4V8Y: 40S ribosomal protein S26-a

Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex. Determined by electron microscopy at 4.3 Å resolution. Released 9 Jul 2014.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 87
Atoms: 214,255
Mol. weight: 3376.54 kDa
Ligands: GCP, OHX, MG, ZN
Released: 9 Jul 2014

Explore 4V8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V8Y contains 549 α-helices and 597 β-strands across 81 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 A0: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	1
β-strand	29-31	3	1
α-helix	32-34	3
β-strand	37-42	6	2
α-helix	50-55	6
β-strand	67-72	6	2
α-helix	76-80	5

Chain A1: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	32-36	5	28
β-strand	44-47	4	28
β-strand	49	1	29
α-helix	54-56	3
β-strand	64-65	2	30
β-strand	70	1	29
β-strand	72-73	2	30
β-strand	78-80	3	28

Chain A2: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	35
β-strand	25-32	8	35
β-strand	39-43	5	35
β-strand	53-56	4	35

Chain A3: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	30-31	2	39
α-helix	33-35	3
β-strand	38-39	2	39
α-helix	40-50	11
β-strand	53	1	36

Chain A4: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	5	1	47
α-helix	13-17	5
α-helix	19-20	2
α-helix	22-25	4
α-helix	28-30	3
α-helix	33-40	8
α-helix	41-45	5

Chain A5: 0 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	107-108	2	51
β-strand	114-115	2	51
β-strand	120	1	52
β-strand	131	1	52
β-strand	132-134	3	53
β-strand	139-141	3	53
β-strand	149-150	2	53

Chain A6: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	57
β-strand	20-24	5	58
β-strand	32-37	6	58
β-strand	42-47	6	58
β-strand	55-60	6	58
β-strand	68-73	6	59
β-strand	79-84	6	59
β-strand	88-93	6	59
β-strand	97-104	8	59
β-strand	110-115	6	60
β-strand	121-126	6	60
β-strand	130-135	6	60
β-strand	140-145	6	60
β-strand	151-156	6	61
α-helix	157-159	3
β-strand	168-173	6	61
β-strand	177-182	6	61
β-strand	187-193	7	61
β-strand	199-204	6	62
β-strand	210-215	6	62
β-strand	219-224	6	62
β-strand	229-235	7	62
β-strand	240-245	6	63
β-strand	251-256	6	63
β-strand	260-265	6	63
β-strand	268-274	7	63
β-strand	289-294	6	57
β-strand	300-305	6	57
β-strand	309-317	9	57

Chain A7: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	22-23	2
α-helix	56-62	7
α-helix	68-72	5
α-helix	75-77	3
α-helix	103-110	8
α-helix	113-115	3
α-helix	116-137	22
α-helix	156-162	7

73 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
40S ribosomal protein S26-a	A0	protein	119	SACCHAROMYCES CEREVISIAE	P39938 (AlphaFold model)
40S ribosomal protein S27-a	A1	protein	82	SACCHAROMYCES CEREVISIAE	P35997 (AlphaFold model)
40S ribosomal protein S28-a	A2	protein	67	SACCHAROMYCES CEREVISIAE	Q3E7X9 (AlphaFold model)
40S ribosomal protein S29-a	A3	protein	56	SACCHAROMYCES CEREVISIAE	P41057 (AlphaFold model)
40S ribosomal protein S30-a	A4	protein	63	SACCHAROMYCES CEREVISIAE	P0CX33
Ubiquitin-40S ribosomal protein S31	A5	protein	152	SACCHAROMYCES CEREVISIAE	P05759
Guanine nucleotide-binding protein subunit beta-like protein	A6	protein	319	SACCHAROMYCES CEREVISIAE	P38011
Suppressor protein STM1	A7	protein	273	SACCHAROMYCES CEREVISIAE	P39015
40S ribosomal protein S0-a	AA	protein	252	SACCHAROMYCES CEREVISIAE	P32905
40S ribosomal protein S1-a	AB	protein	255	SACCHAROMYCES CEREVISIAE	P33442
40S ribosomal protein S2	AC	protein	254	SACCHAROMYCES CEREVISIAE	P25443
40S ribosomal protein S3	AD	protein	240	SACCHAROMYCES CEREVISIAE	P05750

74 more molecules are not listed.

