4XEJ: IRES

Name: PDB 4XEJ: IRES bound to bacterial Ribosome
Published: 2015-02-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

IRES bound to bacterial Ribosome. Determined by X-ray diffraction at 3.8 Å resolution. Released 25 Feb 2015.

Method: X-ray diffraction
Resolution: 3.8 Å
Organisms: Thermus thermophilus HB27, Plautia stali intestine virus
Chains: 106
Atoms: 287,293
Mol. weight: 4366.16 kDa
Ligands: ZN
Released: 25 Feb 2015

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

Secondary structure: helices and β-sheets

4XEJ contains 403 α-helices and 695 β-strands across 98 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 AL02: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	17	1	2
β-strand	18-19	2	1
α-helix	21-23	3
β-strand	36-37	2	3
β-strand	62-63	2	3
β-strand	73	1	4
β-strand	77-83	7	5
β-strand	92-97	6	5
β-strand	102-106	5	5
β-strand	108	1	6
β-strand	119	1	4
β-strand	132	1	7
α-helix	133-135	3
α-helix	137	1
β-strand	142-143	2	8
β-strand	145	1	9
β-strand	155	1	9
β-strand	163	1	8
β-strand	164-169	6	10
β-strand	172-176	5	10
β-strand	182-186	5	10
β-strand	190	1	7
β-strand	192-194	3	8
β-strand	196	1	6
α-helix	199-203	5
β-strand	205	1	2
α-helix	209-215	7
α-helix	223-225	3
β-strand	247	1	11
β-strand	253	1	11
α-helix	267-269	3
β-strand	270-271	2	10

Chain AL03: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	8-11	4	21
β-strand	14-16	3	22
β-strand	19-21	3	22
β-strand	24-27	4	21
β-strand	31-32	2	23
β-strand	33-37	5	24
β-strand	46-51	6	24
α-helix	63-70	8
β-strand	77-82	6	24
β-strand	90-91	2	23
β-strand	101-107	7	20
α-helix	108-109	2
β-strand	113-114	2	25
α-helix	116-119	4
β-strand	158-159	2	25
β-strand	164-171	8	20
β-strand	175-176	2	21
α-helix	177-179	3
β-strand	181-183	3	21
β-strand	195-200	6	20

Chain AL04: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	35
β-strand	16-20	5	35
α-helix	30-43	14
β-strand	65	1	36
β-strand	75	1	36
α-helix	103-120	18
β-strand	124-126	3	35
α-helix	136-146	11
β-strand	154-155	2	37
β-strand	156-157	2	35
α-helix	161-168	8
β-strand	173-174	2	37
β-strand	193-195	3	35
α-helix	199-202	4

Chain AL05: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-15	5
α-helix	16-19	4
β-strand	34-41	8	46
α-helix	45-47	3
α-helix	51-64	14
β-strand	69-71	3	46
α-helix	72-73	2
α-helix	78-80	3
β-strand	89-94	6	46
α-helix	98-105	8
α-helix	106-110	5
β-strand	120	1	47
β-strand	131	1	46
β-strand	134	1	46
β-strand	156	1	46
β-strand	159-161	3	46
α-helix	166-175	10
β-strand	180	1	47

Chain AL06: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	57
β-strand	24-27	4	57
β-strand	32-35	4	57
β-strand	42	1	58
β-strand	45	1	59
β-strand	50	1	59
β-strand	53	1	58
α-helix	59-77	19
β-strand	83-84	2	60
β-strand	88-90	3	61
β-strand	95-99	5	62
β-strand	102-106	5	62
β-strand	114-115	2	62
α-helix	116-118	3
β-strand	130	1	61
β-strand	134-135	2	60
α-helix	138-151	14
β-strand	161-163	3	61

Chain AL09: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	72
β-strand	3-5	3	73
β-strand	20	1	72
α-helix	23-24	2
α-helix	25-29	5
β-strand	36-38	3	73
α-helix	41-73	33
β-strand	78	1	74
α-helix	95-104	10
α-helix	111-113	3
β-strand	114-115	2	74
β-strand	124-130	7	74
β-strand	138-144	7	74

Chain AL11: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	85
α-helix	24-27	4
β-strand	56	1	86
β-strand	57-60	4	85
β-strand	68	1	86
α-helix	71-73	3
α-helix	78-80	3
β-strand	91	1	87
β-strand	94	1	87
α-helix	103-106	4
α-helix	123-126	4
α-helix	132-134	3

