8R57: Wheat 40S ribosomal subunit, head domain

CryoEM structure of wheat 40S ribosomal subunit, head domain. Determined by electron microscopy at 2.55 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 2.55 Å
Organism: Triticum aestivum
Chains: 16
Atoms: 25,048
Mol. weight: 848.23 kDa
Ligands: MG, ZN
Released: 27 Dec 2023

Explore 8R57 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R57 contains 81 α-helices and 98 β-strands across 15 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 c: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-17	12	7
β-strand	23-30	8	7
β-strand	37-43	7	7
β-strand	51-54	4	7

Chain d: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	30-31	2	16
α-helix	33-35	3
β-strand	38-39	2	16
α-helix	40-50	11
β-strand	53	1	10

Chain f: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	30	1	30
β-strand	41	1	30
α-helix	44	1
β-strand	45	1	31
α-helix	46	1
β-strand	56	1	31
β-strand	57-60	4	32
β-strand	63-66	4	32
β-strand	74	1	32

Chain F: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	36-41	6	3
β-strand	46-52	7	3
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-90	7	3
α-helix	98-110	13
α-helix	115-129	15
β-strand	133-140	8	4
β-strand	148-155	8	4
α-helix	164-167	4
β-strand	168-176	9	4
β-strand	181-189	9	4
α-helix	190-191	2
α-helix	203-204	2
β-strand	209-210	2	5

Chain g: 0 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	17
β-strand	21-25	5	18
β-strand	33-38	6	18
β-strand	43-47	5	18
β-strand	64-69	6	18
β-strand	76-81	6	19
β-strand	87-92	6	19
β-strand	97-101	5	19
β-strand	107-111	5	19
β-strand	118-123	6	20
β-strand	129-134	6	20
β-strand	139-143	5	20
β-strand	148	1	20
β-strand	166-168	3	21
β-strand	171	1	21
β-strand	179-184	6	21
β-strand	188-193	6	21
β-strand	198-203	6	21
β-strand	212-215	4	22
β-strand	221-225	5	22
β-strand	230	1	23
β-strand	232-235	4	22
β-strand	240	1	22
β-strand	246	1	23
β-strand	251-256	6	24
β-strand	262-267	6	24
β-strand	271-275	5	24
β-strand	280-285	6	24
β-strand	299-304	6	17
β-strand	310-315	6	17
β-strand	319-325	7	17

Chain h: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-19	13
α-helix	28-34	7
β-strand	39-40	2	5
α-helix	44-63	20

Chain K: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-24	5	1
α-helix	39-51	13
β-strand	55-60	6	1
β-strand	63-68	6	1
α-helix	70-79	10

Chain M: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	28-31	4
α-helix	32-41	10
β-strand	44-46	3	2
α-helix	48-56	9
β-strand	63-66	4	2
α-helix	72-84	13
β-strand	91-92	2	2
α-helix	95-101	7
α-helix	116-118	3
β-strand	121-124	4	2
α-helix	133-142	10

7 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
Plectin/eS10 N-terminal domain-containing protein	K	protein	188	Triticum aestivum	W5AUH7 (AlphaFold model)
40S ribosomal protein S12	M	protein	144	Triticum aestivum	W5FEZ3 (AlphaFold model)
40S ribosomal protein S3	F	protein	227	Triticum aestivum	W5I1R7 (AlphaFold model)
Small ribosomal subunit protein uS7c	P	protein	200	Triticum aestivum	A0A9R1JSD6 (AlphaFold model)
40S ribosomal protein S16	Q	protein	149	Triticum aestivum	W5DS33
Ribosomal protein S20	U	protein	127	Triticum aestivum	U5HTD8
40S ribosomal protein S19	T	protein	155	Triticum aestivum	W5FWF5
40S ribosomal protein S25	Z	protein	108	Triticum aestivum	W5EP45
40S ribosomal protein S28	c	protein	65	Triticum aestivum	W5E8X2
Small ribosomal subunit protein uS14	d	protein	56	Triticum aestivum	Q5I7K3
Ribosomal protein RACK1 subfamily. WD repeat G protein beta family	g	protein	332	Triticum aestivum	W5D4F5
Putative ribosomal protein S18	S	protein	152	Triticum aestivum	Q8L806

4 more molecules are not listed.

