5H5U: 30S ribosomal protein S20

Mechanistic insights into the alternative translation termination by ArfA and RF2. Determined by electron microscopy at 3.01 Å resolution. Released 25 Jan 2017.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Escherichia coli K-12, Escherichia coli
Chains: 57
Atoms: 148,128
Mol. weight: 2233.81 kDa
Released: 25 Jan 2017

Explore 5H5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H5U contains 259 α-helices and 369 β-strands across 52 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 1: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	5-41	37
α-helix	44-64	21
α-helix	69-86	18

Chain 2: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4-5	2	3
α-helix	12-26	15
α-helix	30-33	4
α-helix	41-55	15

Chain 3: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	16-19	4

Chain 4: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
α-helix	27-41	15
α-helix	44-48	5
α-helix	50-83	34
α-helix	85-90	6
α-helix	93-98	6
α-helix	103-118	16
β-strand	128-134	7	16
α-helix	138-156	19
β-strand	162	1	17
β-strand	167-170	4	16
β-strand	176-183	8	16
β-strand	184	1	17
α-helix	189-192	4
β-strand	197-202	6	16
β-strand	203-204	2	18
β-strand	213-214	2	18
β-strand	217-220	4	16
β-strand	222-224	3	16
β-strand	239-243	5	19
α-helix	245-247	3
α-helix	251-256	6
β-strand	261-265	5	19
β-strand	271	1	19
β-strand	274	1	19
α-helix	280-303	24
α-helix	318-321	4
β-strand	322-327	6	16
β-strand	332-335	4	16
α-helix	345-350	6
α-helix	357-363	7

Chain a: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	28
α-helix	18-27	10
β-strand	35-39	5	28
α-helix	42-50	9
α-helix	52-54	3
β-strand	55-58	4	28

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-17	8
α-helix	21-25	5
β-strand	29-30	2	29
β-strand	37-38	2	29
β-strand	42	1	99
β-strand	48-49	2	30
β-strand	52-53	2	30

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	40
β-strand	20-25	6	40
α-helix	33-34	2
β-strand	35-40	6	40
β-strand	45-53	9	40

Chain C: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	31
β-strand	17-19	3	31
β-strand	24	1	32
α-helix	28-30	3
α-helix	31-33	3
β-strand	34-35	2	33
β-strand	43	1	34
β-strand	49	1	34
β-strand	54	1	35
α-helix	61	1
β-strand	62-63	2	33
β-strand	65	1	32
β-strand	76-82	7	32
β-strand	91-96	6	32
β-strand	101-105	5	32
β-strand	107	1	36
β-strand	115-116	2	32
β-strand	118	1	37
β-strand	129-131	3	37
α-helix	136	1
β-strand	140-142	3	37
β-strand	144	1	38
β-strand	154	1	38
β-strand	162-168	7	37
β-strand	171-175	5	37
β-strand	181-185	5	37
β-strand	189-192	4	37
β-strand	195	1	36
α-helix	198-202	5
β-strand	204	1	31
α-helix	208-212	5
β-strand	216	1	35
α-helix	222-224	3
β-strand	245	1	39
β-strand	251	1	39
α-helix	261-263	3
β-strand	269	1	37

44 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
30S ribosomal protein S20	1	protein	86	Escherichia coli K-12	P0A7U7 (AlphaFold model)
30S ribosomal protein S21	2	protein	70	Escherichia coli K-12	P68679 (AlphaFold model)
Alternative ribosome-rescue factor A	3	protein	72	Escherichia coli K-12	P36675 (AlphaFold model)
Peptide chain release factor 2	4	protein	365	Escherichia coli K-12	P07012 (AlphaFold model)
P-site tRNA	5	RNA	76	Escherichia coli
mRNA	7	RNA	6	Escherichia coli
23S rRNA	A	RNA	2903	Escherichia coli K-12
5S Ribosomal RNA	B	RNA	120	Escherichia coli K-12
50S ribosomal protein L2	C	protein	272	Escherichia coli K-12	P60422
50S ribosomal protein L3	D	protein	209	Escherichia coli K-12	P60438
50S ribosomal protein L4	E	protein	201	Escherichia coli K-12	P60723
50S ribosomal protein L5	F	protein	178	Escherichia coli K-12	P62399

45 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5H5U_1 30S ribosomal protein S20 (chains 1)
ANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQ
AAKGLIHKNKAARHKANLTAQINKLA

Sequence of entity 2 (2), FASTA

>5H5U_2 30S ribosomal protein S21 (chains 2)
PVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLA
RENARRTRLY

Sequence of entity 3 (3), FASTA

>5H5U_3 Alternative ribosome-rescue factor A (chains 3)
MSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASGKKVNH
FFTTGLLLSGAC

Sequence of entity 4 (4), FASTA

>5H5U_4 Peptide chain release factor 2 (chains 4)
MFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKER
SSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFS
GEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVT
IKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLR
IDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEM
QKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEAS
LKAGL

Sequence of entity 5 (5), FASTA

>5H5U_5 P-site tRNA (chains 5)
CGCGGGGUGGAGCAGCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAU
CCGGCCCCCGCAACCA

Sequence of entity 6 (7), FASTA

>5H5U_6 mRNA (chains 7)
ACUAUG

Sequence of entity 7 (A), FASTA

>5H5U_7 23S rRNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACCAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU

Sequence of entity 8 (B), FASTA

>5H5U_8 5S Ribosomal RNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 9 (C), FASTA

>5H5U_9 50S ribosomal protein L2 (chains C)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 10 (D), FASTA

>5H5U_10 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 11 (E), FASTA

>5H5U_11 50S ribosomal protein L4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 12 (F), FASTA

>5H5U_12 50S ribosomal protein L5 (chains F)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Primary citation

Mechanistic insights into the alternative translation termination by ArfA and RF2. Ma, C., Kurita, D., Li, N. et al. Nature (2017) 541:550-553. DOI 10.1038/nature20822 · PubMed

Other PDB entries of the same protein (UniProt P0A7U7 (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…
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
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
8CGU 1.89 Å, Gentamicin bound to the 30S body
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA
7K00 1.98 Å, Structure of the Bacterial Ribosome at 2 Angstrom Resolution
8QOA 2.0 Å, Structure of SecM-stalled Escherichia coli 70S ribosome

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