8CSU: 28S ribosomal protein S34, mitochondrial

Human mitochondrial small subunit assembly intermediate (State C*). Determined by electron microscopy at 3.03 Å resolution. Released 14 Dec 2022.

Method
Electron microscopy
Resolution
3.03 Å
Organism
Homo sapiens
Chains
33
Atoms
68,661
Mol. weight
1261.07 kDa
Ligands
SF4, SAM, MG, NAD
Released
14 Dec 2022

Explore 8CSU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CSU contains 353 α-helices and 193 β-strands across 32 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 0: 16 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix10-2516
α-helix27-293
α-helix30-334
β-strand3711
β-strand4211
α-helix481
β-strand4911
α-helix50-512
α-helix52-587
β-strand6212
α-helix64-685
α-helix72-743
β-strand79-8242
α-helix83-886
β-strand94-10292
β-strand112-12092
β-strand123-12422
β-strand129-13022
α-helix1311
β-strand139-14132
α-helix144-1463
α-helix147-1515
β-strand163-16533
α-helix166-1672
α-helix168-18013
α-helix187-1893
β-strand190-19233
α-helix213-2153
Chain 1: 17 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix56-594
α-helix66-694
β-strand8617
α-helix90-912
α-helix96-983
α-helix103-1064
α-helix116-12510
α-helix126-1294
α-helix140-1467
β-strand149-15798
β-strand16219
α-helix166-1694
β-strand171-17668
α-helix177-1793
α-helix184-19411
α-helix195-1973
β-strand198-19928
β-strand204-20968
α-helix215-23319
α-helix240-2423
α-helix257-27216
α-helix287-30115
α-helix306-32015
Chain 3: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix154-18027
α-helix185-1862
Chain 4: 39 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix59-602
β-strand61-65512
α-helix69-779
α-helix93-953
α-helix100-12324
α-helix125-1273
β-strand13419
α-helix138-1403
α-helix154-1629
α-helix166-17813
α-helix185-19814
α-helix236-2383
α-helix243-2508
α-helix256-26813
α-helix272-28413
α-helix291-30313
α-helix309-32517
α-helix332-34312
α-helix346-3494
α-helix350-36213
α-helix369-37911
α-helix392-4009
α-helix412-4143
α-helix415-42612
α-helix429-44012
α-helix444-4485
α-helix451-46818
α-helix471-48111
α-helix490-50213
α-helix506-5083
α-helix509-51810
α-helix521-5233
α-helix525-53612
α-helix542-56019
α-helix573-58614
α-helix589-60214
α-helix605-6073
α-helix608-62114
α-helix624-63613
α-helix642-65211
α-helix657-66610
Chain 5: 19 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix13-175
α-helix18-247
α-helix41-5010
β-strand58-62515
α-helix68-758
β-strand80-85615
α-helix91-10010
β-strand105-109515
α-helix117-1193
α-helix123-1253
β-strand136-140515
α-helix147-16014
α-helix163-1675
β-strand171-177715
α-helix178-1847
α-helix195-2017
β-strand204-212915
α-helix214-2163
β-strand225-232815
α-helix242-25312
α-helix260-2645
α-helix265-2673
α-helix273-28412
α-helix292-2943
α-helix297-31317
α-helix322-3276
Chain 6: 6 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix44-496
α-helix91-10818
α-helix115-1206
β-strand124-129623
β-strand136-141623
α-helix146-16924
α-helix177-1782
β-strand179-184623
α-helix186-19914
Chain 7: 17 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand36-37224
α-helix43-464
α-helix59-602
β-strand61125
α-helix65-7410
α-helix81-9616
α-helix99-1024
α-helix103-11917
α-helix127-13812
α-helix152-18029
β-strand188-192525
α-helix198-20710
β-strand213-217525
α-helix221-23111
β-strand245-248425
β-strand259-265725
α-helix268-2703
α-helix274-28613
β-strand288-2971025
α-helix300-31415
β-strand327-331525
α-helix338-3392
β-strand349-353525
α-helix355-3573
β-strand365-3761225
β-strand387-388226
β-strand393-395326
β-strand398-404726
β-strand410-415626
α-helix417-4204
α-helix422-4309
β-strand436126
β-strand439-440224
Chain B: 14 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix56-583
α-helix59-635
α-helix66-683
α-helix75-784
α-helix81-866
β-strand91-94427
α-helix95-973
α-helix100-1056
β-strand106-110527
β-strand113-116427
α-helix118-13720
β-strand142-145428
α-helix149-1513
α-helix152-16110
β-strand165-167328
α-helix179-1835
α-helix187-1904
β-strand192-195428
β-strand199129
β-strand205129
α-helix207-2148
β-strand219-223528
β-strand234-237428
α-helix243-27331

