6VYS: 50S ribosomal protein L21

Escherichia coli transcription-translation complex A1 (TTC-A1) containing a 21 nt long mRNA spacer, NusG, and fMet-tRNAs at E-site and P-site. Determined by electron microscopy at 3.7 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Escherichia coli, synthetic construct
Chains: 66
Atoms: 175,820
Mol. weight: 2724.03 kDa
Ligands: MG, ZN
Released: 2 Sept 2020

Explore 6VYS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VYS contains 386 α-helices and 548 β-strands across 58 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	6
α-helix	14-23	10
β-strand	28	1	6
α-helix	29-37	9
α-helix	42-62	21
β-strand	70-78	9	6
α-helix	80-81	2
β-strand	82-87	6	7
α-helix	89-91	3
β-strand	93-98	6	7
β-strand	101-108	8	6

Chain 2: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	11-14	4	13
α-helix	18-26	9
β-strand	29-34	6	13
α-helix	40-51	12
β-strand	55-63	9	13
α-helix	64-66	3
β-strand	67-70	4	14
β-strand	73-76	4	14
α-helix	77-79	3
β-strand	80-87	8	13
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
β-strand	65-66	2	18
α-helix	67-69	3
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	3-8	6	29
α-helix	14-22	9
β-strand	25-31	7	29
α-helix	36-37	2
β-strand	38-43	6	29
α-helix	44-52	9
α-helix	55-58	4
β-strand	61-65	5	29
β-strand	69-79	11	29
β-strand	86-93	8	29

Chain 9: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	25	1	45
α-helix	35-46	12
β-strand	85	1	45
α-helix	95-103	9

Chain AA: 56 helices, 91 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	54
α-helix	19-20	2
α-helix	23-26	4
α-helix	29-38	10
α-helix	49-56	8
β-strand	59-60	2	55
β-strand	66-75	10	55
α-helix	82-88	7
β-strand	93-104	12	55
α-helix	113-114	2
β-strand	116-128	13	55
α-helix	129-131	3
β-strand	136-137	2	56
β-strand	142-145	4	56
α-helix	146	1
β-strand	147-151	5	57
α-helix	152	1
β-strand	154-158	5	58
α-helix	164-166	3
β-strand	173-177	5	58
β-strand	180	1	59
β-strand	184-189	6	58
β-strand	193-198	6	58
β-strand	204-205	2	58
α-helix	207-212	6
α-helix	217-224	8
β-strand	227-231	5	60
α-helix	232	1
β-strand	239-240	2	60
α-helix	243-246	4
β-strand	250	1	61
β-strand	255-257	3	62
β-strand	260-263	4	62
β-strand	268	1	61
α-helix	269-270	2
α-helix	271-279	9
β-strand	284-285	2	60
α-helix	286-288	3
α-helix	289-292	4
β-strand	296	1	63
β-strand	297	1	60
β-strand	301-303	3	64
β-strand	308-311	4	64
β-strand	316	1	63
α-helix	319-328	10
β-strand	332-336	5	60
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-386	9
β-strand	396	1	59
α-helix	399-408	10
α-helix	422-437	16
β-strand	451-454	4	57
α-helix	456-480	25
α-helix	496-507	12
β-strand	512-514	3	56
α-helix	520-526	7
β-strand	529-531	3	57
β-strand	558	1	65
β-strand	572-574	3	57
β-strand	575	1	65
β-strand	576	1	66
β-strand	580-581	2	67
β-strand	587-588	2	67
β-strand	589-593	5	68
β-strand	603-606	4	68
α-helix	608-611	4
β-strand	616	1	68
β-strand	623	1	69
β-strand	629	1	69
β-strand	633-637	5	68
β-strand	642-646	5	68
β-strand	652-654	3	68
β-strand	662	1	66
α-helix	676-686	11
β-strand	689	1	70
α-helix	690-692	3
β-strand	700-701	2	54
α-helix	705-711	7
β-strand	717	1	71
β-strand	722	1	72
β-strand	731-735	5	73
β-strand	736	1	72
α-helix	737	1
α-helix	738-740	3
β-strand	748-752	5	73
α-helix	753	1
β-strand	757-758	2	74
β-strand	763	1	75
β-strand	764-765	2	74
β-strand	768-769	2	76
β-strand	777	1	72
β-strand	782	1	71
β-strand	784-785	2	76
β-strand	798-804	7	77
β-strand	816-818	3	77
α-helix	820-824	5
β-strand	830-838	9	75
β-strand	865	1	78
β-strand	871	1	78
β-strand	874-877	4	79
β-strand	882-884	3	80
β-strand	918-919	2	80
α-helix	920-921	2
β-strand	926-928	3	79
β-strand	930-933	4	75
α-helix	944-978	35
α-helix	986-988	3
α-helix	1010-1036	27
β-strand	1050-1058	9	75
β-strand	1065-1067	3	81
β-strand	1073-1075	3	81
β-strand	1076-1079	4	77
β-strand	1087	1	82
β-strand	1088	1	83
α-helix	1092	1
β-strand	1093	1	82
α-helix	1094	1
β-strand	1096-1098	3	77
α-helix	1102-1105	4
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1168-1175	8
β-strand	1182-1183	2	54
α-helix	1192-1201	10
β-strand	1209-1210	2	77
β-strand	1212	1	83
β-strand	1213	1	84
β-strand	1220	1	84
α-helix	1221	1
α-helix	1224	1
β-strand	1225-1232	8	77
β-strand	1233-1234	2	81
β-strand	1235	1	70
α-helix	1239-1241	3
β-strand	1244-1246	3	85
β-strand	1251	1	86
β-strand	1258	1	86
α-helix	1259	1
β-strand	1268-1270	3	87
α-helix	1272-1280	9
α-helix	1284-1288	5
α-helix	1289-1293	5
α-helix	1298-1310	13
α-helix	1321-1331	11
β-strand	1335-1337	3	88

