8UPR: Ribosomal protein L21

Name: PDB 8UPR: Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Published: 2024-05-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome. Determined by electron microscopy at 5.3 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 5.3 Å
Organisms: Escherichia coli, synthetic construct
Chains: 67
Atoms: 177,420
Mol. weight: 2738.64 kDa
Ligands: ZN, MG
Released: 29 May 2024

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

Secondary structure: helices and β-sheets

8UPR contains 404 α-helices and 556 β-strands across 59 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 0: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	10-14	5	1
β-strand	19-23	5	2
β-strand	32-35	4	2
β-strand	38-42	5	1
β-strand	48-49	2	1
β-strand	58-68	11	2
β-strand	72-78	7	3
β-strand	83-89	7	3
β-strand	92-102	11	2

Chain 1: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	7
α-helix	14-24	11
β-strand	28	1	7
α-helix	29-37	9
α-helix	42-62	21
α-helix	66-68	3
β-strand	70-78	9	7
α-helix	80-81	2
β-strand	82-87	6	8
α-helix	89-91	3
β-strand	93-98	6	8
β-strand	101-108	8	7

Chain 2: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	11-14	4	10
α-helix	18-22	5
α-helix	23-27	5
β-strand	29-34	6	10
α-helix	40-51	12
β-strand	55-63	9	10
α-helix	64-66	3
β-strand	67-70	4	11
β-strand	73-76	4	11
α-helix	77-79	3
β-strand	80-87	8	10
α-helix	88	1

Chain 3: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	17
β-strand	22-24	3	17
β-strand	25-29	5	18
β-strand	33-36	4	18
β-strand	41-45	5	19
α-helix	46-48	3
β-strand	49	1	20
α-helix	51-53	3
β-strand	54	1	20
β-strand	58-62	5	19
α-helix	63-64	2
β-strand	65-66	2	18
β-strand	70-72	3	17
β-strand	73-74	2	21
β-strand	79-80	2	21
β-strand	83-87	5	22
β-strand	92-96	5	22
α-helix	101	1
β-strand	102	1	22
α-helix	103	1

Chain 4: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	25
α-helix	14-22	9
β-strand	25-31	7	25
α-helix	36-37	2
β-strand	38-43	6	25
α-helix	44-52	9
α-helix	55-58	4
β-strand	61-65	5	25
β-strand	69-79	11	25
β-strand	86-93	8	25

Chain 9: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-19	13
α-helix	34-46	13
α-helix	95-103	9
α-helix	137-139	3

Chain AA: 53 helices, 96 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11-12	2
β-strand	13-14	2	50
α-helix	19-20	2
α-helix	29-38	10
α-helix	49-55	7
β-strand	59-60	2	51
β-strand	66-75	10	51
α-helix	82-88	7
β-strand	93-104	12	51
β-strand	117-128	12	51
α-helix	129	1
β-strand	136-137	2	52
β-strand	142-145	4	52
β-strand	147-151	5	53
α-helix	152	1
β-strand	154-158	5	54
α-helix	164-166	3
β-strand	173-177	5	54
β-strand	180	1	55
β-strand	184-188	5	54
β-strand	194-197	4	54
β-strand	203-205	3	54
α-helix	207-212	6
α-helix	217-224	8
β-strand	228-231	4	56
β-strand	239-240	2	56
α-helix	243-246	4
β-strand	250	1	57
β-strand	255-257	3	58
β-strand	260-263	4	58
β-strand	268	1	57
α-helix	269-270	2
α-helix	271-279	9
β-strand	284-285	2	56
α-helix	295	1
β-strand	296	1	59
β-strand	297	1	56
β-strand	301-302	2	60
β-strand	309-311	3	60
β-strand	316	1	59
α-helix	319-326	8
β-strand	332-335	4	56
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-388	11
β-strand	396	1	55
α-helix	399-407	9
α-helix	422-437	16
β-strand	451-454	4	53
α-helix	456-479	24
α-helix	496-507	12
β-strand	512-514	3	52
α-helix	520-526	7
β-strand	530-531	2	53
β-strand	558	1	61
β-strand	572-573	2	53
β-strand	575	1	61
β-strand	580-581	2	62
β-strand	587-588	2	62
β-strand	589-594	6	63
β-strand	599-606	8	63
α-helix	610-613	4
β-strand	616-617	2	63
β-strand	623	1	64
β-strand	629	1	64
β-strand	634-637	4	63
β-strand	642-645	4	63
β-strand	652-653	2	63
α-helix	671-673	3
β-strand	674	1	65
α-helix	676-687	12
β-strand	689	1	66
β-strand	700-701	2	50
α-helix	705-710	6
β-strand	717	1	67
β-strand	722-727	6	68
β-strand	731-736	6	68
α-helix	737	1
α-helix	738-740	3
β-strand	748-752	5	68
β-strand	757-758	2	69
β-strand	764-765	2	69
β-strand	768-769	2	70
β-strand	776-777	2	68
β-strand	782	1	67
β-strand	784-785	2	70
β-strand	789-790	2	71
β-strand	793-794	2	71
β-strand	798-804	7	72
β-strand	816-819	4	72
α-helix	820-824	5
β-strand	830-841	12	73
β-strand	842-843	2	74
β-strand	846-847	2	74
β-strand	849	1	75
α-helix	859-862	4
β-strand	865	1	76
β-strand	870	1	77
β-strand	871	1	76
α-helix	872	1
β-strand	876-877	2	78
β-strand	882-884	3	77
β-strand	887	1	75
β-strand	915	1	75
β-strand	918-919	2	77
β-strand	926-927	2	78
β-strand	928-935	8	73
α-helix	940-941	2
α-helix	943-978	36
α-helix	988-990	3
α-helix	1006-1037	32
β-strand	1046-1058	13	73
β-strand	1065	1	79
β-strand	1066-1067	2	80
β-strand	1075	1	79
β-strand	1076-1080	5	72
β-strand	1087	1	81
β-strand	1088	1	82
α-helix	1092	1
β-strand	1093	1	81
α-helix	1094	1
β-strand	1096-1098	3	72
α-helix	1102-1105	4
β-strand	1108	1	65
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1168-1176	9
β-strand	1182-1183	2	50
α-helix	1192-1201	10
β-strand	1209-1210	2	72
α-helix	1211	1
β-strand	1212	1	82
α-helix	1220-1221	2
α-helix	1224	1
β-strand	1225-1232	8	72
β-strand	1233-1234	2	80
β-strand	1235	1	66
β-strand	1244-1246	3	83
β-strand	1251	1	84
β-strand	1258	1	84
β-strand	1269-1270	2	85
α-helix	1272-1280	9
α-helix	1285-1288	4
α-helix	1289-1293	5
α-helix	1298-1309	12
α-helix	1321-1331	11
β-strand	1335-1337	3	86