24 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
28S ribosomal protein S34, mitochondrial0protein218Homo sapiensP82930 (AlphaFold model)
28S ribosomal protein S35, mitochondrial1protein323Homo sapiensP82673 (AlphaFold model)
Aurora kinase A-interacting protein3protein199Homo sapiensQ9NWT8 (AlphaFold model)
Pentatricopeptide repeat domain-containing protein 3, mitochondrial4protein689Homo sapiensQ96EY7 (AlphaFold model)
Dimethyladenosine transferase 1, mitochondrial5protein346Homo sapiensQ8WVM0
Putative ribosome-binding factor A, mitochondrial6protein343Homo sapiensQ8N0V3
Methyltransferase-like protein 17, mitochondrial7protein456Homo sapiensQ9H7H0
12S mitochondrial rRNAARNA955Homo sapiens
28S ribosomal protein S2, mitochondrialBprotein296Homo sapiensQ9Y399
28S ribosomal protein S24, mitochondrialCprotein167Homo sapiensQ96EL2
28S ribosomal protein S5, mitochondrialDprotein430Homo sapiensP82675
28S ribosomal protein S6, mitochondrialEprotein125Homo sapiensP82932

21 more molecules are not listed.

Sequence of entity 1 (0), FASTA
>8CSU_1 28S ribosomal protein S34, mitochondrial (chains 0)
MARKKVRPRLIAELARRVRALREQLNRPRDSQLYAVDYETLTRPFSGRRLPVRAWADVRR
ESRLLQLLGRLPLFGLGRLVTRKSWLWQHDEPCYWRLTRVRPDYTAQNLDHGKAWGILTF
KGKTESEAREIEHVMYHDWRLVPKHEEEAFTAFTPAPEDSLASVPYPPLLRAMIIAERQK
NGDTSTEEPMLNVQRIRMEPWDYPAKQEDKGRAKGTPV
Sequence of entity 2 (1), FASTA
>8CSU_2 28S ribosomal protein S35, mitochondrial (chains 1)
MAAAALPAWLSLQSRARTLRAFSTAVYSATPVPTPSLPERTPGNERPPRRKALPPRTEKM
AVDQDWPSVYPVAAPFKPSAVPLPVRMGYPVKKGVPMAKEGNLELLKIPNFLHLTPVAIK
KHCEALKDFCTEWPAALDSDEKCEKHFPIEIDSTDYVSSGPSVRNPRARVVVLRVKLSSL
NLDDHAKKKLIKLVGERYCKTTDVLTIKTDRCPLRRQNYDYAVYLLTVLYHESWNTEEWE
KSKTEADMEEYIWENSSSERNILETLLQMKAAEKNMEINKEELLGTKEIEEYKKSVVSLK
NEEENENSISQYKESVKRLLNVT
Sequence of entity 3 (3), FASTA
>8CSU_3 Aurora kinase A-interacting protein (chains 3)
MLLGRLTSQLLRAVPWAGGRPPWPVSGVLGSRVCGPLYSTSPAGPGRAASLPRKGAQLEL
EEMLVPRKMSVSPLESWLTARCFLPRLDTGTAGTVAPPQSYQCPPSQIGEGAEQGDEGVA
DAPQIQCKNVLKIRRRKMNHHKYRKLVKKTRFLRRKVQEGRLRRKQIKFEKDLRRIWLKA
GLKEAPEGWQTPKIYLRGK
Sequence of entity 4 (4), FASTA
>8CSU_4 Pentatricopeptide repeat domain-containing protein 3, mitochondrial (chains 4)
MAVVSAVRWLGLRSRLGQPLTGRRAGLCEQARSCRFYSGSATLSKVEGTDVTGIEEVVIP
KKKTWDKVAVLQALASTVNRDTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGENVAKFI
INSYPKYFQKDIAEPHIPCLMPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAG
TTVSLETTNSLLDLLCYYGDQEPSTDYHFQQTGQSEALEEENDETSRRKAGHQFGVTWRA
KNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEA
TVCAINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFARSPALQVLREM
KAIGIEPSLATYHHIIRLFDQPGDPLKRSSFIIYDIMNELMGKRFSPKDPDDDKFFQSAM
SICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYSKFFDLICLMEQIDVTLKWYED
LIPSAYFPHSQTMIHLLQALDVANRLEVIPKIWKDSKEYGHTFRSDLREEILMLMARDKH
PPELQVAFADCAADIKSAYESQPIRQTAQDWPATSLNCIAILFLRAGRTQEAWKMLGLFR
KHNKIPRSELLNELMDSAKVSNSPSQAIEVVELASAFSLPICEGLTQRVMSDFAINQEQK
EALSNLTALTSDSDTDSSSDSDSDTSEGK
Sequence of entity 5 (5), FASTA
>8CSU_5 Dimethyladenosine transferase 1, mitochondrial (chains 5)
MAASGKLSTCRLPPLPTIREIIKLLRLQAAKQLSQNFLLDLRLTDKIVRKAGNLTNAYVY
EVGPGPGGITRSILNADVAELLVVEKDTRFIPGLQMLSDAAPGKLRIVHGDVLTFKVEKA
FSESLKRPWEDDPPNVHIIGNLPFSVSTPLIIKWLENISCRDGPFVYGRTQMTLTFQKEV
AERLAANTGSKQRSRLSVMAQYLCNVRHIFTIPGQAFVPKPEVDVGVVHFTPLIQPKIEQ
PFKLVEKVVQNVFQFRRKYCHRGLRMLFPEAQRLESTGRLLELADIDPTLRPRQLSISHF
KSLCDVYRKMCDEDPQLFAYNFREELKRRKSKNEEKEEDDAENYRL
Sequence of entity 6 (6), FASTA
>8CSU_6 Putative ribosome-binding factor A, mitochondrial (chains 6)
MWAAAGGLWRSRAGLRALFRSRDAALFPGCERGLHCSAVSCKNWLKKFASKTKKKVWYES
