8PPL: MERS-CoV Nsp1

Name: PDB 8PPL: MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
Published: 2023-10-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

MERS-CoV Nsp1 bound to the human 43S pre-initiation complex. Determined by electron microscopy at 2.65 Å resolution. Released 18 Oct 2023.

Method: Electron microscopy
Resolution: 2.65 Å
Organisms: Homo sapiens, Middle East respiratory syndrome-related coronavirus
Chains: 52
Atoms: 118,236
Mol. weight: 2078.2 kDa
Ligands: MET, MG, GTP, ZN
Released: 18 Oct 2023

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

Secondary structure: helices and β-sheets

8PPL contains 473 α-helices and 364 β-strands across 50 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 Aa: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	63
β-strand	29-31	3	63
β-strand	36-43	8	64
α-helix	47-56	10
β-strand	57	1	15
α-helix	62-65	4
β-strand	66-73	8	64
α-helix	75-80	6
α-helix	91-93	3
α-helix	97-99	3

Chain AA: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	61
α-helix	32-37	6
β-strand	38-41	4	61
α-helix	43-45	3
β-strand	47-49	3	61
α-helix	51-66	16
α-helix	71-73	3
β-strand	74-78	5	62
α-helix	81-83	3
α-helix	84-94	11
β-strand	97-100	4	62
α-helix	102-104	3
β-strand	121-124	4	62
α-helix	131-137	7
β-strand	144-148	5	62
β-strand	159-162	4	62
α-helix	168-186	19
α-helix	199-202	4
α-helix	207-216	10

Chain Ab: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	20-22	3
β-strand	32-36	5	50
β-strand	43-47	5	50
β-strand	55	1	67
β-strand	62	1	67
β-strand	64-65	2	68
β-strand	72-73	2	68
α-helix	74	1
β-strand	78-81	4	50
α-helix	82-83	2

Chain AB: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	65
β-strand	43-50	8	65
α-helix	51-52	2
α-helix	58-62	5
β-strand	66-70	5	65
α-helix	71-75	5
β-strand	82-91	10	65
β-strand	96-105	10	65
α-helix	107-113	7
β-strand	118	1	66
β-strand	120-128	9	65
β-strand	134-143	10	65
β-strand	154	1	66
α-helix	158-174	17
α-helix	181-188	8
α-helix	192-200	9
β-strand	207-219	13	65
α-helix	220-223	4
α-helix	225-232	8

Chain Ac: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	72
β-strand	27-34	8	72
β-strand	43-47	5	72
β-strand	55-58	4	72

Chain AC: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	78-83	6
α-helix	92-97	6
α-helix	99-101	3
β-strand	103-115	13	69
β-strand	120-131	12	69
β-strand	136-144	9	69
α-helix	147-160	14
β-strand	162-164	3	69
β-strand	168	1	70
β-strand	179	1	70
β-strand	184-188	5	71
β-strand	191-196	6	71
β-strand	204-205	2	71
α-helix	208-216	9
β-strand	222-227	6	71
α-helix	233-245	13
α-helix	246-249	4
α-helix	253-255	3
α-helix	258-259	2
α-helix	265-268	4
α-helix	270-275	6

Chain Ad: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	16-18	3
β-strand	30-31	2	76
α-helix	33-35	3
β-strand	38-39	2	76
α-helix	40-50	11
β-strand	53	1	44

Chain AD: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-40	7	14
β-strand	46-52	7	14
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	14
α-helix	94-96	3
α-helix	98-110	13
α-helix	115-128	14
β-strand	133-140	8	73
β-strand	148-155	8	73
α-helix	164-167	4
β-strand	168-176	9	73
β-strand	181-189	9	73
β-strand	209-210	2	74
α-helix	211-215	5
α-helix	217-219	3
β-strand	223-226	4	75

