4V5K: Cytotoxic domain of colicin E3

Name: PDB 4V5K: Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome. Determined by X-ray diffraction at 3.2 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Thermus thermophilus HB8, Escherichia coli K-12, synthetic construct
Chains: 116
Atoms: 296,762
Mol. weight: 4561.56 kDa
Ligands: MG, ZN
Released: 9 Jul 2014

Explore 4V5K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V5K contains 380 α-helices and 656 β-strands across 103 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.

Chains AB and CB: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
α-helix	26-28	3
β-strand	34	1	7
α-helix	36-38	3
β-strand	41	1	7
α-helix	44-63	20
β-strand	68-71	4	8
α-helix	75-77	3
α-helix	79-86	8
β-strand	92-93	2	8
α-helix	107-110	4
α-helix	112-115	4
α-helix	132-148	17
β-strand	161-164	4	8
α-helix	167-178	12
β-strand	184-188	5	8
α-helix	194-196	3
β-strand	199-202	4	8
α-helix	208-216	9
α-helix	220-227	8
α-helix	231-233	3

Chain AC: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	16
α-helix	29-47	19
α-helix	48-50	3
β-strand	55-59	5	16
β-strand	63	1	17
β-strand	64-68	5	16
β-strand	70	1	18
α-helix	74-76	3
α-helix	83-94	12
β-strand	98	1	17
β-strand	105	1	18
α-helix	113-125	13
α-helix	130-136	7
β-strand	148-153	6	19
α-helix	157-159	3
β-strand	166-170	5	19
α-helix	178-180	3
β-strand	182-185	4	19
β-strand	191	1	20
β-strand	194	1	20
β-strand	200-203	4	19

Chains AD and CD: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	25-27	3
α-helix	53-68	16
α-helix	72-83	12
α-helix	89-98	10
β-strand	100	1	25
α-helix	101-108	8
α-helix	114-122	9
β-strand	126-128	3	26
β-strand	131	1	26
β-strand	139	1	25
α-helix	140-141	2
β-strand	145	1	27
β-strand	146-148	3	26
α-helix	150-153	4
α-helix	156-163	8
β-strand	175-176	2	27
β-strand	183-184	2	27
α-helix	192-194	3
α-helix	202-206	5

Chains AE and CE: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	32
β-strand	18-20	3	33
β-strand	23-25	3	33
β-strand	28-35	8	32
β-strand	41-48	8	32
α-helix	51-63	13
β-strand	80-81	2	34
β-strand	87-93	7	34
β-strand	100-101	2	34
α-helix	106-110	5
α-helix	111-113	3
β-strand	118-125	8	34
α-helix	128-139	12
α-helix	145-150	6

Chains AF and CF: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	41
β-strand	9-10	2	42
α-helix	16-32	17
β-strand	37	1	41
β-strand	44-47	4	42
β-strand	57-60	4	42
β-strand	63-67	5	41
α-helix	71-81	11
β-strand	85	1	42
β-strand	92	1	41
β-strand	98-99	2	43

Chains AG and CG: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	25-30	6
α-helix	36-53	18
α-helix	60-68	9
β-strand	73-76	4	54
β-strand	79	1	55
β-strand	84	1	55
β-strand	87-90	4	54
α-helix	91-92	2
α-helix	93-109	17
α-helix	116-129	14
α-helix	133-147	15
α-helix	149-153	5

Chains AH and CH: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	30-41	12
β-strand	45-49	5	58
β-strand	52-53	2	59
β-strand	56-57	2	59
β-strand	60-63	4	58
β-strand	65	1	60
β-strand	78	1	60
β-strand	83-85	3	61
β-strand	94-95	2	62
α-helix	103-106	4
β-strand	109-111	3	61
β-strand	112-114	3	63
β-strand	117-119	3	63
α-helix	121-127	7
β-strand	131-132	2	62
β-strand	135-137	3	61

Chains AI and CI: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	70
β-strand	14-21	8	70
β-strand	27-28	2	70
β-strand	31	1	70
α-helix	48-51	4
β-strand	59-63	5	70
β-strand	66	1	70
α-helix	70-81	12
β-strand	118	1	71
β-strand	121	1	71

58 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	AA, CA	RNA	1522	Thermus thermophilus HB8
30S ribosomal protein S2	AB, CB	protein	256	Thermus thermophilus HB8	P80371 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	239	Thermus thermophilus HB8	P80372 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	209	Thermus thermophilus HB8	P80373 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	162	Thermus thermophilus HB8	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus HB8	Q5SLP8
30S ribosomal protein S7	AG, CG	protein	156	Thermus thermophilus HB8	P17291
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus HB8	P0DOY9
30S ribosomal protein S9	AI, CI	protein	128	Thermus thermophilus HB8	P80374
30S ribosomal protein S10	AJ, CJ	protein	105	Thermus thermophilus HB8	Q5SHN7
30S ribosomal protein S11	AK, CK	protein	129	Thermus thermophilus HB8	P80376
30S ribosomal protein S12	AL, CL	protein	135	Thermus thermophilus HB8	Q5SHN3

46 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V5K_1 16S ribosomal RNA (chains AA, CA)
UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCA
AGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUG
GGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGA
CCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU
CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAU
GGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAA
UCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGG
GGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA
AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCC
GGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACG
GCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAA
UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC
ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACC
CGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGC
UAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUG
ACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU
ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGC
CCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCC
CGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGA
CUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC
UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCU
AAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGG
AAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACAC
ACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG
CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGU
GCGGCUGGAUCACCUCCUUUCU

Sequence of entity 2 (AB, CB), FASTA

>4V5K_2 30S RIBOSOMAL PROTEIN S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V5K_3 30S RIBOSOMAL PROTEIN S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V5K_4 30S RIBOSOMAL PROTEIN S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V5K_5 30S RIBOSOMAL PROTEIN S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V5K_6 30S RIBOSOMAL PROTEIN S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V5K_7 30S RIBOSOMAL PROTEIN S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V5K_8 30S RIBOSOMAL PROTEIN S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V5K_9 30S RIBOSOMAL PROTEIN S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V5K_10 30S RIBOSOMAL PROTEIN S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V5K_11 30S RIBOSOMAL PROTEIN S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V5K_12 30S RIBOSOMAL PROTEIN S12 (chains AL, CL)
MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL
TSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKY
GTKKPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2334
ZN	Zinc ion	Zn	4

Primary citation

Structural Basis for 16S Ribosomal RNA Cleavage by the Cytotoxic Domain of Colicin E3. Ng, C.L., Lang, K., Meenan, N.A.G. et al. Nat Struct Mol Biol (2010) 17:1241-1246. DOI 10.1038/nsmb.1896 · PubMed

Other PDB entries of the same protein (UniProt P80371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…

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