5DFE: 70S termination complex containing E. coli RF2

70S termination complex containing E. coli RF2. Determined by X-ray diffraction at 3.1 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Escherichia coli, synthetic construct, Escherichia coli (strain K12)
Chains: 110
Atoms: 296,662
Mol. weight: 4552.15 kDa
Ligands: SF4, ZN, MG
Released: 12 Oct 2016

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

Secondary structure: helices and β-sheets

5DFE contains 542 α-helices and 672 β-strands across 100 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 QB: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	26-31	6
β-strand	32-35	4	50
β-strand	40-42	3	50
α-helix	44-62	19
β-strand	68-71	4	51
α-helix	78-87	10
β-strand	92-93	2	51
α-helix	105-121	17
α-helix	132-149	18
β-strand	161-164	4	51
α-helix	171-179	9
β-strand	184-188	5	51
α-helix	194-196	3
β-strand	199-202	4	51
α-helix	208-225	18

Chain QC: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	65
β-strand	16	1	65
β-strand	20-21	2	66
α-helix	29-46	18
β-strand	52-59	8	66
β-strand	63-70	8	66
α-helix	73-77	5
α-helix	82-95	14
β-strand	98-105	8	66
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	67
α-helix	157-159	3
β-strand	164-171	8	67
β-strand	180-190	11	67
β-strand	195-206	12	67

Chain QD: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	25-27	3
α-helix	32-35	4
α-helix	47-48	2
α-helix	50-52	3
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	79
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	80
β-strand	131-132	2	80
β-strand	139	1	79
β-strand	144-148	5	80
α-helix	150-152	3
α-helix	156-163	8
β-strand	174-177	4	80
β-strand	182-185	4	80
α-helix	188-190	3
α-helix	200-207	8

Chain QE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-20	14	86
β-strand	23-35	13	86
β-strand	40-48	9	86
α-helix	51-64	14
β-strand	67-68	2	86
β-strand	72	1	87
β-strand	75	1	87
β-strand	80-84	5	88
β-strand	87-93	7	88
β-strand	100-101	2	88
α-helix	104-112	9
β-strand	118-125	8	88
α-helix	128-139	12
α-helix	145-151	7

Chain QF: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	97
α-helix	16-32	17
α-helix	35	1
β-strand	36-47	12	97
β-strand	57-67	11	97
α-helix	72-79	8
β-strand	85-92	8	97
β-strand	98-99	2	98

Chain QG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-69	12
β-strand	73-80	8	107
β-strand	83-90	8	107
α-helix	93-108	16
α-helix	116-129	14
α-helix	132-147	16
α-helix	149-154	6

Chain QH: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	23-27	5	120
α-helix	30-41	12
β-strand	47-53	7	120
β-strand	56-62	7	120
α-helix	63	1
β-strand	65	1	121
α-helix	75-77	3
β-strand	78	1	121
β-strand	83-85	3	122
β-strand	94-95	2	122
α-helix	97-99	3
α-helix	103-106	4
β-strand	109-114	6	122
β-strand	117-120	4	122
α-helix	121-127	7
β-strand	131-137	7	122

Chain QI: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	130
β-strand	13-21	9	130
β-strand	26-28	3	130
β-strand	31-32	2	130
α-helix	33-36	4
α-helix	48-52	5
β-strand	59-66	8	130
α-helix	70-88	19
α-helix	90-92	3
α-helix	97-99	3
α-helix	109-113	5
α-helix	121-124	4

80 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
P-site tRNA fMet	QV, XV	RNA	77	Escherichia coli
messenger RNA	QX, XX	RNA	25	synthetic construct
Peptide chain release factor 2	QY, XY	protein	380	Escherichia coli (strain K12)	P07012 (AlphaFold model)
T23S rRNA	RA, YA	RNA	2915	Thermus thermophilus HB8
5S rRNA	RB, YB	RNA	122	Thermus thermophilus HB8
50S ribosomal protein L2	RD, YD	protein	276	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	P60405 (AlphaFold model)
50S ribosomal protein L3	RE, YE	protein	206	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Q5SHN8 (AlphaFold model)
50S ribosomal protein L4	RF, YF	protein	210	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Q5SHN9 (AlphaFold model)
50S ribosomal protein L5	RG, YG	protein	182	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Q5SHQ0
50S ribosomal protein L6	RH, YH	protein	180	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	P0DOY8
50S ribosomal protein L9	RI, YI	protein	148	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Q5SLQ1
50S ribosomal protein L13	RN, YN	protein	140	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	P60488

43 more molecules are not listed.

Sequence of entity 1 (QV, XV), FASTA

>5DFE_1 P-site tRNA fMet (chains QV, XV)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 2 (QX, XX), FASTA

>5DFE_2 messenger RNA (chains QX, XX)
GGCAAGGAGGUAAAAAUGUAACAGA

Sequence of entity 3 (QY, XY), FASTA

>5DFE_3 Peptide chain release factor 2 (chains QY, XY)
MGSSHHHHHHSEDPAMFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPD
VWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDA
LEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEI
IEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPE
VDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKD
QAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNT
QAVLDGSLDQFIEASLKAGL

Sequence of entity 4 (RA, YA), FASTA

>5DFE_4 T23S rRNA (chains RA, YA)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC

Sequence of entity 5 (RB, YB), FASTA

>5DFE_5 5S rRNA (chains RB, YB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
UU

Sequence of entity 6 (RD, YD), FASTA

>5DFE_6 50S ribosomal protein L2 (chains RD, YD)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK

Sequence of entity 7 (RE, YE), FASTA

>5DFE_7 50S ribosomal protein L3 (chains RE, YE)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK

Sequence of entity 8 (RF, YF), FASTA

>5DFE_8 50S ribosomal protein L4 (chains RF, YF)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA

Sequence of entity 9 (RG, YG), FASTA

>5DFE_9 50S ribosomal protein L5 (chains RG, YG)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK

Sequence of entity 10 (RH, YH), FASTA

>5DFE_10 50S ribosomal protein L6 (chains RH, YH)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK

Sequence of entity 11 (RI, YI), FASTA

>5DFE_11 50S ribosomal protein L9 (chains RI, YI)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE

Sequence of entity 12 (RN, YN), FASTA

>5DFE_12 50S ribosomal protein L13 (chains RN, YN)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	2
ZN	Zinc ion	Zn	12
MG	Magnesium ion	Mg	2513

Primary citation

Uniformity of Peptide Release Is Maintained by Methylation of Release Factors. Pierson, W.E., Hoffer, E.D., Keedy, H.E. et al. Cell Rep (2016) 17:11-18. DOI 10.1016/j.celrep.2016.08.085 · PubMed

Other PDB entries of the same protein (UniProt P07012 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GQE 1.81 Å, Polypeptide Chain Release Factor 2 (RF2) from Escherichia coli
7O1C 2.6 Å, Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome-RF2 complex stalled in…
8P16 2.77 Å, E167K RF2 on E. coli 70S release complex with UGG (Structure I)
8P18 2.77 Å, E167K RF2 on E. coli 70S release complex with UGG (Structure III)
8QK7 2.77 Å, E167K RF2 on E. coli 70S release complex with UAA
8P17 2.78 Å, E167K RF2 on E. coli 70S release complex with UGG (Structure II)
8ZTV 2.9 Å, 70S ribosome arrested by PepNL with RF2
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
6C4H 3.1 Å, Conformation of methylated GGQ in the peptidyl transferase center during translation…

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