5IT9: Ribosomal protein uS2

Name: PDB 5IT9: Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.
Published: 2016-05-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES. Determined by electron microscopy at 3.8 Å resolution. Released 18 May 2016.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Kluyveromyces lactis, Cricket paralysis virus
Chains: 35
Atoms: 80,144
Mol. weight: 1183.86 kDa
Ligands: MG, ZN
Released: 18 May 2016

Explore 5IT9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IT9 contains 176 α-helices and 252 β-strands across 33 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	4
β-strand	29-31	3	4
β-strand	37-43	7	5
α-helix	49-56	8
β-strand	66-72	7	5
α-helix	75-79	5
α-helix	90-93	4
α-helix	97	1

Chain A: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37	1	1
α-helix	40-41	2
α-helix	47	1
β-strand	48	1	1
α-helix	49	1
α-helix	50-66	17
β-strand	73-75	3	2
β-strand	76-77	2	3
α-helix	80-92	13
β-strand	98-99	2	3
β-strand	120-122	3	2
α-helix	130-137	8
β-strand	143-145	3	2
β-strand	157-159	3	2
α-helix	169-183	15
α-helix	199-201	3

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	8
β-strand	43-47	5	8
β-strand	54	1	9
β-strand	64-65	2	9
α-helix	71	1
β-strand	72-73	2	9
β-strand	78-80	3	8

Chain B: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	6
β-strand	44-48	5	6
α-helix	57-61	5
β-strand	65-69	5	6
α-helix	70-74	5
α-helix	77-79	3
β-strand	83-91	9	6
β-strand	96-104	9	6
α-helix	107-113	7
β-strand	120-121	2	7
β-strand	125-128	4	6
β-strand	134-137	4	6
β-strand	140-142	3	7
α-helix	143-144	2
α-helix	155-157	3
α-helix	158-175	18
α-helix	182-188	7
α-helix	192-201	10
β-strand	208-211	4	7
β-strand	215-217	3	6
α-helix	225-231	7

Chain c: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	15
β-strand	12-19	8	16
β-strand	25-31	7	16
β-strand	39-44	6	16
β-strand	53-56	4	15

Chain C: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	45-52	8
α-helix	58-63	6
α-helix	72-77	6
β-strand	82-94	13	10
β-strand	99-110	12	10
β-strand	115-116	2	11
β-strand	117-123	7	10
α-helix	126-140	15
β-strand	142-143	2	11
β-strand	146-147	2	12
β-strand	158-159	2	12
β-strand	163-164	2	13
β-strand	170-171	2	14
β-strand	173-176	4	13
β-strand	183-184	2	13
α-helix	187-196	10
β-strand	201-203	3	13
β-strand	206-207	2	14
α-helix	212-226	15
α-helix	232-234	3
α-helix	237-238	2
α-helix	241-243	3
α-helix	244-247	4

Chain d: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	21
α-helix	33-35	3
β-strand	38-39	2	21
α-helix	40-46	7
β-strand	53-54	2	75

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-41	8	17
β-strand	46-52	7	17
α-helix	55-59	5
α-helix	65-77	13
β-strand	84-89	6	17
α-helix	99-111	13
α-helix	115-129	15
β-strand	131-140	10	18
β-strand	148-155	8	18
β-strand	168-176	9	18
β-strand	181-190	10	18
α-helix	192-194	3
β-strand	207	1	19
α-helix	208-211	4
β-strand	223-224	2	20

25 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
Ribosomal protein uS2	A	protein	206	Kluyveromyces lactis	Q6CN12 (AlphaFold model)
Ribosomal protein eS1	B	protein	214	Kluyveromyces lactis	Q6CWD0 (AlphaFold model)
Ribosomal protein uS5	C	protein	217	Kluyveromyces lactis	Q6CKL3 (AlphaFold model)
Ribosomal protein uS3	D	protein	223	Kluyveromyces lactis	Q6CRK7 (AlphaFold model)
Ribosomal protein eS4	E	protein	260	Kluyveromyces lactis	Q6CWJ2
Ribosomal protein uS7	F	protein	206	Kluyveromyces lactis	Q6CRA3
Ribosomal protein eS6	G	protein	226	Kluyveromyces lactis	Q6CM04
Ribosomal protein eS7	H	protein	184	Kluyveromyces lactis	Q6CTD6
Ribosomal protein eS8	I	protein	200	Kluyveromyces lactis	Q6CMG3
Ribosomal protein uS4	J	protein	182	Kluyveromyces lactis	Q6CM18
Ribosomal protein eS10	K	protein	96	Kluyveromyces lactis	Q6CVZ5
Ribosomal protein uS17	L	protein	155	Kluyveromyces lactis	Q6CX80

