9I78: PDB entry 9I78

Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon. Determined by electron microscopy at 2.2 Å resolution. Released 12 Nov 2025.

Method
Electron microscopy
Resolution
2.2 Å
Organism
Thermochaetoides thermophila DSM 1495
Chains
50
Atoms
133,840
Mol. weight
2121.45 kDa
Ligands
MG
Released
12 Nov 2025

Explore 9I78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I78 contains 412 α-helices and 323 β-strands across 47 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 1: 22 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix11-166
β-strand18-2031
α-helix21-233
α-helix29-4820
β-strand5012
β-strand7612
α-helix77-793
α-helix83-9816
α-helix108-13629
β-strand13813
β-strand14013
α-helix142-1454
α-helix147-17024
α-helix171-1755
α-helix180-19819
β-strand202-20434
β-strand209-21134
α-helix214-22411
α-helix228-23710
α-helix244-26118
β-strand264-27185
β-strand278-28475
α-helix291-31424
α-helix318-3236
β-strand325-32846
β-strand335-33956
α-helix341-3455
α-helix347-3482
α-helix351-3544
α-helix358-38225
α-helix387-39711
β-strand399-40025
α-helix406-43833
α-helix444-46320
Chain 2: 4 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand29115
α-helix38-403
α-helix44-5815
α-helix68-714
β-strand91-9331
α-helix95-12127
Chain 3: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix7-2519
β-strand2715
α-helix28-292
α-helix31-6636
Chain 4: 20 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix77-11640
β-strand119-120221
α-helix135-14814
α-helix149-1524
β-strand154-157421
β-strand160-166721
β-strand168121
β-strand171-179921
α-helix186-19813
β-strand208-215821
α-helix220-2234
α-helix225-2262
α-helix230-2345
α-helix238-2392
β-strand247-251521
α-helix252-2543
α-helix255-2617
α-helix264-2674
β-strand269-271321
β-strand280-284521
α-helix287-2937
α-helix296-30510
α-helix306-3083
β-strand309-315721
α-helix321-3222
β-strand333-339721
α-helix340-3412
α-helix350-3578
α-helix359-3668
α-helix371-41747
α-helix421-44323
Chain 6: 14 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix5-1915
α-helix28-5932
β-strand64-69623
α-helix70-712
β-strand80-85623
α-helix86-10924
α-helix110-1145
α-helix121-1244
α-helix127-1348
α-helix1371
α-helix138-1436
α-helix149-1513
α-helix155-1573
α-helix161-1666
α-helix168-1703
β-strand171123
α-helix174-1818
Chain 7: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix176-19924
α-helix201-2033
Chain La: 8 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix3-53
α-helix7-104
α-helix42-476
α-helix65-684
β-strand72-74324
α-helix79-813
α-helix84-929
β-strand98-103625
α-helix104-1074
β-strand111-113324
β-strand124-127425
β-strand129-130224
α-helix132-14110
β-strand144-147425
Chain LA: 11 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix3-53
α-helix6-105
α-helix14-163
α-helix18-192
α-helix34-385
β-strand40-491026
β-strand58-64726
β-strand71-77726
α-helix781
β-strand79127
β-strand83128
β-strand87-91526
β-strand101-103326
α-helix104-1063
β-strand112-114326
β-strand116129
β-strand126129
β-strand134-140726
β-strand145-149526
β-strand155-159526
β-strand163-166426
β-strand169127
α-helix174-1763
α-helix182-1909
α-helix201-2033
β-strand224-225230
α-helix229-2302
β-strand237-238230

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Translocon Sec61/SecY plug domain-containing protein1protein476Thermochaetoides thermophila DSM 1495G0SHC8 (AlphaFold model)
SEC61 beta subunit2protein124Thermochaetoides thermophila DSM 1495
SEC61 gamma subunit3protein70Thermochaetoides thermophila DSM 1495G0SFD9 (AlphaFold model)
CCDC474protein455Thermochaetoides thermophila DSM 1495G0S5M5 (AlphaFold model)
Putative inorganic phosphate transporter protein6protein224Thermochaetoides thermophila DSM 1495G0RYQ7 (AlphaFold model)
Translocon-associated protein subunit alpha7protein278Thermochaetoides thermophila DSM 1495G0SGC8
60S ribosomal protein L2-like proteinLAprotein254Thermochaetoides thermophila DSM 1495G0S4P8
60S ribosomal protein L3-like proteinLBprotein392Thermochaetoides thermophila DSM 1495G0RXW1
60S ribosomal protein L4-like proteinLCprotein365Thermochaetoides thermophila DSM 1495G0SFC3
60S ribosomal protein l5-like proteinLDprotein304Thermochaetoides thermophila DSM 1495G0SEG2
60S ribosomal protein L6LEprotein200Thermochaetoides thermophila DSM 1495G0S0D6
60S ribosomal protein l7-like proteinLFprotein249Thermochaetoides thermophila DSM 1495G0SFL0

