9HM0: Translational activator Aep3

Name: PDB 9HM0: Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome
Published: 2025-12-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome. Determined by electron microscopy at 3.0 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Saccharomyces cerevisiae W303, Saccharomyces cerevisiae
Chains: 77
Atoms: 213,189
Mol. weight: 3642.6 kDa
Ligands: MG, GTP
Released: 17 Dec 2025

Explore 9HM0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HM0 contains 832 α-helices and 532 β-strands across 74 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 00: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	57-58	2	64
β-strand	69-74	6	64
β-strand	77-82	6	64
α-helix	86-88	3
β-strand	90-91	2	64

Chain 1: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	80-99	20
α-helix	101-108	8

Chain 11: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	37-43	7
α-helix	58-63	6
α-helix	66-67	2
α-helix	71-94	24
α-helix	98-109	12
α-helix	113-120	8
α-helix	137-146	10
α-helix	147-151	5
α-helix	152-161	10
α-helix	164-168	5
β-strand	176-181	6	77
α-helix	183-186	4
β-strand	191	1	77
α-helix	192-193	2
β-strand	196-197	2	78
β-strand	208-213	6	77
β-strand	224-235	12	78
β-strand	240-252	13	78
β-strand	260-261	2	77
α-helix	268-270	3
β-strand	271-273	3	78
α-helix	280-281	2
β-strand	282	1	79
β-strand	287-295	9	78
α-helix	322-329	8
β-strand	332-341	10	78
α-helix	346-354	9
α-helix	356-360	5
β-strand	361	1	79
β-strand	362	1	80

Chain 2: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	32-34	3
α-helix	41-48	8
α-helix	53-55	3
α-helix	56-59	4
α-helix	63-68	6
α-helix	71-77	7
α-helix	81-95	15
α-helix	114-124	11
α-helix	125-129	5

Chain 22: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-49	13
α-helix	63-108	46
α-helix	110-117	8
α-helix	130-132	3
β-strand	133	1	93
β-strand	135	1	94

Chain 3: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	10
α-helix	17-22	6
α-helix	31-34	4
α-helix	35-40	6
α-helix	41-53	13
α-helix	57-60	4
α-helix	63-70	8
α-helix	77-96	20
α-helix	108-110	3
α-helix	117-126	10
α-helix	132-146	15
β-strand	151-157	7	11
β-strand	163-169	7	11
α-helix	177-179	3
α-helix	191-205	15
β-strand	219-225	7	11
α-helix	228-231	4
α-helix	240-249	10
α-helix	253-259	7

Chain 33: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
β-strand	63-64	2	101
β-strand	70-71	2	101
α-helix	74-76	3
β-strand	78-80	3	102
β-strand	93-95	3	103
α-helix	99-101	3
β-strand	102-104	3	104
α-helix	111-113	3
α-helix	115-128	14
α-helix	131-133	3
α-helix	134-137	4
β-strand	143-145	3	104

Chain 4: 21 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	34-37	4
α-helix	38-42	5
α-helix	43-54	12
α-helix	64-70	7
α-helix	75-77	3
α-helix	78-95	18
β-strand	97	1	15
α-helix	103-104	2
α-helix	109-111	3
α-helix	114-117	4
α-helix	119-120	2
α-helix	130-133	4
α-helix	136-146	11
α-helix	149-162	14
β-strand	167-176	10	16
β-strand	192-202	11	16
α-helix	215-234	20
α-helix	240-256	17
β-strand	265-274	10	16
α-helix	277-284	8
α-helix	289-298	10
β-strand	300	1	15
α-helix	302-308	7
α-helix	309-310	2
β-strand	311-312	2	16
α-helix	314-318	5