42 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
Eukaryotic translation initiation factor 3 subunit K	I3	protein	218	Homo sapiens	Q9UBQ5 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit F	I4	protein	357	Homo sapiens	O00303 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit L	I5	protein	564	Homo sapiens	Q9Y262 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit M	I6	protein	374	Homo sapiens	Q7L2H7 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit H	I8	protein	352	Homo sapiens	O15372
Eukaryotic translation initiation factor 3 subunit G	Io	protein	320	Homo sapiens	O75821
Eukaryotic translation initiation factor 1	Ip	protein	113	Homo sapiens	P41567
Eukaryotic translation initiation factor 1A, X-chromosomal	Iq	protein	144	Homo sapiens	P47813
Eukaryotic translation initiation factor 2 subunit 1	Ir	protein	315	Homo sapiens	P05198
Eukaryotic translation initiation factor 2 subunit 2	Is	protein	333	Homo sapiens	P20042
Eukaryotic translation initiation factor 2 subunit 3	It	protein	472	Homo sapiens	P41091
Eukaryotic translation initiation factor 3 subunit A	Iu	protein	1382	Homo sapiens	Q14152

40 more molecules are not listed.

Sequence of entity 1 (I3), FASTA

>8PPL_1 Eukaryotic translation initiation factor 3 subunit K (chains I3)
MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAF
FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA
LDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWS
ADESGQIFICSQEESIKPKNIVEKIDFDSVSSIMASSQ

Sequence of entity 2 (I4), FASTA

>8PPL_2 Eukaryotic translation initiation factor 3 subunit F (chains I4)
MATPAVPVSAPPATPTPVPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPG
QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTL
LGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDIT
EHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYA
YYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSA
DNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL

Sequence of entity 3 (I5), FASTA

>8PPL_3 Eukaryotic translation initiation factor 3 subunit L (chains I5)
MSYPADDYESEAAYDPYAYPSDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFH
KTVSDLIDQKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAP
QVGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPN
QWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNI
NRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELN
KKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMI
NKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKF
LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLD
LTEQEFRIQLLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYG
DFFIRQIHKFEELNRTLKKMGQRP

Sequence of entity 4 (I6), FASTA

>8PPL_4 Eukaryotic translation initiation factor 3 subunit M (chains I6)
MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDV
ESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVR
YTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDA
ASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDL
LTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQE
LQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQN
LNKVKNSLLSLSDT

Sequence of entity 5 (I8), FASTA

>8PPL_5 Eukaryotic translation initiation factor 3 subunit H (chains I8)
MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGT
EVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWY
QSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEK
DFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLG
KNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEED
LSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN

Sequence of entity 6 (Io), FASTA

>8PPL_6 Eukaryotic translation initiation factor 3 subunit G (chains Io)
MPTGDFDSKPSWADQVEEEGEDDKCVTSELLKGIPLATGDTSPEPELLPGAPLPPPKEVI
NGNIKTVTEYKIDEDGKKFKIVRTFRIETRKASKAVARRKNWKKFGNSEFDPPGPNVATT
TVSDDVSMTFITSKEDLNCQEEEDPMNKLKGQKIVSCRICKGDHWTTRCPYKDTLGPMQK
ELAEQLGLSTGEKEKLPGELEPVQATQNKTGKYVPPSLRDGASRRGESMQPNRRADDNAT
IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV
SGFGYDHLILNVEWAKPSTN

Sequence of entity 7 (Ip), FASTA

>8PPL_7 Eukaryotic translation initiation factor 1 (chains Ip)
MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLV
KAFKKKFACNGTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF

Sequence of entity 8 (Iq), FASTA

>8PPL_8 Eukaryotic translation initiation factor 1A, X-chromosomal (chains Iq)
MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCH
IRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDT
FGPGDDDEIQFDDIGDDDEDIDDI

Sequence of entity 9 (Ir), FASTA

>8PPL_9 Eukaryotic translation initiation factor 2 subunit 1 (chains Ir)
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN
KLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE
YTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNI
NRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTT
TLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEV
DGDDDAEEMEAKAED

Sequence of entity 10 (Is), FASTA

>8PPL_10 Eukaryotic translation initiation factor 2 subunit 2 (chains Is)
MSGDEMIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEED
TRKKDASDDLDDLNFFNQKKKKKKTKKIFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIM
LGNKKKKKKNVKFPDEDEILEKDEALEDEDNKKDDGISFSNQTGPAWAGSERDYTYEELL
NRVFNIMREKNPDMVAGEKRKFVMKPPQVVRVGTKKTSFVNFTDICKLLHRQPKHLLAFL
LAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLYFL
QCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN

Sequence of entity 11 (It), FASTA

>8PPL_11 Eukaryotic translation initiation factor 2 subunit 3 (chains It)
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKA
ISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGT
KGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIM
KLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIV
KKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGI
VSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGA
VGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAV
KADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD

