6ZU9: Yeast ABCE1-bound 48S initiation complex

Structure of a yeast ABCE1-bound 48S initiation complex. Determined by electron microscopy at 6.2 Å resolution. Released 28 Oct 2020.

Method: Electron microscopy
Resolution: 6.2 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 44
Atoms: 78,384
Mol. weight: 1681.18 kDa
Ligands: MG, ZN, ADP, ATP
Released: 28 Oct 2020

Explore 6ZU9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZU9 contains 314 α-helices and 369 β-strands across 41 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	62
β-strand	8	1	62
α-helix	13-14	2
β-strand	15-16	2	63
β-strand	23-24	2	63
β-strand	32-39	8	64
β-strand	45-55	11	64
α-helix	57-61	5
α-helix	65-75	11

Chain A: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	33-41	9	89
β-strand	47-51	5	89
β-strand	55-61	7	89
β-strand	76-81	6	89
α-helix	82	1
β-strand	88-94	7	89
α-helix	97-106	10

Chain b: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	24-27	4	32
α-helix	32-43	12
β-strand	50-53	4	32
β-strand	60-64	5	32
β-strand	72-74	3	66
β-strand	80-81	2	66
α-helix	83-93	11
β-strand	101-106	6	66
β-strand	109-112	4	66
α-helix	113-119	7
β-strand	123-129	7	66

Chain B: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
α-helix	29-32	4
β-strand	37-42	6	107
β-strand	45-52	8	107
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-90	7	107
α-helix	94-96	3
α-helix	98-111	14
α-helix	115-128	14
β-strand	131-141	11	108
β-strand	147-155	9	108
α-helix	162-167	6
β-strand	168-177	10	108
β-strand	180-190	11	108
β-strand	207-208	2	109
α-helix	209-213	5
β-strand	221-223	3	37

Chain c: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-24	13
α-helix	28-34	7
α-helix	36-39	4
β-strand	48-57	10	83
α-helix	59	1
β-strand	60	1	84
α-helix	61	1
β-strand	68	1	84
β-strand	71-76	6	83
β-strand	82-86	5	83
α-helix	92-95	4
β-strand	101-106	6	83
β-strand	122-127	6	83
β-strand	130-131	2	83
α-helix	132-136	5

Chain C: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-38	8
α-helix	82-85	4
α-helix	89-97	9
α-helix	101-103	3
α-helix	107-123	17
α-helix	129-139	11
β-strand	144-149	6	45
β-strand	156-161	6	45
α-helix	164-183	20
α-helix	190-203	14
α-helix	209-223	15

Chain d: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	86
β-strand	20-28	9	86
α-helix	37-48	12
α-helix	52-54	3
β-strand	55-62	8	86
α-helix	63	1
β-strand	68-76	9	86
α-helix	79-85	7
α-helix	88-93	6
α-helix	105-115	11
α-helix	123-132	10

Chain D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-22	3	110
α-helix	39-51	13
β-strand	55-56	2	110
β-strand	65-68	4	110
α-helix	70-80	11

33 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
18S ribosomal RNA	2	RNA	1800	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
40S ribosomal protein S0-A	P	protein	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32905 (AlphaFold model)
40S ribosomal protein S1-A	Q	protein	255	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33442 (AlphaFold model)
40S ribosomal protein S2	R	protein	254	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25443 (AlphaFold model)
40S ribosomal protein S4-A	S	protein	261	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX35 (AlphaFold model)
40S ribosomal protein S6-A	T	protein	236	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX37
40S ribosomal protein S7-A	U	protein	190	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P26786
40S ribosomal protein S8-A	V	protein	200	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX39
40S ribosomal protein S9-A	W	protein	197	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	O13516
40S ribosomal protein S11-A	X	protein	155	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX47
40S ribosomal protein S13	Y	protein	151	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05756
40S ribosomal protein S14-A	Z	protein	136	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P06367

32 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6ZU9_1 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUG
UGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUA
UUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCU
UAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCC
CUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGC
CGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAU
UGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCC
UGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGG
AUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (P), FASTA

>6ZU9_2 40S ribosomal protein S0-A (chains P)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 3 (Q), FASTA

>6ZU9_3 40S ribosomal protein S1-A (chains Q)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 4 (R), FASTA

>6ZU9_4 40S ribosomal protein S2 (chains R)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 5 (S), FASTA

>6ZU9_5 40S ribosomal protein S4-A (chains S)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 6 (T), FASTA

>6ZU9_6 40S ribosomal protein S6-A (chains T)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 7 (U), FASTA

>6ZU9_7 40S ribosomal protein S7-A (chains U)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 8 (V), FASTA

>6ZU9_8 40S ribosomal protein S8-A (chains V)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 9 (W), FASTA

>6ZU9_9 40S ribosomal protein S9-A (chains W)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 10 (X), FASTA

>6ZU9_10 40S ribosomal protein S11-A (chains X)
STELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFT
GLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGD
IVTVGQCRPISKTVRFNVVKVSAAAAKANKQFAKF

Sequence of entity 11 (Y), FASTA

>6ZU9_11 40S ribosomal protein S13 (chains Y)
MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV
TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVAVLPPNWKYESATASALVN

Sequence of entity 12 (Z), FASTA

>6ZU9_12 40S ribosomal protein S14-A (chains Z)
SNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAM
LAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPV
PSDSTRKKGGRRGRRL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
ZN	Zinc ion	Zn	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
SF4	Iron/sulfur cluster	Fe4 S4	2

Primary citation

A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Kratzat, H., Mackens-Kiani, T., Ameismeier, M. et al. EMBO J (2021) 40:e105179-e105179. DOI 10.15252/embj.2020105179 · PubMed

Other PDB entries of the same protein (UniProt P32905 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
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…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing

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