5MDY: ArfA and TtRF2

Name: PDB 5MDY: Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)
Published: 2016-12-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state). Determined by electron microscopy at 3.35 Å resolution. Released 21 Dec 2016.

Method: Electron microscopy
Resolution: 3.35 Å
Organisms: Escherichia coli K-12, Escherichia coli, Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Chains: 58
Atoms: 149,460
Mol. weight: 2262.72 kDa
Ligands: MG, FME, ZN
Released: 21 Dec 2016

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

Secondary structure: helices and β-sheets

5MDY contains 267 α-helices and 345 β-strands across 53 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 6: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	23-25	3
β-strand	28-29	2	19

Chain 7: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	18-30	13
α-helix	32-41	10
α-helix	42-46	5
α-helix	49-52	4
α-helix	55-89	35
α-helix	104-119	16
β-strand	129-135	7	19
α-helix	140-159	20
β-strand	163-171	9	19
β-strand	177-185	9	19
α-helix	189-193	5
β-strand	200-205	6	19
β-strand	214-225	12	19
β-strand	240-243	4	21
β-strand	262-266	5	21
β-strand	271	1	21
β-strand	274-275	2	21
α-helix	281-311	31
β-strand	325-327	3	19
β-strand	328	1	22
α-helix	329-331	3
β-strand	333	1	22
β-strand	334-336	3	19
α-helix	338-340	3
β-strand	341-343	3	19
α-helix	346-351	6
α-helix	355-368	14

Chain a: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	23
β-strand	21-26	6	23
β-strand	32-34	3	23
α-helix	43-49	7
α-helix	56-62	7

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
β-strand	29-30	2	33
β-strand	37-38	2	33
β-strand	42	1	90
β-strand	48	1	34
β-strand	53	1	34

Chain B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	24
α-helix	6-7	2
β-strand	17-19	3	24
α-helix	31-33	3
β-strand	34-36	3	25
β-strand	43	1	26
β-strand	49	1	26
β-strand	54	1	27
β-strand	61-63	3	25
β-strand	65	1	28
β-strand	72	1	29
β-strand	75-83	9	28
β-strand	90-96	7	28
β-strand	101-105	5	28
β-strand	107	1	30
β-strand	115-117	3	28
β-strand	118	1	29
β-strand	129	1	29
α-helix	136	1
β-strand	140-142	3	29
β-strand	144	1	31
β-strand	154	1	31
β-strand	162-168	7	29
β-strand	171-175	5	29
β-strand	181-185	5	29
β-strand	191-192	2	29
β-strand	195	1	30
α-helix	198-202	5
β-strand	204	1	24
α-helix	208-213	6
β-strand	216	1	27
β-strand	245	1	32
β-strand	251	1	32
β-strand	267-269	3	29

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	39
β-strand	20-26	7	39
α-helix	33-34	2
β-strand	35-40	6	39
β-strand	45-53	9	39

Chain C: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	35
β-strand	21-28	8	35
β-strand	32-38	7	36
β-strand	47-52	6	36
α-helix	62-71	10
β-strand	78-83	6	36
β-strand	95-96	2	36
α-helix	98-103	6
β-strand	106-107	2	37
β-strand	110-112	3	35
α-helix	113-114	2
β-strand	115-119	5	38
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-166	4	38
β-strand	169-171	3	35
β-strand	175-176	2	37
β-strand	177-181	5	35
β-strand	186-190	5	35
β-strand	200-203	4	35
β-strand	205	1	37

Chain d: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-23	6
α-helix	25-37	13

45 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
23S ribosomal RNA	1	RNA	2904	Escherichia coli K-12
16S ribosomal RNA	2	RNA	1534	Escherichia coli K-12
5S ribosomal RNA	3	RNA	120	Escherichia coli K-12
mRNA	4	RNA	18	Escherichia coli
fMet-NH-tRNA(fMet)	5	RNA	78	Escherichia coli
Alternative ribosome-rescue factor A	6	protein	61	Escherichia coli K-12	P36675 (AlphaFold model)
Peptide chain release factor 2	7	protein	378	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Q5SM01 (AlphaFold model)
50S ribosomal protein L2	B	protein	273	Escherichia coli K-12	P60422 (AlphaFold model)
50S ribosomal protein L3	C	protein	209	Escherichia coli K-12	P60438 (AlphaFold model)
50S ribosomal protein L4	D	protein	201	Escherichia coli K-12	P60723
50S ribosomal protein L5	E	protein	179	Escherichia coli K-12	P62399
50S ribosomal protein L6	F	protein	177	Escherichia coli K-12	P0AG55

46 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5MDY_1 23S ribosomal RNA (chains 1)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAACCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU

Sequence of entity 2 (2), FASTA

>5MDY_2 16S ribosomal RNA (chains 2)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA

Sequence of entity 3 (3), FASTA

>5MDY_3 5S ribosomal RNA (chains 3)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 4 (4), FASTA

>5MDY_4 mRNA (chains 4)
GGCAAGGAGGUAAAAAUG

Sequence of entity 5 (5), FASTA

>5MDY_5 fMet-NH-tRNA(fMet) (chains 5)
CGCGGGGUUGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAA
UCCGGCCCCCGCAACCAM

Sequence of entity 6 (6), FASTA

>5MDY_6 Alternative ribosome-rescue factor A (chains 6)
HMSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASGKKVN
H

Sequence of entity 7 (7), FASTA

>5MDY_7 Peptide chain release factor 2 (chains 7)
MRLASQSAILVKVWTWNASRNAWKASGGIFDIPQKETRLKELERRLEDPSLWNDPEAARK
VSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLL
NFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYA
QILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEEL
RIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELE
RKKREEELKALRGEVRPIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWA
GLEWKAGRRQGTEEVEAE

Sequence of entity 8 (B), FASTA

>5MDY_8 50S ribosomal protein L2 (chains B)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 9 (C), FASTA

>5MDY_9 50S ribosomal protein L3 (chains C)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 10 (D), FASTA

>5MDY_10 50S ribosomal protein L4 (chains D)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 11 (E), FASTA

>5MDY_11 50S ribosomal protein L5 (chains E)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 12 (F), FASTA

>5MDY_12 50S ribosomal protein L6 (chains F)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	450
FME	N-formylmethionine	C6 H11 N O3 S	1
ZN	Zinc ion	Zn	2

Primary citation

Translational termination without a stop codon. James, N.R., Brown, A., Gordiyenko, Y. et al. Science (2016) 354:1437-1440. DOI 10.1126/science.aai9127 · 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
5U9F 3.2 Å, 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure II)
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…
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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