7WTT: Human pre-40S ribosomal subunit - State RRP12-A1

Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1). Determined by electron microscopy at 3.1 Å resolution. Released 19 Oct 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 34
Atoms: 83,677
Mol. weight: 1515.51 kDa
Ligands: SAH, ZN
Released: 19 Oct 2022

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

Secondary structure: helices and β-sheets

7WTT contains 301 α-helices and 247 β-strands across 33 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: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	30
β-strand	17-26	10	30
β-strand	29-36	8	30
β-strand	42-49	8	30
α-helix	57-66	10
α-helix	74-75	2
β-strand	76-82	7	30
β-strand	85-91	7	30
β-strand	96	1	31
α-helix	97-103	7
α-helix	110-129	20
β-strand	132-133	2	32
β-strand	142-144	3	31
α-helix	147-151	5
β-strand	153-155	3	31
α-helix	158-160	3
β-strand	162-163	2	32
β-strand	165	1	33
β-strand	172	1	33
α-helix	173-175	3
α-helix	190-194	5
α-helix	196-198	3
α-helix	200-216	17
α-helix	229-241	13
α-helix	246-249	4
α-helix	254-264	11
α-helix	274-287	14
α-helix	297-304	8

Chain b: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	8
β-strand	43-47	5	8
α-helix	53	1
β-strand	54-55	2	9
β-strand	62-65	4	9
β-strand	72-73	2	9
β-strand	75	1	10
β-strand	77	1	10
β-strand	78-81	4	8

Chain B: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	29-34	6	11
β-strand	43-49	7	11
α-helix	50-52	3
α-helix	58-61	4
β-strand	65-70	6	11
α-helix	71-73	3
β-strand	82-91	10	11
β-strand	96-105	10	11
α-helix	107-113	7
β-strand	118	1	12
β-strand	120-127	8	11
β-strand	135-142	8	11
β-strand	143	1	13
β-strand	154	1	12
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	207	1	13
β-strand	211-215	5	11
α-helix	225-232	8

Chain c: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	16
β-strand	27-34	8	16
β-strand	41-47	7	16
β-strand	55-58	4	16

Chain e: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	26-28	3
α-helix	31-38	8
α-helix	39-43	5

Chain E: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	19
α-helix	11-13	3
α-helix	16-18	3
β-strand	27-28	2	19
α-helix	31-32	2
β-strand	42-43	2	20
α-helix	44-45	2
α-helix	46-51	6
α-helix	58-65	8
β-strand	71-72	2	21
β-strand	75-76	2	21
β-strand	83-84	2	20
β-strand	89-92	4	21
β-strand	97-100	4	21
β-strand	103	1	22
β-strand	109	1	22
β-strand	113	1	21
α-helix	118-120	3
β-strand	121-125	5	23
β-strand	126-132	7	24
β-strand	136-141	6	24
β-strand	146-148	3	24
β-strand	159-163	5	23
β-strand	169-173	5	23
β-strand	180-183	4	25
α-helix	186-188	3
β-strand	192-199	8	25
β-strand	207-212	6	25
β-strand	217-221	5	25
α-helix	222-224	3
β-strand	225-227	3	25
β-strand	229-230	2	26
β-strand	233-234	2	26
α-helix	248-261	14

Chain f: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
α-helix	91-93	3
β-strand	106	1	27
β-strand	116	1	27
β-strand	120	1	28
β-strand	131	1	28
β-strand	132-135	4	29
β-strand	138-141	4	29
β-strand	147-148	2	29

Chain F: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	34
β-strand	23-24	2	34
α-helix	33-35	3
β-strand	40	1	35
α-helix	62-64	3
β-strand	67	1	35
α-helix	68-75	8
α-helix	86-104	19
α-helix	108-119	12
β-strand	123-129	7	16
β-strand	134-141	8	16
α-helix	143-161	19
α-helix	169-181	13
α-helix	188-202	15

25 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
18S rRNA	2	RNA	1873	Homo sapiens
40S ribosomal protein S17	R	protein	135	Homo sapiens	P08708 (AlphaFold model)
40S ribosomal protein S27	b	protein	84	Homo sapiens	P42677 (AlphaFold model)
40S ribosomal protein S3a	B	protein	264	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S28	c	protein	69	Homo sapiens	P62857 (AlphaFold model)
40S ribosomal protein S4, X isoform	E	protein	263	Homo sapiens	P62701
40S ribosomal protein S30	e	protein	59	Homo sapiens	P62861
40S ribosomal protein S5	F	protein	204	Homo sapiens	P46782
40S ribosomal protein S7	H	protein	194	Homo sapiens	P62081
40S ribosomal protein S6	G	protein	249	Homo sapiens	P62753
40S ribosomal protein S25	Z	protein	125	Homo sapiens	P62851
40S ribosomal protein S24	Y	protein	133	Homo sapiens	P62847

22 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>7WTT_1 18S rRNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUAACGG

Sequence of entity 2 (R), FASTA

>7WTT_2 40S ribosomal protein S17 (chains R)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV

Sequence of entity 3 (b), FASTA

>7WTT_3 40S ribosomal protein S27 (chains b)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH

Sequence of entity 4 (B), FASTA

>7WTT_4 40S ribosomal protein S3a (chains B)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (c), FASTA

>7WTT_5 40S ribosomal protein S28 (chains c)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR

Sequence of entity 6 (E), FASTA

>7WTT_6 40S ribosomal protein S4, X isoform (chains E)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (e), FASTA

>7WTT_7 40S ribosomal protein S30 (chains e)
KVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS

Sequence of entity 8 (F), FASTA

>7WTT_8 40S ribosomal protein S5 (chains F)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 9 (H), FASTA

>7WTT_9 40S ribosomal protein S7 (chains H)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 10 (G), FASTA

>7WTT_10 40S ribosomal protein S6 (chains G)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 11 (Z), FASTA

>7WTT_11 40S ribosomal protein S25 (chains Z)
MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCK
EVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPA
AGEDA

Sequence of entity 12 (Y), FASTA

>7WTT_12 40S ribosomal protein S24 (chains Y)
MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGF
RTHFGGGKTTGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGT
AKANVGAGKKPKE

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
ZN	Zinc ion	Zn	1

Primary citation

The nucleoplasmic phase of pre-40S formation prior to nuclear export. Cheng, J., Lau, B., Thoms, M. et al. Nucleic Acids Res (2022) 50:11924-11937. DOI 10.1093/nar/gkac961 · PubMed

Other PDB entries of the same protein (UniProt P08708 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)
8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
9O3V 2.2 Å, Human 80S ribosome stalled on MYC nascent chain

Browse structure collections

About this viewer

MolViewer shows 7WTT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.