Sequence of entity 12 (Iu), FASTA

>8PPL_12 Eukaryotic translation initiation factor 3 subunit A (chains Iu)
MPAYFQRPENALKRANEFLEVGKKQPALDVLYDVMKSKKHRTWQKIHEPIMLKYLELCVD
LRKSHLAKEGLYQYKNICQQVNIKSLEDVVRAYLKMAEEKTEAAKEESQQMVLDIEDLDN
IQTPESVLLSAVSGEDTQDRTDRLLLTPWVKFLWESYRQCLDLLRNNSRVERLYHDIAQQ
AFKFCLQYTRKAEFRKLCDNLRMHLSQIQRHHNQSTAINLNNPESQSMHLETRLVQLDSA
ISMELWQEAFKAVEDIHGLFSLSKKPPKPQLMANYYNKVSTVFWKSGNALFHASTLHRLY
HLSREMRKNLTQDEMQRMSTRVLLATLSIPITPERTDIARLLDMDGIIVEKQRRLATLLG
LQAPPTRIGLINDMVRFNVLQYVVPEVKDLYNWLEVEFNPLKLCERVTKVLNWVREQPEK
EPELQQYVPQLQNNTILRLLQQVSQIYQSIEFSRLTSLVPFVDAFQLERAIVDAARHCDL
QVRIDHTSRTLSFGSDLNYATREDAPIGPHLQSMPSEQIRNQLTAMSSVLAKALEVIKPA
HILQEKEEQHQLAVTAYLKNSRKEHQRILARRQTIEERKERLESLNIQREKEELEQREAE
LQKVRKAEEERLRQEAKEREKERILQEHEQIKKKTVRERLEQIKKTELGAKAFKDIDIED
LEELDPDFIMAKQVEQLEKEKKELQERLKNQEKKIDYFERAKRLEEIPLIKSAYEEQRIK
DMDLWEQQEEERITTMQLEREKALEHKNRMSRMLEDRDLFVMRLKAARQSVYEEKLKQFE
ERLAEERHNRLEERKRQRKEERRITYYREKEEEEQRRAEEQMLKEREERERAERAKREEE
LREYQERVKKLEEVERKKRQRELEIEERERRREEERRLGDSSLSRKDSRWGDRDSEGTWR
KGPEADSEWRRGPPEKEWRRGEGRDEDRSHRRDEERPRRLGDDEDREPSLRPDDDRVPRR
GMDDDRGPRRGPEEDRFSRRGADDDRPSWRNTDDDRPPRRIADEDRGNWRHADDDRPPRR
GLDEDRGSWRTADEDRGPRRGMDDDRGPRRGGADDERSSWRNADDDRGPRRGLDDDRGPR
RGMDDDRGPRRGMDDDRGPRRGMDDDRGPRRGLDDDRGPWRNADDDRIPRRGAEDDRGPW
RNMDDDRLSRRADDDRFPRRGDDSRPGPWRPLVKPGGWREKEKAREESWGPPRESRPSEE
REWDREKERDRDNQDREENDKDPERERDRERDVDREDRFRRPRDEGGWRRGPAEESSSWR
DSSRRDDRDRDDRRRERDDRRDLRERRDLRDDRDRRGPPLRSEREEVSSWRRADDRKDDR
VEERDPPRRVPPPALSRDRERDRDREREGEKEKASWRAEKDRESLRRTKNETDEDGWTTV
RR

Ligands and cofactors

ID	Name	Formula	Copies
MET	Methionine	C5 H11 N O2 S	1
MG	Magnesium ion	Mg	116
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
ZN	Zinc ion	Zn	4

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

Primary citation

Universal features of Nsp1-mediated translational shutdown by coronaviruses. Schubert, K., Karousis, E.D., Ban, I. et al. Mol Cell (2023) 83:3546-3557.e8. DOI 10.1016/j.molcel.2023.09.002 · PubMed

Other PDB entries of the same protein (UniProt Q9UBQ5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RZ4 2.1 Å, Crystal Structure of Human eIF3k
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
9KZU 3.0 Å, Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome…
8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
9KN5 3.2 Å, Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3
9KRP 3.2 Å, Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3
6YBD 3.3 Å, Structure of a human 48S translational initiation complex - eIF3

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