66 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
Small ribosomal subunit protein mS38	1	protein	111	Saccharomyces cerevisiae W303	P32344 (AlphaFold model)
Small ribosomal subunit protein mS41	2	protein	130	Saccharomyces cerevisiae W303	P38783 (AlphaFold model)
Small ribosomal subunit protein mS42	3	protein	266	Saccharomyces cerevisiae W303	P47141 (AlphaFold model)
Small ribosomal subunit protein mS43	4	protein	321	Saccharomyces cerevisiae W303	P10662 (AlphaFold model)
Small ribosomal subunit protein mS27	5	protein	339	Saccharomyces cerevisiae W303	P12686
Small ribosomal subunit protein mS45	6	protein	345	Saccharomyces cerevisiae W303	P53292
Small ribosomal subunit protein mS46	7	protein	361	Saccharomyces cerevisiae W303	Q03430
Small ribosomal subunit protein mS47	8	protein	500	Saccharomyces cerevisiae W303	P28817
Small ribosomal subunit protein bS1m	A	protein	344	Saccharomyces cerevisiae W303	Q02950
Small ribosomal subunit protein uS2m	B	protein	394	Saccharomyces cerevisiae W303	P32902
Small ribosomal subunit protein uS3m	C	protein	398	Saccharomyces cerevisiae W303	P02381
Small ribosomal subunit protein uS4m	D	protein	486	Saccharomyces cerevisiae W303	P27929

65 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>9HM0_1 Small ribosomal subunit protein mS38 (chains 1)
MLGRALRPGWLGITRTVVKKPSCGSYFNRTFQTAINTTMPPMQEGMLSTMMMMTATATRI
TGTVSEPLNGSNIVMQLDSVMRKRKKKMKKHKLRKRRKREKAERRKLSQGR

Sequence of entity 2 (2), FASTA

>9HM0_2 Small ribosomal subunit protein mS41 (chains 2)
MIPSRISHKFPLFLRSSLAAPKAAYRFSSTIPKPSDQVPDVDAFLNKIGRNCNELKDTFE
NNWNNLFQWDSKILKEKGVNIQQRKYILKQVHNYRNNRPIHEIKLGKKSFFGGERKRKAF
TAKWKAENKQ

Sequence of entity 3 (3), FASTA

>9HM0_3 Small ribosomal subunit protein mS42 (chains 3)
MLVFKRGIHVVPKLPNSKALLQNGVPNILSSSGFKTVWFDYQRYLCDKLTLATAGQSLES
YYPFHILLKTAGNPLQSNIFNLASSIHNNHLFVENILPSAVEHGTNSNAVVKTEPSRLFL
SKIKDSFNGSDWEVVKEEMIYRAENEVLGQGWLFLVENNEKKLFILTSNNNGTPYYFPRN
QSFDLNSAISIDEFATLKQMKELIGKSTKLNGKVQDWTMPIICVNLWDHAYLHDYGVGNR
SKYVKNVLDNLNWSVVNNRIFSGISK

Sequence of entity 4 (4), FASTA

>9HM0_4 Small ribosomal subunit protein mS43 (chains 4)
MLRFTGARAIRKYSTRYALEHLKEGAPLKGLFSIEGLQKAWFDRVKYLDAKLNDCTNEAQ
QKPLETLIHENSKSASKKHIVNYASSLYNLKFSMSSLQGCIRTPPEECPRLGPEALLQTP
DFNRTISNEPLTTGNERLQAALISSFGSLMEFRTLLINSNLAISGDGFTWLVARRQLDKR
AMRNDMPNRDIEYDKLFILNTYNAGTPFNFSTSGVMNELNNQYTNMEKQRAKEAGNLEDS
EMTAKQAKTKFIYETQQKGFSGKEVSYIPLLAIDASPKTWLTDYGVFGKREYLERVWDSI
EWKIVESRLPQRTKIQAFNTL

Sequence of entity 5 (5), FASTA

>9HM0_5 Small ribosomal subunit protein mS27 (chains 5)
MGTITVVINEGPILLIRALHRATTNKKMFRSTVWRRFASTGEIAKAKLDEFLIYHKTDAK
LKPFIYRPKNAQILLTKDIRDPKTREPLQPRPPVKPLSKQTLNDFIYSVEPNSTELLDWF
KEWTGTSIRKRAIWTYISPIHVQKMLTASFFKIGKYAHMVGLLYGIEHKFLKAQNPSVFD
IEHFFNTNIMCALHRNRLKDYKDAEIAQRKLQVAWKKVLNRKNNTGLANILVATLGRQIG
FTPELTGLQPVDISLPDIPNSSSGAELKDLLSKYEGIYLIARTLLDIDQHNAQYLELQEF
IRQYQNALSESSDPYDTHLKALGLLETPPPQESTEKEEK