Chain AB: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	90
α-helix	14-22	9
β-strand	28-29	2	90
β-strand	32-38	7	91
β-strand	43-49	7	91
β-strand	54-59	6	90
α-helix	66-69	4
β-strand	77-78	2	90
α-helix	86-89	4
α-helix	91-95	5
β-strand	139-143	5	92
β-strand	150-154	5	92

51 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
Ribosomal protein L21	0	protein	103	Escherichia coli	P0AG48 (AlphaFold model)
50S ribosomal protein L22	1	protein	110	Escherichia coli	P61175 (AlphaFold model)
50S ribosomal protein L23	2	protein	100	Escherichia coli	P0ADZ0 (AlphaFold model)
50S ribosomal protein L24	3	protein	104	Escherichia coli	P60624 (AlphaFold model)
50S ribosomal protein L25	4	protein	94	Escherichia coli	P68919
NT DNA ops	5	DNA	38	synthetic construct
T DNA ops	6	DNA	38	synthetic construct
mRNA with 21 nt long spacer	7	RNA	38	synthetic construct
50S ribosomal protein L10	9	protein	165	Escherichia coli	P0A7J3
E-site and P-site tRNA (fMet)	A, B	RNA	76	Escherichia coli
DNA-directed RNA polymerase subunit beta	AA	protein	1342	Escherichia coli	P0A8V2
Transcription antitermination protein RfaH	AB	protein	162	Escherichia coli	P0AFW0

53 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8UPR_1 Ribosomal protein L21 (chains 0)
MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIK
AEVVAHGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGISA

Sequence of entity 2 (1), FASTA

>8UPR_2 50S ribosomal protein L22 (chains 1)
METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEH
NDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR

Sequence of entity 3 (2), FASTA

>8UPR_3 50S ribosomal protein L23 (chains 2)
MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNT
LVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE

Sequence of entity 4 (3), FASTA

>8UPR_4 50S ribosomal protein L24 (chains 3)
MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVE
KEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK

Sequence of entity 5 (4), FASTA

>8UPR_5 50S ribosomal protein L25 (chains 4)
MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEV
LTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Sequence of entity 6 (5), FASTA

>8UPR_6 NT DNA ops (chains 5)
CCGTCATGATCATAGGCGGTAGCGTGCGCCAGACAGGG

Sequence of entity 7 (6), FASTA

>8UPR_7 T DNA ops (chains 6)
CCCTGTCTGGCGTCCTCTCACCCCTATGATCATGACGG

Sequence of entity 8 (7), FASTA

>8UPR_8 mRNA with 21 nt long spacer (chains 7)
AUGUUUUUUUUUUUUUUUUUUUUUGAUUUGGUGAGAGG

Sequence of entity 9 (9), FASTA

>8UPR_9 50S ribosomal protein L10 (chains 9)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA

Sequence of entity 10 (A, B), FASTA

>8UPR_10 E-site and P-site tRNA (fMet) (chains A, B)
CGCGGGGUGGAGCAGCCGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAU
CCGGCCCCCGCAACCA

Sequence of entity 11 (AA), FASTA

>8UPR_11 DNA-directed RNA polymerase subunit beta (chains AA)
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQ
SYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ
EVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRL
SALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTR
ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV
VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERG
DVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVS
RDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDE
LKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKIN
PIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAK
LREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMP
ESFNVLLKEIRSLGINIELEDE

Sequence of entity 12 (AB), FASTA

>8UPR_12 Transcription antitermination protein RfaH (chains AB)
MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFD
PEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITE
GAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	1

Primary citation

Structural basis of RfaH-mediated transcription-translation coupling. Molodtsov, V., Wang, C., Zhang, J. et al. Nat Struct Mol Biol (2024) 31:1932-1941. DOI 10.1038/s41594-024-01372-w · PubMed

Other PDB entries of the same protein (UniProt P0AG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
8CGV 1.66 Å, Tiamulin bound to the 50S subunit
8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
8CAM 1.86 Å, Evernimicin bound to the 50S subunit
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)

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