9GUP: 30S mRNA delivery complex

Name: PDB 9GUP: 30S mRNA delivery complex (open head)
Published: 2024-11-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

30S mRNA delivery complex (open head). Determined by electron microscopy at 2.8 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Escherichia coli K-12, synthetic construct
Chains: 23
Atoms: 53,689
Mol. weight: 865.66 kDa
Ligands: MG
Released: 20 Nov 2024

Explore 9GUP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GUP contains 116 α-helices and 115 β-strands across 21 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 B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
β-strand	23-31	9	1
β-strand	35-39	5	1
β-strand	47-49	3	1
α-helix	50-53	4
β-strand	54	1	2
β-strand	60	1	2
β-strand	67-74	8	1
β-strand	83-85	3	1
α-helix	86-104	19
β-strand	108-115	8	3
β-strand	119-124	6	3
β-strand	127-132	6	3
α-helix	133-135	3
α-helix	145-147	3
β-strand	151-154	4	3
β-strand	158-160	3	3
α-helix	161-163	3
β-strand	165-167	3	3

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	4
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-34	4	4
β-strand	38-41	4	4
α-helix	43-62	20
β-strand	67-70	4	5
α-helix	77-85	9
β-strand	90-92	3	5
α-helix	104-121	18
α-helix	132-148	17
β-strand	160-164	5	5
α-helix	170-178	9
β-strand	183-187	5	5
β-strand	198-201	4	5
α-helix	207-226	20

Chain D: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	12	1	6
β-strand	16	1	6
β-strand	20	1	7
α-helix	26-46	21
β-strand	52-58	7	7
β-strand	64-70	7	7
α-helix	73-77	5
α-helix	82-95	14
β-strand	99-105	7	7
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-154	7	8
α-helix	157-159	3
β-strand	165-171	7	8
β-strand	180-191	12	8
β-strand	194-206	13	8

Chain E: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	28-31	4
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-96	11
β-strand	97	1	9
α-helix	98-105	8
α-helix	111-119	9
β-strand	123-125	3	10
β-strand	128-129	2	10
β-strand	136	1	9
α-helix	137-138	2
β-strand	142-145	4	10
α-helix	147-150	4
α-helix	153-164	12
α-helix	166-168	3
β-strand	171-174	4	10
β-strand	179-182	4	10
α-helix	197-205	9

Chain F: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-25	14	11
β-strand	28-40	13	11
β-strand	45-53	9	11
α-helix	56-68	13
β-strand	72-73	2	11
β-strand	77	1	12
β-strand	80	1	12
β-strand	85-89	5	13
β-strand	92-98	7	13
β-strand	105-106	2	13
α-helix	109-118	10
β-strand	123-129	7	13
α-helix	133-145	13
α-helix	150-157	8
α-helix	161-164	4

Chain G: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	14
α-helix	12-14	3
α-helix	18-31	14
β-strand	35-45	11	14
β-strand	51	1	15
β-strand	54	1	15
β-strand	57-65	9	14
α-helix	68-80	13
β-strand	84-92	9	14

Chain H: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-54	19
α-helix	58-69	12
β-strand	73-79	7	16
β-strand	84-90	7	16
α-helix	91-92	2
α-helix	93-109	17
α-helix	116-128	13
α-helix	133-147	15

Chain I: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	17
α-helix	31-43	13
β-strand	46-52	7	17
β-strand	58-63	6	17
β-strand	65	1	18
β-strand	70	1	18
β-strand	75-77	3	19
β-strand	80	1	20
β-strand	83	1	20
β-strand	86-87	2	19
α-helix	89-91	3
α-helix	95-98	4
β-strand	101-107	7	19
β-strand	109-112	4	19
α-helix	113-119	7
β-strand	123-129	7	19