Chain AB: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	93
α-helix	19-32	14
α-helix	36-38	3
β-strand	39-43	5	93
β-strand	68-73	6	93
α-helix	77-85	9
β-strand	89-92	4	93
α-helix	100-102	3
α-helix	105-116	12

50 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
50S 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	5	DNA	36	synthetic construct
T DNA	6	DNA	36	synthetic construct
mRNA with 21 nt long spacer	7	RNA	37	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 termination/antitermination protein NusG	AB	protein	181	Escherichia coli	P0AFG0

52 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>6VYS_1 50S ribosomal protein L21 (chains 0)
MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIK
AEVVAHGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGISA

Sequence of entity 2 (1), FASTA

>6VYS_2 50S ribosomal protein L22 (chains 1)
METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEH
NDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR

Sequence of entity 3 (2), FASTA

>6VYS_3 50S ribosomal protein L23 (chains 2)
MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNT
LVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE

Sequence of entity 4 (3), FASTA

>6VYS_4 50S ribosomal protein L24 (chains 3)
MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVE
KEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK

Sequence of entity 5 (4), FASTA

>6VYS_5 50S ribosomal protein L25 (chains 4)
MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEV
LTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Sequence of entity 6 (5), FASTA

>6VYS_6 NT DNA (chains 5)
CCGTCATGATCATATTATTTTTTACGCCAGACAGGG

Sequence of entity 7 (6), FASTA

>6VYS_7 T DNA (chains 6)
CCCTGTCTGGCGTCCTCTCACCTATGATCATGACGG

Sequence of entity 8 (7), FASTA

>6VYS_8 mRNA with 21 nt long spacer (chains 7)
AUGUUUUUUUUUUUUUUUUUUUUGAUUUGGUGAGAGG

Sequence of entity 9 (9), FASTA

>6VYS_9 50S ribosomal protein L10 (chains 9)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA

Sequence of entity 10 (A, B), FASTA

>6VYS_10 E-site and P-site tRNA (fMet) (chains A, B)
CGCGGGGUGGAGCAGCCGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAU
CCGGCCCCCGCAACCA

Sequence of entity 11 (AA), FASTA

>6VYS_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

>6VYS_12 Transcription termination/antitermination protein NusG (chains AB)
MSEAPKKRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVMVPTEEVVEIRGGQRRKS
ERKFFPGYVLVQMVMNDASWHLVRSVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGD
KPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEK
A

Ligands and cofactors

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

Primary citation

Structural basis of transcription-translation coupling. Wang, C., Molodtsov, V., Firlar, E. et al. Science (2020) 369:1359-1365. DOI 10.1126/science.abb5317 · 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)

Browse structure collections

About this viewer

MolViewer shows 6VYS 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.