5U9F: 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex

Name: PDB 5U9F: 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure II)
Published: 2017-03-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure II). Determined by electron microscopy at 3.2 Å resolution. Released 22 Mar 2017.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Escherichia coli
Chains: 60
Atoms: 152,819
Mol. weight: 2305.5 kDa
Ligands: MG, ZN
Released: 22 Mar 2017

Explore 5U9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U9F contains 249 α-helices and 366 β-strands across 54 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 03: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	23-31	9
β-strand	42-48	7	15
β-strand	60-63	4	16
β-strand	75	1	17
β-strand	76-79	4	18
α-helix	83-88	6
β-strand	94-97	4	18
α-helix	101-105	5
β-strand	113	1	17
β-strand	116	1	19
α-helix	121-124	4
α-helix	132-134	3
β-strand	145	1	19
α-helix	149-156	8
β-strand	161-164	4	16
β-strand	170-176	7	15
α-helix	182-191	10
α-helix	193-198	6
β-strand	209-216	8	15
β-strand	222-223	2	15

Chain 04: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	24
β-strand	16-18	3	24
α-helix	30-32	3
β-strand	33-34	2	25
β-strand	42	1	26
β-strand	48	1	26
β-strand	53	1	27
β-strand	61-62	2	25
β-strand	64	1	28
β-strand	72-81	10	28
α-helix	89	1
β-strand	90-95	6	28
β-strand	99-104	6	28
α-helix	105	1
β-strand	106	1	29
β-strand	114-117	4	28
β-strand	128-130	3	28
α-helix	135	1
β-strand	139-141	3	28
β-strand	143	1	30
β-strand	153	1	30
β-strand	161-167	7	28
β-strand	170-174	5	28
β-strand	180-184	5	28
β-strand	188-191	4	28
β-strand	194	1	29
α-helix	197-201	5
β-strand	203	1	24
α-helix	208-211	4
β-strand	215	1	27
α-helix	216-220	5
β-strand	266	1	28

Chain 05: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	33
β-strand	21-28	8	33
β-strand	32-38	7	34
β-strand	47-51	5	34
α-helix	62-71	10
α-helix	74-76	3
β-strand	79	1	34
β-strand	82-83	2	34
β-strand	95-96	2	34
α-helix	98-102	5
β-strand	106-112	7	35
α-helix	113-115	3
β-strand	118-119	2	36
α-helix	121-125	5
α-helix	127-129	3
β-strand	163-164	2	36
β-strand	169-176	8	35
β-strand	177-179	3	33
β-strand	188-190	3	33
β-strand	200-203	4	33
β-strand	204-205	2	35

Chain 06: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	39
β-strand	12-13	2	39
α-helix	16-19	4
α-helix	25-39	15
α-helix	98-115	18
β-strand	118-121	4	40
α-helix	131-140	10
β-strand	146-150	5	40
α-helix	155-160	6
β-strand	167-171	5	40
α-helix	179-182	4
β-strand	186-189	4	40
α-helix	190-199	10

Chain 07: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	6-11	6
α-helix	12-16	5
β-strand	30-34	5	41
β-strand	37-38	2	42
α-helix	41-43	3
α-helix	47-59	13
α-helix	63-64	2
β-strand	65-68	4	42
β-strand	83-87	5	42
β-strand	89-90	2	41
α-helix	93-103	11
β-strand	116	1	43
β-strand	127-130	4	41
β-strand	152-157	6	41
α-helix	162-170	9
β-strand	176	1	43

Chain 08: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	45
β-strand	15-19	5	46
β-strand	22-26	5	46
β-strand	31-35	5	46
β-strand	40-44	5	45
β-strand	48-53	6	45
α-helix	54	1
α-helix	60-63	4
α-helix	65-79	15
β-strand	82-87	6	47
β-strand	94-98	5	48
β-strand	101-105	5	48
β-strand	112-115	4	48
β-strand	121	1	47
β-strand	129-134	6	47
α-helix	137-148	12
α-helix	152-154	3
β-strand	162-163	2	47

