGFMDIISIPKTGENYRLLYDTKGRFRLHSVRDEDAK
FKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLETNKIVDFIKFDVGNV
VMVTGGRNTGRVGVIKNREKHKGTFETIHVEDAQGHQFATRLGNVFTIGKGTKPWVSLPK
GKGIKLTIIEEQRKRDAAAQAAAKA

Sequence of entity 4 (O), FASTA

>8R6F_4 30S ribosomal protein S11, chloroplastic (chains O)
MSSKRKTREPKEENVTLGPAVREGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGM
KVKADRDESSPYAAMLASQDVATRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALA
RSGMKIGRIEDVTPVPTDSTRRKGGRRGRRL

Sequence of entity 5 (W), FASTA

>8R6F_5 Small ribosomal subunit protein uS8c (chains W)
MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLIVMQKHGYIGEFEYVDDHRSGK
IVVELNGRLNKCGVISPRFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKN
VGGKVLGFFY

Sequence of entity 6 (b), FASTA

>8R6F_6 40S ribosomal protein S27 (chains b)
MVLQNDIDLLNPPAELEKLKHKKKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCPG
CQTVLCQPTGGKARLTEGCSFRRKGD

Sequence of entity 7 (e), FASTA

>8R6F_7 40S ribosomal protein S30 (chains e)
MGKVHGSLARAGKVRGQTPKVAKQDKKKQPRGRAHKRIQYNRRFVTAVVGFGKKRGPNSS
EK

Sequence of entity 8 (k), FASTA

>8R6F_8 Small ribosomal subunit protein uS2 (chains k)
MAAAAGEAPRALSQKEQDIQMMLAADVHLGTKNCDFQMERYAYKRRSDGIYIINLGKTWE
KLQLAARVIVAIENPQDIIVQSARPYGQRAVLKFAQHTGANAIAGRHTPGTFTNQMQTSF
SEPRLLILTDPRTDHQPIKESALGNIPTIAFCDTDSPMRYVDIGIPANNKGRNSIGCLYW
LLARMVLQMRGTILPGHKWDVMVDLFFYRDPEEAKEQEDEAAGAPEYAAITDYGAAAGQW
GGDQWTSDAPAPPPVTGGEWPMAEAPVAGGDGWDAAGAPVAVEGAVPAPVVAATGWDAAV
QPPAQGWE

Sequence of entity 9 (B), FASTA

>8R6F_9 Small ribosomal subunit protein eS1 (chains B)
MAVGKNKRISKGRKGSKKKAVDPFTKKQWYDIKAPLLFTSRNVGKTLVSRTQGTKIASEG
LKHRVFEVSLADLQNDEDQAYRKIRLRAEDVQGMNVLTNFWGMDFTTDKLRSLVRKWQTL
IEAHVDVKTTDNYMLRMFAIGFTKRRPNQVKRTCYAQASQIRQIRRKMVEIMVNQAASCD
LKELVNKFIPEVIGKEIEKATSSIFPLQNVYVRKVKILKAPKFDLGKLMEVHGDYKEDVG
VKLDRPADGDEVIPGAEEVAAAE

Sequence of entity 10 (V), FASTA

>8R6F_10 Genome assembly, chromosome: II (chains V)
MQNEVGDMVDLYVPRKCSATNRIITAKDHASVQINIGHVDANGLYNGSFTTFALSGFVRA
QGDADGSLDRLWQQKRAEIKQ

Sequence of entity 11 (a), FASTA

>8R6F_11 40S ribosomal protein S26 (chains a)
MTFKRRNGGRNKHGRGHVKYIRCSNCAKCCPKDKAIKRFLVRNIVEQAAVRDVQEACVHD
GYVLPKLYAKVHHCVSCAIHAHIVRVRSRENRRNREPPQRFRRRDDGPRPGQGGPPRAGG
PGGAPAGAGAVPGAPAPRV

Sequence of entity 12 (J), FASTA

>8R6F_12 30S ribosomal protein S4, chloroplastic (chains J)
MVHVNFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNAARH
LLTLDEKNPRRIFEGAALLRRMNRYGLLAEGQDKLDYVLALTAENFLARRLQTLVFKAGM
AKSIHHARVLIRQRHIRVGRQIVNVPSFMVRVESEKHIDFSLTSPFGGGPAGRVKRKNQK
KASGGGDAGGDEEEE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	32

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

Primary citation

High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit. Kravchenko, O.V., Baymukhametov, T.N., Afonina, Z.A. et al. Int J Mol Sci (2023) 24. DOI 10.3390/ijms242417453 · PubMed

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