9F9S: Yeast SDD1 Disome with Mbf1

Yeast SDD1 Disome with Mbf1. Determined by electron microscopy at 2.9 Å resolution. Released 4 Dec 2024.

Method
Electron microscopy
Resolution
2.9 Å
Organism
Saccharomyces cerevisiae
Chains
164
Atoms
406,583
Mol. weight
6403.53 kDa
Ligands
SPD, ZN, MG
Released
4 Dec 2024

Explore 9F9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F9S contains 981 α-helices and 1,039 β-strands across 151 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 CN: 9 helices, 5 β-strands

ElementResiduesLengthSheet
β-strand9-10224
β-strand24-25225
α-helix29-3810
β-strand41-46625
α-helix54-552
α-helix59-679
α-helix71-755
α-helix79-9113
α-helix96-1027
α-helix107-1148
α-helix119-1202
α-helix122-13211
β-strand134126
β-strand144126
Chain La: 3 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand17-182279
β-strand22-254280
β-strand271281
β-strand31-399280
α-helix48-503
β-strand51-522279
β-strand57-659280
β-strand701280
β-strand73-808280
β-strand85-862213
β-strand92-954213
β-strand99-1024280
β-strand1031282
β-strand1091282
β-strand1141281
β-strand1181283
α-helix120-1256
α-helix127-1326
β-strand1331281
β-strand1361283
Chain LA: 7 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix10-123
α-helix15-195
β-strand38-42587
β-strand50188
β-strand51-57787
β-strand62-66587
α-helix69-724
β-strand77-80487
α-helix81-833
β-strand84-90787
α-helix110-1123
α-helix133-14917
α-helix155-1606
β-strand162188
Chain Lb: 3 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix9-135
α-helix20-3314
β-strand37-382295
β-strand45-495295
β-strand54-574295
β-strand63-653295
α-helix74-9118
Chain LB: 12 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix28-7144
β-strand75-773100
α-helix78-814
β-strand83-886101
α-helix97-1059
β-strand113-1186101
α-helix121-1299
α-helix131-1333
β-strand134-1374101
α-helix141-15111
β-strand153-1553102
β-strand160-1623102
α-helix166-1738
α-helix174-1763
α-helix181-1899
α-helix195-2017
β-strand2021102
α-helix203-2042
β-strand205-2062101
β-strand2221103
β-strand2291103
β-strand230-2312101
α-helix236-2438
Chain Lc: 3 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand7-126310
β-strand19-246310
β-strand271310
α-helix32-343
α-helix38-4710
β-strand67-748310
β-strand80-878310
α-helix96-983
Chain LC: 13 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix47-493
β-strand511117
α-helix54-6815
β-strand70-712118
α-helix721
α-helix84-9613
α-helix98-1003
α-helix102-11413
α-helix115-1195
β-strand133-1342119
α-helix136-1449
β-strand150-1534119
α-helix160-1623
α-helix166-1727
β-strand177-1793119
α-helix183-1875
β-strand197-2004119
α-helix208-22215
β-strand234-2352118
α-helix240-25314
Chain Ld: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix3-2119

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Uncharacterized protein YEL057CCCprotein233Saccharomyces cerevisiaeP39983 (AlphaFold model)
mRNACMRNA41Saccharomyces cerevisiae
Multiprotein-bridging factor 1CNprotein151Saccharomyces cerevisiaeO14467 (AlphaFold model)
tRNA P-site, stalledCPRNA76Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C 25S ribosomal RNA (RDN25-1)L1RNA3396Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C 5.8S ribosomal RNAL2, M2RNA158Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C 5S ribosomal RNAL3, M3RNA121Saccharomyces cerevisiae
60S ribosomal protein L6-BLAprotein176Saccharomyces cerevisiaeP05739 (AlphaFold model)
60S ribosomal protein L7-ALB, MBprotein244Saccharomyces cerevisiaeP05737 (AlphaFold model)
60S ribosomal protein L8-ALC, MCprotein256Saccharomyces cerevisiaeP17076
60S ribosomal protein L9-ALD, MDprotein191Saccharomyces cerevisiaeP05738
60S ribosomal protein L10LE, MEprotein221Saccharomyces cerevisiaeP41805

79 more molecules are not listed.

Sequence of entity 1 (CC), FASTA
>9F9S_1 Uncharacterized protein YEL057C (chains CC)
MANDGIQRNDNRKGFKTVQFSAYSKEIDVIMKKISFLERNITQQLDTLPHFPKTLPPNHK
DCVSRKHRARRGWSSQLKNLLGIYSKEEIFTLDNLAATLHDQVLKLQATLFPNAILKQVH
LDNANIENKRILKEITYKYLSNENCKEENKFGTFIVKRIFFGDLSLGVSVLINRIAFESA
TSSIMVVRSSFIESDFFYEDYLIFDCRAKRRKKLKRKILFISTTMNFNYQTKV
Sequence of entity 2 (CM), FASTA
>9F9S_2 mRNA (chains CM)
UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUAAACGACGAA
Sequence of entity 3 (CN), FASTA
>9F9S_3 Multiprotein-bridging factor 1 (chains CN)
MSDWDTNTIIGSRARAGGSGPRANVARSQGQINAARRQGLVVSVDKKYGSTNTRGDNEGQ
RLTKVDRETDIVKPKKLDPNVGRAISRARTDKKMSQKDLATKINEKPTVVNDYEAARAIP
NQQVLSKLERALGVKLRGNNIGSPLGAPKKK
Sequence of entity 4 (CP), FASTA
>9F9S_4 tRNA P-site, stalled (chains CP)
UUCCUCGUGGCCCAAUGGUCACGGCGUCUGGCUICGAACCAGAAGAUUCCAGGUUCAAGU
CCUGGCGGGGAAGCCA
Sequence of entity 5 (L1), FASTA
>9F9S_5 Saccharomyces cerevisiae S288C 25S ribosomal RNA (RDN25-1) (chains L1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 6 (L2, M2), FASTA
>9F9S_6 Saccharomyces cerevisiae S288C 5.8S ribosomal RNA (chains L2, M2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 7 (L3, M3), FASTA
>9F9S_7 Saccharomyces cerevisiae S288C 5S ribosomal RNA (chains L3, M3)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U
Sequence of entity 8 (LA), FASTA
>9F9S_8 60S ribosomal protein L6-B (chains LA)
MTAQQAPKWYPSEDVAAPKKTRKAVRPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLVTGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQTKEIKTERVEDQKVVDKALLAEIKKTPLLKQYLSASFSLKNGDKPHLLKF
Sequence of entity 9 (LB, MB), FASTA
>9F9S_9 60S ribosomal protein L7-A (chains LB, MB)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 10 (LC, MC), FASTA
>9F9S_10 60S ribosomal protein L8-A (chains LC, MC)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 11 (LD, MD), FASTA
>9F9S_11 60S ribosomal protein L9-A (chains LD, MD)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL
Sequence of entity 12 (LE, ME), FASTA
>9F9S_12 60S ribosomal protein L10 (chains LE, ME)
MARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQL
SSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWG
KPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPE
YLKKREAGEVKDDGAFVKFLSKKGSLENNIREFPEYFAAQA

Ligands and cofactors

IDNameFormulaCopies
SPDSpermidineC7 H19 N33
ZNZinc ionZn13
MGMagnesium ionMg295

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

Primary citation

Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes. Kim, K.Q., Li, J.J., Nanjaraj Urs, A.N. et al. Mol Cell (2024) 84:4594. DOI 10.1016/j.molcel.2024.10.029 · PubMed

Other PDB entries of the same protein (UniProt P39983 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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