Sequence of entity 6 (6), FASTA

>9HM0_6 Small ribosomal subunit protein mS45 (chains 6)
MSYGLTGTSSKLRGTSSIFSWTQVRHFSRRRIAYPFYPFKKLGRQHPKKHDTNLKTAMRQ
FLGPKNYKGEYVMNKYFTVPTNHVPNYIKPDLERGQSLEHPVTKKPLQLRYDGTLGPPPV
ENKRLQNIFKDRLLQPFPSNPHCKTNYVLSPQLKQSIFEEITVEGLSAQQVSQKYGLKIP
RVEAIVKLVSVENSWNRRNRVSSDLKTMDETLYRMFPVFDSDASFKRENLSEIPVPQKTL
ASRFLTIAESEPFGPVDAAHVLELEPAVETLRNLSTVGEHSSGHQQSTNKNTKVIYGELV
EGERSQYKFTNAKVGKVGYRYGSGNRDNKKDRRIGFNKLGQMVYI

Sequence of entity 7 (7), FASTA

>9HM0_7 Small ribosomal subunit protein mS46 (chains 7)
MRSSMFRCVSRAHYSTSVTEDFINSILARAQEATAKASSNALKLDKMKEGRMQNKRRNGN
QNRNSMNNKESRGREGNQGERNMRLKNRSSDSVRANKQQWNKGANTSFVKNPTGNTVVMQ
PQFKKMQNGKNNLKGDARVEDDLLDVFNSSMEQKPVNFNGTPKSKARFQKKSHILTASKR
RKAPQQQLQKVIKRPVSSEYVLEEPTPLSLLEYTPQVFPTKESRLVNFTLDSLKKSNYPI
YRSPNLGILKVHDFTLNTPNFGKYTPGSSLIFAKEPQLQNLLIEEDPEDFHRQVTGEYQL
LKPYVKKDFEKLTKSKDTVSKLVQNSQVVRLSLQSVVMGSEEKKLVYDVCSGMKPISELQ
Q

Sequence of entity 8 (8), FASTA

>9HM0_8 Small ribosomal subunit protein mS47 (chains 8)
MLRNTLKCAQLSSKYGFKTTTRTFMTTQPQLNVTDAPPVLFTVQDTARVITLNRPKKLNA
LNAEMSESMFKTLNEYAKSDTTNLVILKSSNRPRSFCAGGDVATVAIFNFNKEFAKSIKF
FTDEYSLNFQIATYLKPIVTFMDGITMGGGVGLSIHTPFRIATENTKWAMPEMDIGFFPD
VGSTFALPRIVTLANSNSQMALYLCLTGEVVTGADAYMLGLASHYVSSENLDALQKRLGE
ISPPFNNDPQSAYFFGMVNESIDEFVSPLPKDYVFKYSNEKLNVIEACFNLSKNGTIEDI
MNNLRQYEGSAEGKAFAQEIKTKLLTKSPSSLQIALRLVQENSRDHIESAIKRDLYTAAN
MCMNQDSLVEFSEATKHKLIDKQRVPYPWTKKEQLFVSQLTSITSPKPSLPMSLLRNTSN
VTWTQYPYHSKYQLPTEQEIAAYIEKRTNDDTGAKVTEREVLNHFANVIPSRRGKLGIQS
LCKIVCERKCEEVNDGLRWK

Sequence of entity 9 (A), FASTA

>9HM0_9 Small ribosomal subunit protein bS1m (chains A)
MTLAELLGRSRIAQVANNHKPLTYTGKKFHPTHQIIETKPSTLYRQEWGLKSAIPSKIKS
RYLVYNDLDTLERITTFEPRGGTQWNRLRFQEMGVPIVSNIGRQNPFFKYISRPEDESHA
KLSLFKEMKGDTDISPAAMKKRLKKITALIRSFQDEFKEWLVENHPDELKLNSNKLEDYV
VKFLNKKLETKTNKKFNTEIIGTGGLSYSLPGKLKNSPNGVIQRTVVPGRILNVVKENND
NKWLAAIGGFVADVVFFQSPPSSFNSMGDFIRMKTFLFEILEASMEKNGSVSMHARLLEP
QNDKTREFFNKRPIYKPLTSRRARRPSVGNIQEANNLLNIIKGN