Sequence of entity 1 (K), FASTA

>8R57_1 Plectin/eS10 N-terminal domain-containing protein (chains K)
MIISKKNRNEICKYLFQEGVLYAKKDYNLAKHPQIDVPNLQVIKLMQSFKSKEYVRETFS
WQHYYWYLTNDGIEFLRNFLNLPSEIVPATLKKSARPPGRPLGSGPPGDRPRGPPRFEGD
RPRYGDRDGYRGGPRGAPGDFGGEKGGAPAEFQPSFRSSGGGGFGRGGGGGFGRGGGGGG
GFGASPME

Sequence of entity 2 (M), FASTA

>8R57_2 40S ribosomal protein S12 (chains M)
MAEENAPVEVAAPVAAPTPVLGEPMDLMTALQLVMKKSSAHDGLVKGLREAAKAIEKHAA
QICVLAEDCDQPDYVKLVKALCAEHNVHLVTVPSAKTLGEWAGLCKIDSEGKARKVVGCS
CVVVKDYGEDSEGLHIVQEYVKSH

Sequence of entity 3 (F), FASTA

>8R57_3 40S ribosomal protein S3 (chains F)
MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG
EKGRRIRELTSVVQKRFNFPENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFVMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQG
VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEEDELRPPALVEV

Sequence of entity 4 (P), FASTA

>8R57_4 Small ribosomal subunit protein uS7c (chains P)
MAVVEPVPGGDVKLFNRWTFEDVQVSDISLNDYLAVTSMKHYTFLPHSAGRYSAKRFRKA
QCPIIERLTNSLMMHGRNNGKKIMAVRIIKHTMEIIHLLTDANPIQIIVDAIINSGPRED
ATRIGSAGVVRRQAVDISPLRRVNQAIYLLTTGARESAFRNVKTIAECLADELINAAKGS
SNSYAIKKKDEIERVAKANR

Sequence of entity 5 (Q), FASTA

>8R57_5 40S ribosomal protein S16 (chains Q)
MAAVLTRPTPGTVQCFGRKKTAVAVAYCKPGRGLIKVNGAPIELIRPEMLRLKAFEPILL
AGRSRFKDIDMRIRVRGGGKTSQIYSIRQAIAKSLVAYYQKYVDEAAKKEVKEIFGRYDR
TLLVADPRRCEPKKFGGRGARARFQKSYR

Sequence of entity 6 (U), FASTA

>8R57_6 Ribosomal protein S20 (chains U)
MATELAYAPPMKSGKLGFEGTQEVQHRIRITLSSKSVKNLEKVCSDLVKGAKEKQLKVKG
PVRMPTKVLNITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSPDVVKQITSITIEPGVEV
EVTISDQ

Sequence of entity 7 (T), FASTA

>8R57_7 40S ribosomal protein S19 (chains T)
MATVPAPAAETAASTARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPP
SDADWYYIRAASMARKIYLRQGIGIGGFQKIYGGRQRNGSRPPHFCKSSGAVSRNILQEL
QKMGIIDVDPKGGRLITSQGRRDLDQVAGTVPAEF

Sequence of entity 8 (Z), FASTA

>8R57_8 40S ribosomal protein S25 (chains Z)
MAPKKEKAPAASSKPAKSGGGKQKKKKWSKGKQKEKVNNAVLFDQATYDKLLTEVPKYKQ
ITPSVLSERLRINGSLARRAIKDLMERGLIRMVSIHSSQQIFTRATNT

Sequence of entity 9 (c), FASTA

>8R57_9 40S ribosomal protein S28 (chains c)
MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDILTLLESERE
ARRLR

Sequence of entity 10 (d), FASTA

>8R57_10 Small ribosomal subunit protein uS14 (chains d)
MGHSNVWNSHPKNYGAGSRVCRVCGNSHGLIRKYGLMCCRQCFRSDAKDIGFIKYR

Sequence of entity 11 (g), FASTA

>8R57_11 Ribosomal protein RACK1 subfamily. WD repeat G protein beta family (chains g)
MAGAQESLVYAGVMRGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPIQATQDSSS
EYGVPFRRLTGHGHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDVLS
VAFSIDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHTGWVSCVRFSPNNFAPTI
VSGSWDRSVKVWNLTNCKLRCTLDGHGGYVSAVAVSPDGSLCASGGKDGVTLLWDLTEGK
RLYSLDAGSIINSLCFSPNRYWLCAATQDSIKIWDLESKHIVQDLRPEVPVSTKQMLYCT
CLSWSADGSTLYAGYTDGTIRIYKISGFSYSS

Sequence of entity 12 (S), FASTA

>8R57_12 Putative ribosomal protein S18 (chains S)
MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELS
AEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNH
RGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	20
ZN	Zinc ion	Zn	2

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

Other PDB entries of the same protein (UniProt W5AUH7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JIW 2.88 Å, Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
8IP8 2.9 Å, Wheat 80S ribosome stalled on AUG-Stop boron dependently
8IP9 3.0 Å, Wheat 40S ribosome in complex with a tRNAi
8IPA 3.4 Å, Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide
8IPB 3.4 Å, Wheat 80S ribosome pausing on AUG-Stop with cycloheximide

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