PSLGSHSTYKPSKLEFLMRSTSKKTRKEDHARLRALNGLLYKALTDLLCTPEVSQELYDL
NVELSKVSLTPDFSACRAYWKTTLSAEQNAHMEAVLQRSAAHMRHLLMSQQTLRNVPPIV
FVQDKGNAALAELDQLLAVADFGPRDERDNFVQNDFRDPDAPQPCGTTEPTTSSSLCGID
HEALNKQIMEYKRRKDKGLGGLVWQGQVAELTTQMKKGRKRAKPRLEQDSSLKSYLSGEE
VEDDLDLVGAPEYECYAPDTEELEAERGGGRTEDGHSCGASRE
Sequence of entity 7 (7), FASTA
>8CSU_7 Methyltransferase-like protein 17, mitochondrial (chains 7)
MAAALKCLLTLGRWCPGLGVAPQARALAALVPGVTQVDNKSGFLQKRPHRQHPGILKLPH
VRLPQALANGAQLLLLGSAGPTMENQVQTLTSYLWSRHLPVEPEELQRRARHLEKKFLEN
PDLSQTEEKLRGAVLHALRKTTYHWQELSYTEGLSLVYMAARLDGGFAAVSRAFHEIRAR
NPAFQPQTLMDFGSGTGSVTWAAHSIWGQSLREYMCVDRSAAMLVLAEKLLKGGSESGEP
YIPGVFFRQFLPVSPKVQFDVVVSAFSLSELPSKADRTEVVQTLWRKTGHFLVLVENGTK
AGHSLLMDARDLVLKGKEKSPLDPRPGFVFAPCPHELPCPQLTNLACSFSQAYHPIPFSW
NKKPKEEKFSMVILARGSPEEAHRWPRITQPVLKRPRHVHCHLCCPDGHMQHAVLTARRH
GRDLYRCARVSSWGDLLPVLTPSAFPPSTAQDPSES
Sequence of entity 8 (A), FASTA
>8CSU_8 12S mitochondrial rRNA (chains A)
AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCC
CGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGC
AGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAA
CCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG
UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUU
UUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUG
ACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCA
AACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAA
CUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAU
AUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUG
CUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAG
UACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACA
UUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUA
GCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCC
CGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAU
AGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAACC
Sequence of entity 9 (B), FASTA
>8CSU_9 28S ribosomal protein S2, mitochondrial (chains B)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL
Sequence of entity 10 (C), FASTA
>8CSU_10 28S ribosomal protein S24, mitochondrial (chains C)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL
Sequence of entity 11 (D), FASTA
>8CSU_11 28S ribosomal protein S5, mitochondrial (chains D)
MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPY
ASLSRALQTQCCISSPSHLMSQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKK
KKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQRSKEEQEKVEADMIQQREEWD
RKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS
IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKR
THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRS
VWSNLKRAAT
Sequence of entity 12 (E), FASTA
>8CSU_12 28S ribosomal protein S6, mitochondrial (chains E)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Ligands and cofactors

IDNameFormulaCopies
SF4Iron/sulfur clusterFe4 S41
SAMS-adenosylmethionineC15 H22 N6 O5 S1
MGMagnesium ionMg26
NADNicotinamide-adenine-dinucleotideC21 H27 N7 O14 P21
ZNZinc ionZn1
FESFE2/S2 (inorganic) clusterFe2 S22
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P21

Water and common crystallization additives (K) are not listed.

Primary citation

Principles of mitoribosomal small subunit assembly in eukaryotes. Harper, N.J., Burnside, C., Klinge, S. Nature (2023) 614:175-181. DOI 10.1038/s41586-022-05621-0 · PubMed

Other PDB entries of the same protein (UniProt P82930 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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