13 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
16S ribosomal RNA	A	RNA	1541	Escherichia coli K-12
30S ribosomal protein S1	B	protein	557	Escherichia coli K-12	P0AG67 (AlphaFold model)
30S ribosomal protein S2	C	protein	241	Escherichia coli K-12	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	D	protein	233	Escherichia coli K-12	P0A7V3 (AlphaFold model)
Small ribosomal subunit protein uS4	E	protein	206	Escherichia coli K-12	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	F	protein	156	Escherichia coli K-12	P0A7W1
Small ribosomal subunit protein bS6	G	protein	131	Escherichia coli K-12	P02358
30S ribosomal protein S7	H	protein	156	Escherichia coli K-12	P02359
30S ribosomal protein S8	I	protein	130	Escherichia coli K-12	P0A7W7
30S ribosomal protein S9	J	protein	130	Escherichia coli K-12	P0A7X3
30S ribosomal protein S10	K	protein	103	Escherichia coli K-12	P0A7R5
30S ribosomal protein S11	L	protein	129	Escherichia coli K-12	P0A7R9

11 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9GUP_1 16S ribosomal RNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGUACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUU

Sequence of entity 2 (B), FASTA

>9GUP_2 30S ribosomal protein S1 (chains B)
MTESFAQLFEESLKEIETRPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFKNAQGEL
EIQVGDEVDVALDAVEDGFGETLLSREKAKRHEAWITLEKAYEDAETVTGVINGKVKGGF
TVELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRRAVIESENSA
ERDQLLENLQEGMEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVNVGDE
ITVKVLKFDRERTRVSLGLKQLGEDPWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGV
EGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAET
HNKGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWNVAGEEAVREYKKGDEIAAVVL
QVDAERERISLGVKQLAEDPFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRA
SEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDEADEKDAIATVNKQEDA
NFSNNAMAEAFKAAKGE

Sequence of entity 3 (C), FASTA

>9GUP_3 30S ribosomal protein S2 (chains C)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 4 (D), FASTA

>9GUP_4 Small ribosomal subunit protein uS3 (chains D)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 5 (E), FASTA

>9GUP_5 Small ribosomal subunit protein uS4 (chains E)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 6 (F), FASTA

>9GUP_6 30S ribosomal protein S5 (chains F)
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARR
NMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYG
STNPINVVRATIDGLENMNSPEMVAAKRGKSVEEIL

Sequence of entity 7 (G), FASTA

>9GUP_7 Small ribosomal subunit protein bS6 (chains G)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDADAGDSEE

Sequence of entity 8 (H), FASTA

>9GUP_8 30S ribosomal protein S7 (chains H)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Sequence of entity 9 (I), FASTA

>9GUP_9 30S ribosomal protein S8 (chains I)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 10 (J), FASTA

>9GUP_10 30S ribosomal protein S9 (chains J)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 11 (K), FASTA

>9GUP_11 30S ribosomal protein S10 (chains K)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 12 (L), FASTA

>9GUP_12 30S ribosomal protein S11 (chains L)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	86

Primary citation

Molecular basis of mRNA delivery to the bacterial ribosome. Webster, M.W., Chauvier, A., Rahil, H. et al. Science (2024) 386:eado8476-eado8476. DOI 10.1126/science.ado8476 · PubMed

Other PDB entries of the same protein (UniProt P0AG67 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BH8 1.9 Å, Combinatorial Protein 1b11
9GUU 2.5 Å, 30S mRNA delivery complex (consensus)
9IOT 2.7 Å, Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant
9GUT 2.8 Å, 30S mRNA delivery complex (bS1 resolved)
4Q7J 2.9 Å, Complex structure of viral RNA polymerase
6H4N 3.0 Å, Structure of a hibernating 100S ribosome reveals an inactive conformation of the…
9GUV 3.0 Å, 30S mRNA delivery complex (closed-head)
6X7K 3.1 Å, Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B3…
8URY 3.1 Å, Escherichia coli transcription-translation coupled complex class B (TTC-B) containing…
9GUQ 3.1 Å, 30S PIC (Pre-Initiation complex)
9GUW 3.1 Å, 30S-TEC (TEC in expressome position) Inactive state 2
6X6T 3.2 Å, Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B1…

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