5MDV: ArfA and RF2

Name: PDB 5MDV: Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)
Published: 2016-12-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state). Determined by electron microscopy at 2.97 Å resolution. Released 14 Dec 2016.

Method: Electron microscopy
Resolution: 2.97 Å
Organism: Escherichia coli
Chains: 58
Atoms: 149,892
Mol. weight: 2260.99 kDa
Ligands: ZN, FME, MG
Released: 14 Dec 2016

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

Secondary structure: helices and β-sheets

5MDV contains 280 α-helices and 337 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, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	18
α-helix	15-20	6
β-strand	28-29	2	19
α-helix	30-32	3

Chain 7: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	27-42	16
α-helix	44-48	5
α-helix	50-85	36
α-helix	86-90	5
α-helix	93-118	26
β-strand	128-134	7	19
α-helix	139-159	21
β-strand	162-170	9	19
α-helix	171	1
β-strand	176-184	9	19
α-helix	188-192	5
α-helix	193-195	3
β-strand	197-204	8	19
β-strand	213-224	12	19
α-helix	232-235	4
β-strand	239-244	6	21
α-helix	245-246	2
α-helix	252-256	5
β-strand	260-265	6	21
β-strand	271-274	4	21
α-helix	280-317	38
α-helix	318-321	4
β-strand	322-327	6	19
β-strand	332-335	4	19
β-strand	341-342	2	19
α-helix	345-351	7
α-helix	354-363	10

Chain a: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-15	6	22
β-strand	22-26	5	22
α-helix	31	1
β-strand	32-33	2	22
α-helix	46-49	4
α-helix	56-64	9

Chain b: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-17	8
α-helix	18-20	3
α-helix	21-25	5
β-strand	29-30	2	32
β-strand	37-38	2	32
β-strand	42	1	87
β-strand	48-49	2	33
β-strand	52-53	2	33

Chain B: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	23
α-helix	6-7	2
β-strand	17-19	3	23
β-strand	24	1	24
α-helix	31-33	3
β-strand	34-35	2	25
β-strand	43	1	26
β-strand	49	1	26
β-strand	54	1	27
β-strand	62-63	2	25
β-strand	65	1	24
β-strand	72	1	28
β-strand	76-82	7	24
β-strand	91-96	6	24
β-strand	101-105	5	24
β-strand	107	1	29
β-strand	115-116	2	24
β-strand	118	1	28
β-strand	129-131	3	28
α-helix	136	1
β-strand	140-142	3	28
β-strand	144	1	30
β-strand	154	1	30
β-strand	162-168	7	28
β-strand	171-175	5	28
β-strand	181-185	5	28
β-strand	189-192	4	28
β-strand	195	1	29
α-helix	198-202	5
β-strand	204	1	23
α-helix	208-213	6
β-strand	216	1	27
α-helix	217-221	5
α-helix	222-224	3
α-helix	243-244	2
β-strand	245	1	31
β-strand	251	1	31
α-helix	264-266	3
β-strand	267-269	3	28

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	37
β-strand	20-25	6	37
α-helix	33-34	2
β-strand	35-40	6	37
β-strand	45-53	9	37

Chain C: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	34
β-strand	21-28	8	34
β-strand	32-38	7	35
β-strand	47-52	6	35
α-helix	62-71	10
β-strand	78-83	6	35
α-helix	84-85	2
β-strand	95-96	2	35
α-helix	98-103	6
β-strand	106-112	7	34
β-strand	117-119	3	36
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-165	3	36
β-strand	169-181	13	34
β-strand	186-190	5	34
α-helix	192-193	2
β-strand	200-205	6	34

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
16S ribosomal RNA	2	RNA	1534	Escherichia coli
5S ribosomal RNA	3	RNA	120	Escherichia coli
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	P36675 (AlphaFold model)
Peptide chain release factor 2	7	protein	365	Escherichia coli	P07012 (AlphaFold model)
50S ribosomal protein L2	B	protein	273	Escherichia coli	P60422 (AlphaFold model)
50S ribosomal protein L3	C	protein	209	Escherichia coli	P60438 (AlphaFold model)
50S ribosomal protein L4	D	protein	201	Escherichia coli	P60723
50S ribosomal protein L5	E	protein	179	Escherichia coli	P62399
50S ribosomal protein L6	F	protein	177	Escherichia coli	P0AG55

46 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5MDV_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

>5MDV_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

>5MDV_3 5S ribosomal RNA (chains 3)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 4 (4), FASTA

>5MDV_4 mRNA (chains 4)
GGCAAGGAGGUAAAAAUG

Sequence of entity 5 (5), FASTA

>5MDV_5 fMet-NH-tRNA(fMet) (chains 5)
CGCGGGGUUGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAA
UCCGGCCCCCGCAACCAM

Sequence of entity 6 (6), FASTA

>5MDV_6 Alternative ribosome-rescue factor A (chains 6)
HMSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASGKKVN
H

Sequence of entity 7 (7), FASTA

>5MDV_7 Peptide chain release factor 2 (chains 7)
MFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKER
SSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFS
GEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVT
IKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLR
IDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEM
QKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEAS
LKAGL

Sequence of entity 8 (B), FASTA

>5MDV_8 50S ribosomal protein L2 (chains B)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 9 (C), FASTA

>5MDV_9 50S ribosomal protein L3 (chains C)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 10 (D), FASTA

>5MDV_10 50S ribosomal protein L4 (chains D)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 11 (E), FASTA

>5MDV_11 50S ribosomal protein L5 (chains E)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 12 (F), FASTA

>5MDV_12 50S ribosomal protein L6 (chains F)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
FME	N-formylmethionine	C6 H11 N O3 S	1
MG	Magnesium ion	Mg	440

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:

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…
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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