Sequence of entity 10 (B), FASTA

>9HM0_10 Small ribosomal subunit protein uS2m (chains B)
MQRHVFARNFRRLSLLRNPSLTKRFQSSASGAANTPNNNDEVMLLQQKLLYDEIRSELKS
LSQVPEDEILPELKKSLEQDKLSDKEQQLEAELSDFFRNYALLNKLFDSKTLDGQSSTTT
AAATPTKPYPNLIPSANDKPYSSQELFLRQLNHSMRTAKLGATISKVYYPHKDIFYPPLP
ENITVESLMSAGVHLGQSTSLWRSSTQSYIYGEYKGIHIIDLNQTLSYLKRAAKVVEGVS
ESGGIILFLGTRQGQKRGLEEAAKKTHGYYVSTRWIPGTLTNSTEISGIWEKQEIDSNDN
PTERALSPNETSKQVKPDLLVVLNPTENRNALLEAIKSRVPTIAIIDTDSEPSLVTYPIP
GNDDSLRSVNFLLGVLARAGQRGLQNRLARNNEK

Sequence of entity 11 (C), FASTA

>9HM0_11 Small ribosomal subunit protein uS3m (chains C)
MKLKLLNMILSMMNKTNNNNNIIINNTLDSLMNKKLLLKNMLLDMNNKKMNNMKRMLNNN
NMNPAGANPVVHRIGPAGNINNKLQHLNNMNNWNTQIYNYNKNMEIMNTMNDKLINKLLY
KMMTLKLNNMNINKIIMSKTINQHSLNKLNIKFYYYNNDINNNNNNNNNNYYMNMMNKLM
NIMNNNMNNNLCNILSYYYKKKVTIEPIKLSYIYLNSDIFSKYISLNDMDKYNNGILTNY
QRMLNNIMPKLNDHNISMNYINNINNINNNKYNNMINLLNNNNNINNNNNYNNNNNNYIG
NINNIYNNMTIDNIPMDILMYKYLVGWSIKFKGRLSNNNGRTSTTNLLNGTFNNKKYLWS
NINNNYKLNYIPSNHNLYNNSNINKNGKYNIKVKLNFI

Sequence of entity 12 (D), FASTA

>9HM0_12 Small ribosomal subunit protein uS4m (chains D)
MPRKANLLKSLARGRVRTSFNKYNLFNLYKKGGVDLKSKSLYQQKWTAKQETRAYHGEHL
TEKRWQTVFKPKLDSVAQLDASLRGGEIKETPFLLQTFAVLEKRLDFALFRAMFASSVRQ
ARQFILHGNVRVNGVKIKHPSYTLKPGDMFSVKPDKVLEALGAKKPSFQEALKIDKTQIV
LWNKYVKEAKTEPKEVWEKKLENFEKMSDSNPKKLQFQEFLRQYNKNLESQQYNALKGCT
QEGILRKLLNVEKEIGKSNNEPLSIDELKQGLPEIQDSQLLESLNNAYQEFFKSGEIRRE
IISKCQPDELISLATEMMNPNETTKKELSDGAKSALRSGKRIIAESVKLWTKNITDHFKT
RMSDISDGSLTFDPKWAKNLKYHDPIKLSELEGDEPKARKLINLPWQKNYVYGRQDPKKP
FFTPWKPRPFLSPFAILPHHLEISFKTCHAVYLRDPVARPGQSEVISPFDVPVHERAYMY
YLRNGK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	317
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation. Bridgers, J.B., Carlstrom, A., Sherpa, D. et al. Nat Struct Mol Biol (2026) 33:245-258. DOI 10.1038/s41594-025-01726-y · PubMed

Other PDB entries of the same protein (UniProt P32344 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OM4 2.32 Å, Small subunit of yeast mitochondrial ribosome.
8OM2 2.57 Å, Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22.
8OM3 2.87 Å, Small subunit of yeast mitochondrial ribosome in complex with IF3/Aim23.
8UXA 3.2 Å, Glucose treated mitochondrial ribosome of saccharomyces cerevisiae class I
9HLZ 3.2 Å, Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast…
5MRC 3.25 Å, Structure of the yeast mitochondrial ribosome - Class A
8UX4 3.3 Å, Mitochondrial ribosome of saccharomyces cerevisiae class II from YEP with Dextrose culture
5MRE 3.75 Å, Structure of the yeast mitochondrial ribosome - Class B
5MRF 4.97 Å, Structure of the yeast mitochondrial ribosome - Class C

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