6WDE: 50S ribosomal protein L2

Name: PDB 6WDE: Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-B)
Published: 2020-07-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-B). Determined by electron microscopy at 3.0 Å resolution. Released 1 Jul 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Escherichia coli, Escherichia coli K-12
Chains: 58
Atoms: 150,220
Mol. weight: 2238.32 kDa
Ligands: MET, PHE
Released: 1 Jul 2020

Explore 6WDE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WDE contains 238 α-helices and 326 β-strands across 51 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 a: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	20-22	3
α-helix	23-29	7
β-strand	41-48	8	101
α-helix	55-57	3
β-strand	60-64	5	102
β-strand	160-164	5	102
β-strand	170-177	8	101
α-helix	182-196	15
β-strand	209-216	8	101
β-strand	221-223	3	101

Chain b: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	16-18	3	1
β-strand	23	1	2
α-helix	30-32	3
β-strand	33-34	2	3
β-strand	42	1	4
β-strand	48	1	4
β-strand	53	1	5
β-strand	61-62	2	3
β-strand	64	1	2
β-strand	75-80	6	2
β-strand	90-94	5	2
β-strand	100-104	5	2
β-strand	106	1	6
β-strand	114-115	2	2
β-strand	117	1	7
β-strand	128-130	3	7
α-helix	135	1
β-strand	139-141	3	7
β-strand	143	1	8
β-strand	153	1	8
β-strand	161-167	7	7
β-strand	170-174	5	7
β-strand	180-184	5	7
β-strand	188-191	4	7
β-strand	194	1	6
α-helix	197-201	5
β-strand	203	1	1
α-helix	207-211	5
β-strand	215	1	5
α-helix	221-223	3
β-strand	244	1	9
β-strand	250	1	9
β-strand	268	1	7

Chain B: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	20-22	3
β-strand	28	1	103
β-strand	37	1	103
β-strand	47-48	2	104
β-strand	51-52	2	104

Chain c: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	8-15	8	13
β-strand	21-27	7	13
β-strand	28	1	14
β-strand	32-38	7	15
β-strand	47-52	6	15
α-helix	62-71	10
β-strand	77-83	7	15
α-helix	94	1
β-strand	95-96	2	15
α-helix	98-101	4
β-strand	106-112	7	12
β-strand	117-119	3	16
α-helix	121-124	4
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-165	3	16
β-strand	169-176	8	12
β-strand	177-179	3	13
α-helix	182-184	3
β-strand	186	1	14
β-strand	188-190	3	13
β-strand	200-205	6	12

Chain C: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	10
β-strand	19-24	6	10
α-helix	32-33	2
β-strand	36-39	4	11
β-strand	44-47	4	11
β-strand	49-51	3	10

Chain d: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	17
β-strand	12-13	2	17
α-helix	25-37	13
α-helix	98-113	16
β-strand	118-121	4	18
α-helix	131-140	10
β-strand	148-150	3	18
α-helix	155-159	5
β-strand	169-171	3	18
α-helix	177-182	6
β-strand	186-189	4	18
α-helix	192-197	6

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-21	4
α-helix	25-37	13

Chain e: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	7-11	5
α-helix	12-16	5
α-helix	24-26	3
β-strand	32-36	5	20
β-strand	37	1	21
α-helix	41-43	3
α-helix	46-59	14
α-helix	63-64	2
β-strand	65-68	4	21
β-strand	83-87	5	21
β-strand	89-90	2	20
α-helix	94-101	8
α-helix	102-106	5
α-helix	107-109	3
β-strand	121	1	20
β-strand	127-131	5	20
α-helix	134-136	3
β-strand	151-156	6	20
α-helix	162-171	10

43 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
50S ribosomal protein L2	b	protein	271	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 (AlphaFold model)
50S ribosomal protein L5	e	protein	177	Escherichia coli	P62399 (AlphaFold model)
50S ribosomal protein L6	f	protein	176	Escherichia coli	P0AG55
50S ribosomal protein L9	g	protein	149	Escherichia coli	P0A7R1
50S ribosomal protein L10	h	protein	131	Escherichia coli	P0A7J3
50S ribosomal protein L11	i	protein	141	Escherichia coli	P0A7J7
50S ribosomal protein L13	j	protein	142	Escherichia coli	P0AA10
50S ribosomal protein L14	k	protein	122	Escherichia coli	P0ADY3
50S ribosomal protein L15	l	protein	143	Escherichia coli	P02413
50S ribosomal protein L16	m	protein	136	Escherichia coli	P0ADY7

45 more molecules are not listed.

Sequence of entity 1 (b), FASTA

>6WDE_1 50S ribosomal protein L2 (chains b)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS

Sequence of entity 2 (c), FASTA

>6WDE_2 50S ribosomal protein L3 (chains c)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 3 (d), FASTA

>6WDE_3 50S ribosomal protein L4 (chains d)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 4 (e), FASTA

>6WDE_4 50S ribosomal protein L5 (chains e)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR

Sequence of entity 5 (f), FASTA

>6WDE_5 50S ribosomal protein L6 (chains f)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 6 (g), FASTA

>6WDE_6 50S ribosomal protein L9 (chains g)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 7 (h), FASTA

>6WDE_7 50S ribosomal protein L10 (chains h)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPT

Sequence of entity 8 (i), FASTA

>6WDE_8 50S ribosomal protein L11 (chains i)
AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITV
YADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGAD
IEAMTRSIEGTARSMGLVVED

Sequence of entity 9 (j), FASTA

>6WDE_9 50S ribosomal protein L13 (chains j)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI

Sequence of entity 10 (k), FASTA

>6WDE_10 50S ribosomal protein L14 (chains k)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV

Sequence of entity 11 (l), FASTA

>6WDE_11 50S ribosomal protein L15 (chains l)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE

Sequence of entity 12 (m), FASTA

>6WDE_12 50S ribosomal protein L16 (chains m)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM

Ligands and cofactors

ID	Name	Formula	Copies
MET	Methionine	C5 H11 N O2 S	1
PHE	Phenylalanine	C9 H11 N O2	1

Primary citation

Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Loveland, A.B., Demo, G., Korostelev, A.A. Nature (2020) 584:640-645. DOI 10.1038/s41586-020-2447-x · PubMed

Other PDB entries of the same protein (UniProt P60422 (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…
8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
8CGV 1.66 Å, Tiamulin bound to the 50S subunit
8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
8CAM 1.86 Å, Evernimicin bound to the 50S subunit
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
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142

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