Chain 09: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	50
β-strand	18-19	2	50
α-helix	23-25	3
α-helix	26-30	5
α-helix	31-33	3
β-strand	36-38	3	50
α-helix	45	1
α-helix	46-51	6
α-helix	55-70	16
β-strand	77-82	6	51
β-strand	87	1	52
β-strand	89	1	52
α-helix	99-102	4
α-helix	104-106	3
β-strand	115-116	2	51
β-strand	127-132	6	51
β-strand	140-148	9	51

Chain 10: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	27	1	53
α-helix	36-38	3
α-helix	40-44	5
α-helix	72-77	6
β-strand	83	1	53
α-helix	95-104	10

46 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	1539	Escherichia coli
23S ribosomal RNA	01	RNA	2903	Escherichia coli
5S ribosomal RNA	02	RNA	119	Escherichia coli
Alternative ribosome-rescue factor A	Y	protein	72	Escherichia coli	P36675 (AlphaFold model)
fMet-tRNA (P- and E-site)	W, X	RNA	77	Escherichia coli
50S ribosomal protein L1	03	protein	234	Escherichia coli	P0A7L0 (AlphaFold model)
50S ribosomal protein L2	04	protein	273	Escherichia coli	P60422 (AlphaFold model)
50S ribosomal protein L3	05	protein	209	Escherichia coli	P60438 (AlphaFold model)
50S ribosomal protein L4	06	protein	201	Escherichia coli	P60723
50S ribosomal protein L5	07	protein	179	Escherichia coli	P62399
50S ribosomal protein L6	08	protein	177	Escherichia coli	P0AG55
50S ribosomal protein L9	09	protein	149	Escherichia coli	P0A7R1

47 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5U9F_1 16S ribosomal RNA (chains A)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGG
GAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGG
GAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUU
CGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUG
ACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGG
GUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCG
UAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG
GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAA
ACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCC
UUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUU
CGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGA
AUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA
AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCC
GGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGA
CCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACU
CGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUU
CCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Sequence of entity 2 (01), FASTA

>5U9F_2 23S ribosomal RNA (chains 01)
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
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGGAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU

Sequence of entity 3 (02), FASTA

>5U9F_3 5S ribosomal RNA (chains 02)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCA

Sequence of entity 4 (Y), FASTA

>5U9F_4 Alternative ribosome-rescue factor A (chains Y)
MSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASGKKVNH
FFTTGLLLSGAC

Sequence of entity 5 (W, X), FASTA

>5U9F_5 fMet-tRNA (P- and E-site) (chains W, X)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 6 (03), FASTA

>5U9F_6 50S ribosomal protein L1 (chains 03)
MAKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVR
GATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDA
MRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDF
DADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLSASVN

Sequence of entity 7 (04), FASTA

>5U9F_7 50S ribosomal protein L2 (chains 04)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 8 (05), FASTA

>5U9F_8 50S ribosomal protein L3 (chains 05)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 9 (06), FASTA

>5U9F_9 50S ribosomal protein L4 (chains 06)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 10 (07), FASTA

>5U9F_10 50S ribosomal protein L5 (chains 07)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 11 (08), FASTA

>5U9F_11 50S ribosomal protein L6 (chains 08)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 12 (09), FASTA

>5U9F_12 50S ribosomal protein L9 (chains 09)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	360
ZN	Zinc ion	Zn	1

Primary citation

Mechanism of ribosome rescue by ArfA and RF2. Demo, G., Svidritskiy, E., Madireddy, R. et al. Elife (2017) 6. DOI 10.7554/eLife.23687 · PubMed

Other PDB entries of the same protein (UniProt P36675 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MDV 2.97 Å, Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)
5H5U 3.01 Å, Mechanistic insights into the alternative translation termination by ArfA and RF2
5MDW 3.06 Å, Structure of ArfA(A18T) and RF2 bound to the 70S ribosome (pre-accommodated state)
5MGP 3.1 Å, Structural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAs
5U9G 3.2 Å, 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure I)
6C4I 3.24 Å, Conformation of methylated GGQ in the peptidyl transferase center during translation…
5MDY 3.35 Å, Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)
5U4I 3.5 Å, Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
7OJ0 3.5 Å, Cryo-EM structure of 70S ribosome stalled with TnaC peptide and RF2
5U4J 3.7 Å, Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome

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