Sequence of entity 1 (A0), FASTA

>4V8Y_1 40S RIBOSOMAL PROTEIN S26-A (chains A0)
MPKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVRDLSEASVYP
EYALPKTYNKLHYCVSCAIHARIVRVRSREDRKNRAPPQRPRFNRENKVSPADAAKKAL

Sequence of entity 2 (A1), FASTA

>4V8Y_2 40S RIBOSOMAL PROTEIN S27-A (chains A1)
MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCS
TILCTPTGGKAKLSEGTSFRRK

Sequence of entity 3 (A2), FASTA

>4V8Y_3 40S RIBOSOMAL PROTEIN S28-A (chains A2)
MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESE
REARRLR

Sequence of entity 4 (A3), FASTA

>4V8Y_4 40S RIBOSOMAL PROTEIN S29-A (chains A3)
MAHENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFNKFR

Sequence of entity 5 (A4), FASTA

>4V8Y_5 40S RIBOSOMAL PROTEIN S30-A (chains A4)
MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGP
SVQ

Sequence of entity 6 (A5), FASTA

>4V8Y_6 UBIQUITIN-40S RIBOSOMAL PROTEIN S31 (chains A5)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGGKKRKXXXXXXXXXXXXXXXXXXXXVLSYYKVDAEGKVTKLRRE
CSNPTCGAGVFLANHKDRLYCGKCHSVYKVNA

Sequence of entity 7 (A6), FASTA

>4V8Y_7 GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN (chains A6)
MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRS
FKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKAS
MIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKA
WNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEV
FSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQT
LFAGYTDNVIRVWQVMTAN

Sequence of entity 8 (A7), FASTA

>4V8Y_8 SUPPRESSOR PROTEIN STM1 (chains A7)
MSNPFDLLXXXXXXXXXXXXPPKEIVKSNTSSKKADVPPPSADPSKARKNRPRPSGNEGA
IRDKTAGRRNNRSKDVTDSATTKKSNTRRATDRHSRTGKTDTKKKVNQGWGDDKKELSAE
KEAQADAAAEIAEDAAEAEDAGKPKTAQLSXXXXXXXXXXXXXXXXXXXXXXXXXXERIE
TAEKEAYVPATKVKNVKSKQLKTKEYLEFDATFVESNTRKNFGDRNNNSRNNFNNRRGGR
GARKGNNTANATNSANTVQKNRNIDVSNLPSLA

Sequence of entity 9 (AA), FASTA

>4V8Y_9 40S RIBOSOMAL PROTEIN S0-A (chains AA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 10 (AB), FASTA

>4V8Y_10 40S RIBOSOMAL PROTEIN S1-A (chains AB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 11 (AC), FASTA

>4V8Y_11 40S RIBOSOMAL PROTEIN S2 (chains AC)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 12 (AD), FASTA

>4V8Y_12 40S RIBOSOMAL PROTEIN S3 (chains AD)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
OHX	osmium (III) hexammine	H12 N6 Os	197
MG	Magnesium ion	Mg	191
ZN	Zinc ion	Zn	6

Primary citation

Molecular architecture of a eukaryotic translational initiation complex. Fernandez, I.S., Bai, X.C., Hussain, T. et al. Science (2013) 342:1240585-1240585. DOI 10.1126/science.1240585 · PubMed

Other PDB entries of the same protein (UniProt P39938 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
7MPJ 2.7 Å, Stm1 bound vacant 80S structure isolated from wild-type
8CDL 2.72 Å, 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex
6SNT 2.8 Å, Yeast 80S ribosome stalled on SDD1 mRNA.
9F9S 2.9 Å, Yeast SDD1 Disome with Mbf1
9R9O 2.9 Å, Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state
4V88 3.0 Å, The structure of the eukaryotic ribosome at 3.0 A resolution.
8CAH 3.0 Å, Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex
9R9P 3.0 Å, Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state
8UTI 3.13 Å, Eukaryotic 80S ribosome with Reh1 and A/P site tRNA

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