38 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>9I78_1 Translocon Sec61/SecY plug domain-containing protein (chains 1)
MSSLRFLDLVKPFVPFLPEVQQPESKIPFNQKLMWTGLTLLIFLVMSQMPLYGIVSSDSS
DPLYWLRMMMASNRGTLMELGITPIISSGMVFQLLAGTHMIDVNLDLKSDRELYQSAQKL
FALILSVGTATVYVFTGLYGPPSELGAGIVFLLILQLVLAGMIVILLDELLQKGYGLGSG
ISLFIATNICESIMWKAFSPTSINTGRGPEYEGAVIALFHLLMTWPNKQRALQEAFYRQN
LPNIMNLLATIVVFAAVIYLQGFRVEIPVKSSRQRGARGSYPVRLFYTSNMPIMLQSTLS
SNIFLISQMLYSRFSDNLLVRLFGVWEAKDGSSQLSAVSGLVYYMSPPLNFKEALLDPIH
TFVYIAYMLTACAIFSKTWIEVSGSSPRDVAKQLKDQGLVMAGHRDQSMYKELKRVIPTA
AAFGGACIGALSVASDLMGALGSGTGTLLAVTIIYGYFEIAAKEGDLAGMKGMIMG
Sequence of entity 2 (2), FASTA
>9I78_2 SEC61 beta subunit (chains 2)
MASPRATSPAPAGEKGSATGASTSASPGVLGGPRGSSPPPPGGARTAIRRRAAADQKERL
ANQRPNSTRAAGAGGSSNTMLKLYTDESPGLKVDPVVVLVLSLVFIFSVVALHVIAKITR
KFSS
Sequence of entity 3 (3), FASTA
>9I78_3 SEC61 gamma subunit (chains 3)
MADQIQELLDVPREFLKDGIQFINRAQKPDRREFIKISQAVGVGFLIMGAVGYFVKLIHV
PLNNILVGGA
Sequence of entity 4 (4), FASTA
>9I78_4 CCDC47 (chains 4)
MANVLNNLFGGGKPSVSPDPLVAGDDFADFSQAAEPSPVTVQPLATTPSAVPLQPARPYT
DYKDDDDKKWYRLHERYTWSDFKSEGIILCIISVFIILHVIGASLNRRKAKKWIRAHAAP
LAAEFAVVGYSGIPKNVSDKKGEELVKALQDSNIAQGDNLIKERSLFEFATYATGRANVA
FLEVKIALTKRFNPLTAFFESVLGFFFESGPEVGDRVEATLYPFDGKEADVVPDFPGAAE
LRSKDPKSTYDNFVWAIVHKECMKKARNDRYDLSLTYTKDHAKLPNWLAVMSESAEITDA
LLTPELIKAAEAAGDLFEYLVVTDQPEDKPKTLNETRPRKRVILKYRVPSNDDYTSLLPI
FEYFLRMPDHLVQVAHFRPEVLRKVKVVRDEEIRKIQKAEEESKAEERAQEREKAKKAKR
DQELSQLDAKAQKKYLEREREKELKRSMKKATIRA
Sequence of entity 5 (6), FASTA
>9I78_5 Putative inorganic phosphate transporter protein (chains 6)
MALSPQITNLIIIFGMMQVSKKIPFDDPNVLNMCRAAYLASNLIILCISLYIKSVVDKKK
DMTTLKYIEPAPPGSSEEGKLVTTTVHAYDVEQVKILIKSQLFGIGMMAFMHLYLKYTNP
LLIQSIIPLKGALESNMAKIHLWGMPATGDLKRPFKQPGGLLGGLFGQSVQADKKAVEAA
ERAGRGGVKEEGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK
Sequence of entity 6 (7), FASTA
>9I78_6 Translocon-associated protein subunit alpha (chains 7)
MVNFKWSALALLALRVAAVFAQEESADAEPGVLKEVSPDELKVSIDTTFPDADIFGVKLV
NGRPTKAIIEITNHEEVPVDVAFIGGILKTTKPLPEDAPHYASIVRNLTAVRYGVQVPAG
EKHQLPYQFVLDMMPQDVNLVLSAVITNAAAGKIYEVEAHSGPASIVDPPTSIFDPQIIF
LYLFLTAFFSGIAYWVYKTWLEQFFPQAKPSRAAGPAKGKKARRAGGATSDAEPVSGSES
AGGNTSGAGEKEYDESWIPAHHINRPVARKVKGGSKSK
Sequence of entity 7 (LA), FASTA
>9I78_7 60S ribosomal protein L2-like protein (chains LA)
MGRVIRNQRKGRGSVFTAHTRLRKAPAKFRPLDYAERHGYIRGIVKEIIHDPGRGAPLAR
VVFRSPYKYKQITETFIANEGMYTGQFIYAGKNAALTVGNILPLSSVPEGTVVSNVEEKP
GDRGALGRTSGNYVTVVGHNPDEGKTRIKLPSGAKKVVPSSSRGMIGIVAGGGRTDKPLL
KASRAKHKFAVKRNRWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRYAAQGQKAGLIAA
RRTGLLRGTQKTKE
Sequence of entity 8 (LB), FASTA
>9I78_8 60S ribosomal protein L3-like protein (chains LB)
MSHRKYEAPRHGSLAFLPRKRAARHRGRVKSFPKDDPKKPVHLTAAMGYKAGMTTIVRDL
DRPGAKAHKKEVVEAVTIIDCPPMVVVGLVGYIETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYAKKYAENNGASITRELERIKKYCTVVRVLAHTQIRKTPLKQKKAHLM
EIQINGGSVADKVEFGRSLFEKPVTIDTIFEKDEMIDVIAVTKGHGFVGVTARWGTKKLP
RKTHKGLRKVACIGAWHPSHVQWTVARAGQMGYHHRTSVNHKIYRIGKGDDEANASTETD
LTKKKITPMGGFVRYGEVNNDYVMIKGSVPGVKKRIMTLRKSLFTHTSRKALEKVELKWI
DTSSEFGHGAFQTAAEKKQFMGTLKKDLQTSA
Sequence of entity 9 (LC), FASTA
>9I78_9 60S ribosomal protein L4-like protein (chains LC)
MASRPTVTVFGADGKPTGATEVLPKVFSAPIRPDIVKHVHTGMAKNKRQPYAVSEKAGHQ
TSAESWGTGRAVARIPRVSGGGTHRAGQGAFGNMCRSGRMFAPTKIWRKWHVKINQGQKR
FATASALAASAVAPLLMARGHQVSTVPEVPLVVDSAAVAGDAVAKTAAAYKLLKAIGAGP
DVEKVKKSKKLRAGKGKMRGRRHRQRRGPLIVYSPEHDGKELVKGFRNIPGVETCPVDAL
NLLQLAPGGHLGRFIVWTSAAIKQLDAVYESKKGFFLPANIVSQADLSRLINSTEIQSVL
RAPKGEARTKRACVQKKNPLRNKQIMLRLNPYASTFAKEKLGEVKAEEGKPPKVPASFKE
LLHEA
Sequence of entity 10 (LD), FASTA
>9I78_10 60S ribosomal protein l5-like protein (chains LD)
MAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAKNKYNAPKYRLVVRFTNRDI
ITQMVTSEINGDKIFAAAYSHELRAYGINHGLTNWAAAYATGLLLARRVLAKLGLDKTFT
GVEEPNGEYTLTEAAETEDGERRPFKAILDVGLARTSTGARVFGVMKGASDGGIFIPHSE
NRFPGYDIETEELDTEVLKKYIYGGHVAEYMETLADDDEERYKSQFVKYIEDDVEADSLE
ELYAEAHKQIRADPFRKYVSDAPKKSKEEWKAESLKYKKAKLSREERKARVEAKIKQLLA
EQDE
Sequence of entity 11 (LE), FASTA
>9I78_11 60S ribosomal protein L6 (chains LE)
MSAAPTTKTFGKGTRTVPAPSEKAQKWYPAEDEAQPKKVRKAVRPWTPRKSLQPGTVLIL
LAGRFRGKRVVLLKCLDQGVLLVTGPFKINGVPLRRVNARYVIATSVKVDLTGVDQAKID
EVAQPKYFTAEKAKEKASEEAFFKQGEKPQKKPVSSTRAADQKAIDKALIANIKKVDMLA
SYLASSFSLRKGDKPHLMKF
Sequence of entity 12 (LF), FASTA
>9I78_12 60S ribosomal protein l7-like protein (chains LF)
MSSTTVPTQNDILVPETLLKKRKSQEKARAERAAALEKRKQANKEKRQVIFKRAEKYVKE
YREQEREKIRLARIAKQQGSFHIPAEAKLVFVIRIKGINKIPPKPRKILQLLRLRQINNG
VFVKVTKATAEMIKIVEPWVAYGYPNLKSVRELIYKRGYGKVNGQRIPLTDNAIIEENLG
KYGIICIEDLIHEIFTVGPNFKQAANFLWPFKLSNPNGGFRPRKFKHFIEGGDLGNREEH
INALIRAMN

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg379

Primary citation

SND3 is the membrane insertase within a distinct SEC61 translocon complex. Yang, T.J., Mukherjee, S., Langer, J.D. et al. Nat Commun (2025) 16:9566-9566. DOI 10.1038/s41467-025-65357-z · PubMed

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