Chain AL13: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	37-39	3	94
α-helix	46-55	10
β-strand	75-77	3	94
α-helix	89-92	4
β-strand	94-98	5	95
β-strand	105-109	5	95
α-helix	110-115	6
α-helix	118-120	3
α-helix	121-127	7
α-helix	134-141	8
β-strand	144-145	2	94
β-strand	159	1	94

90 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	AL02, BL02	protein	271	Thermus thermophilus HB27	Q72I07 (AlphaFold model)
50S ribosomal protein L3	AL03, BL03	protein	204	Thermus thermophilus HB27	Q72I04 (AlphaFold model)
50S ribosomal protein L4	AL04, BL04	protein	202	Thermus thermophilus HB27	Q72I05 (AlphaFold model)
50S ribosomal protein L5	AL05, BL05	protein	181	Thermus thermophilus HB27	Q72I16 (AlphaFold model)
50S ribosomal protein L6	AL06, BL06	protein	159	Thermus thermophilus HB27	Q72I19
50S ribosomal protein L9	AL09, BL09	protein	145	Thermus thermophilus HB27	Q72GV5
50S ribosomal protein L11	AL11, BL11	protein	147	Thermus thermophilus HB27	P62442
50S ribosomal protein L13	AL13, BL13	protein	137	Thermus thermophilus HB27	Q72IN1
50S ribosomal protein L14	AL14, BL14	protein	122	Thermus thermophilus HB27	Q72I14
50S ribosomal protein L15	AL15, BL15	protein	146	Thermus thermophilus HB27	Q72I23
50S ribosomal protein L16	AL16, BL16	protein	134	Thermus thermophilus HB27	Q72I11
50S ribosomal protein L17	AL17, BL17	protein	117	Thermus thermophilus HB27	Q72I33

41 more molecules are not listed.

Sequence of entity 1 (AL02, BL02), FASTA

>4XEJ_1 50S ribosomal protein L2 (chains AL02, BL02)
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRL
YRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGP
DAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGE
LRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP
RGRPPASPWGWQTKGLKTRKRRKPSSRFIIA

Sequence of entity 2 (AL03, BL03), FASTA

>4XEJ_2 50S ribosomal protein L3 (chains AL03, BL03)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKA

Sequence of entity 3 (AL04, BL04), FASTA

>4XEJ_3 50S ribosomal protein L4 (chains AL04, BL04)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIG

Sequence of entity 4 (AL05, BL05), FASTA

>4XEJ_4 50S ribosomal protein L5 (chains AL05, BL05)
PLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELA
LITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLN
PNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFR
K

Sequence of entity 5 (AL06, BL06), FASTA

>4XEJ_5 50S ribosomal protein L6 (chains AL06, BL06)
PKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSLHGLTRTL
IANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRV
RVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVR

Sequence of entity 6 (AL09, BL09), FASTA

>4XEJ_6 50S ribosomal protein L9 (chains AL09, BL09)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVV

Sequence of entity 7 (AL11, BL11), FASTA

>4XEJ_7 50S ribosomal protein L11 (chains AL11, BL11)
MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIY
ADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDL
EAAARMIAGSARSMGVEVVGAPEVKDA

Sequence of entity 8 (AL13, BL13), FASTA

>4XEJ_8 50S ribosomal protein L13 (chains AL13, BL13)
KTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIR
VTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK
VYAGPDHPHQAQRPEKL

Sequence of entity 9 (AL14, BL14), FASTA

>4XEJ_9 50S ribosomal protein L14 (chains AL14, BL14)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Sequence of entity 10 (AL15, BL15), FASTA

>4XEJ_10 50S ribosomal protein L15 (chains AL15, BL15)
DLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLMRLPK
RGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEAKPLK
VVAHAFSKSALEKLKAAGGEPVLLEA

Sequence of entity 11 (AL16, BL16), FASTA

>4XEJ_11 50S ribosomal protein L16 (chains AL16, BL16)
RMKYRKQQRGRLKGATKGGDYVAFGDFGLVALEPAWITAQQIEAARVAMVRHFRRGGKIF
IRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRIAGHKL
PIKTKIVRRDAYDE

Sequence of entity 12 (AL17, BL17), FASTA

>4XEJ_12 50S ribosomal protein L17 (chains AL17, BL17)
RHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDHLIHLAKRGDLH
ARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKLAERRRGDGAPLALVELVE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Colussi, T.M., Costantino, D.A., Zhu, J. et al. Nature (2015) 519:110-113. DOI 10.1038/nature14219 · PubMed

Other PDB entries of the same protein (UniProt Q72I07 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
4V63 3.21 Å, Structural basis for translation termination on the 70S ribosome.
5V8I 3.25 Å, Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
4V84 3.4 Å, Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S…
4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
4V9Q 3.4 Å, Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…

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