23 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5IT9_1 Ribosomal protein uS2 (chains A)
SLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLAA
RIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALPDRTQPWAIMPDLYFYRNP

Sequence of entity 2 (B), FASTA

>5IT9_2 Ribosomal protein eS1 (chains B)
VVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDSLKGRVVEVCLADLQGSEDH
SFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFA
IAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNSTLAQLTSKLIPEVINKEIEN
ATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHG

Sequence of entity 3 (C), FASTA

>5IT9_3 Ribosomal protein uS5 (chains C)
GWVPVTKLGRLVKAGKISSIEEIFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTSGKCGSVSVRLIPAPRGSGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKA
AFVAIGNTYGFLTPNLWEVQALTPSPMDVYADYATAS

Sequence of entity 4 (D), FASTA

>5IT9_4 Ribosomal protein uS3 (chains D)
AIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVGEN
GRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQGVL
GIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDY

Sequence of entity 5 (E), FASTA

>5IT9_5 Ribosomal protein eS4 (chains E)
ARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEASY
KLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKLV
YVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPKG
KGIKLTISEERDRRRAQHGL

Sequence of entity 6 (F), FASTA

>5IT9_6 Ribosomal protein uS7 (chains F)
FVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASLVDYIQISKPIYVAHTAGRYAN
KRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTLEIINVLTDQNPLQVVVDAIIN
SGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 7 (G), FASTA

>5IT9_7 Ribosomal protein eS6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEV

Sequence of entity 8 (H), FASTA

>5IT9_8 Ribosomal protein eS7 (chains H)
PQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAVFVP
VPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 9 (I), FASTA

>5IT9_9 Ribosomal protein eS8 (chains I)
GISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRIE
TGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQSL
GKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 10 (J), FASTA

>5IT9_10 Ribosomal protein uS4 (chains J)
PRAPRTYSKTYSTPKRPYESARLDAELKLAGEYGLKNKREIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRIGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLISQRHIAVGKQIVNIPSFMVRLESEKHIDFARTSPFGGARPGRVARKRAAAAG
GE

Sequence of entity 11 (K), FASTA

>5IT9_11 Ribosomal protein eS10 (chains K)
MLIPKEDRKKIYQHLFQEGVLVAKKDFNQPKHEEIDTKNLFVIKALQSLTSKGFVKTQFS
WQYYYYTLTEEGVVYLREYLNLPEHIFPATYLAGQS

Sequence of entity 12 (L), FASTA

>5IT9_12 Ribosomal protein uS17 (chains L)
STELTVQSERAFQKQPHIFTNPKAKANRKTKRWYKNVGLGFKTPKTAIEGSYIDKKCPFT
GLVSIRGKILTGTVVSTRMHRTIVIRRDYLHYVPKYNRYEKRHKNVPAHVSPAFRVQVGD
IVTVGQCRPISKTVRFNVLKVASATGKANKQFAKF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	80
ZN	Zinc ion	Zn	3

Primary citation

Structural characterization of ribosome recruitment and translocation by type IV IRES. Murray, J., Savva, C.G., Shin, B.S. et al. Elife (2016) 5. DOI 10.7554/eLife.13567 · PubMed

Other PDB entries of the same protein (UniProt Q6CN12 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FYY 3.02 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
8RW1 3.35 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation
8S8D 3.45 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
3JAM 3.46 Å, CryoEM structure of 40S-eIF1A-eIF1 complex from yeast
6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
5IT7 3.6 Å, Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis…
6UZ7 3.6 Å, K.lactis 80S ribosome with p/PE tRNA and eIF5B
3J80 3.75 Å, CryoEM structure of 40S-eIF1-eIF1A preinitiation complex
8S8E 3.85 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
8S8F 3.95 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex
8S8G 4.0 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…

Browse structure collections

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