6ZP4: SARS-CoV-2 Nsp1

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2. Determined by electron microscopy at 2.9 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 54
Atoms: 117,784
Mol. weight: 2160.44 kDa
Ligands: MG, GTP, ZN
Released: 29 Jul 2020

Explore 6ZP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZP4 contains 449 α-helices and 457 β-strands across 52 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 4: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	176-183	8
α-helix	205-207	3
β-strand	209-211	3	120
β-strand	217-219	3	120
α-helix	223-228	6
α-helix	233-243	11
β-strand	248-250	3	120
β-strand	256-258	3	120
α-helix	264-278	15
β-strand	290-293	4	121
β-strand	298-301	4	121
β-strand	308-309	2	121
α-helix	311-313	3

Chain a: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	12-21	10
β-strand	25	1	1
α-helix	35-37	3
β-strand	38-41	4	1
α-helix	46	1
β-strand	47-49	3	1
α-helix	51-66	16
α-helix	71-73	3
β-strand	74-78	5	2
α-helix	84-94	11
β-strand	97-100	4	2
β-strand	121-124	4	2
α-helix	131-136	6
α-helix	137-139	3
β-strand	144-148	5	2
β-strand	159-162	4	2
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-202	4
α-helix	207-213	7

Chain A: 35 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	24-35	12
α-helix	47-60	14
α-helix	64-77	14
α-helix	84-115	32
α-helix	126-132	7
α-helix	137-145	9
α-helix	147-163	17
α-helix	171-187	17
α-helix	191-210	20
α-helix	217-219	3
α-helix	223-242	20
α-helix	246-262	17
α-helix	269-285	17
α-helix	289-302	14
α-helix	313-326	14
α-helix	337-340	4
α-helix	353-356	4
α-helix	364-365	2
α-helix	368-371	4
α-helix	373-376	4
α-helix	379-382	4
α-helix	390-395	6
α-helix	403-415	13
α-helix	428-446	19
β-strand	447-451	5	84
α-helix	452-458	7
α-helix	464-476	13
β-strand	482-485	4	84
β-strand	490-493	4	84
α-helix	500-502	3
α-helix	515-519	5
α-helix	522-537	16
α-helix	540-559	20
α-helix	564-599	36
α-helix	603-638	36
α-helix	643-684	42
α-helix	708-724	17

Chain b: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
α-helix	30-32	3
β-strand	34-41	8	102
β-strand	46-52	7	102
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-76	13
α-helix	79-80	2
β-strand	84-90	7	102
α-helix	94-96	3
α-helix	98-111	14
α-helix	115-128	14
β-strand	133-140	8	103
β-strand	148-155	8	103
α-helix	164-167	4
β-strand	168-176	9	103
β-strand	181-189	9	103
β-strand	209-210	2	100
α-helix	211-215	5
β-strand	223-226	4	42

Chain B: 10 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	188-189	2	64
α-helix	192-194	3
α-helix	200-211	12
β-strand	219-221	3	65
β-strand	224-225	2	66
β-strand	228-229	2	66
β-strand	233	1	64
β-strand	234-236	3	65
α-helix	242-248	7
β-strand	254	1	67
β-strand	260	1	67
β-strand	263-264	2	64
α-helix	290-293	4
α-helix	304-305	2
β-strand	306-308	3	68
β-strand	310	1	69
β-strand	317-319	3	68
β-strand	342	1	70
β-strand	349	1	70
α-helix	350	1
β-strand	357-361	5	70
β-strand	366-371	6	70
β-strand	378-381	4	71
β-strand	388-391	4	71
β-strand	404-407	4	71
β-strand	414-418	5	71
β-strand	430-431	2	72
β-strand	437-439	3	72
β-strand	449-450	2	72
β-strand	455-456	2	72
β-strand	470-472	3	73
β-strand	478-482	5	73
β-strand	493-497	5	73
β-strand	503-507	5	73
β-strand	516-519	4	74
β-strand	525-529	5	74
β-strand	542-548	7	74
β-strand	556-561	6	74
α-helix	564	1
β-strand	565-568	4	75
α-helix	570-571	2
β-strand	576-581	6	75
β-strand	587	1	76
β-strand	588-594	7	75
β-strand	600-604	5	75
β-strand	609-610	2	76
β-strand	613-614	2	77
β-strand	622-624	3	78
β-strand	625-626	2	77
β-strand	633-634	2	79
β-strand	637-639	3	78
β-strand	645	1	78
β-strand	650-651	2	79
β-strand	658-659	2	80
β-strand	666-667	2	80
β-strand	684	1	80
β-strand	699	1	69
β-strand	704	1	68
α-helix	714-720	7
α-helix	734-742	9

Chain c: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	22-35	14
α-helix	41-60	20
α-helix	68-84	17
α-helix	97-99	3
α-helix	102-106	5
β-strand	109	1	53
α-helix	110-116	7
α-helix	123-131	9
β-strand	135-137	3	54
β-strand	141	1	54
α-helix	147	1
β-strand	148	1	53
α-helix	149-150	2
β-strand	157-159	3	54
α-helix	172-176	5

Chain C: 37 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	52-72	21
α-helix	76-92	17
α-helix	97-99	3
α-helix	104-121	18
α-helix	137-148	12
α-helix	326-336	11
α-helix	347-360	14
α-helix	369-383	15
α-helix	392-394	3
α-helix	395-412	18
β-strand	419-421	3	86
β-strand	439-442	4	86
α-helix	445-458	14
α-helix	468-472	5
α-helix	473-475	3
α-helix	476-489	14
β-strand	490	1	87
β-strand	493	1	87
α-helix	500-507	8
α-helix	514-515	2
α-helix	545-557	13
α-helix	563-578	16
α-helix	583-592	10
α-helix	594-597	4
α-helix	598-600	3
α-helix	603-622	20
α-helix	626-632	7
α-helix	634-638	5
α-helix	662-666	5
α-helix	670-672	3
α-helix	673-675	3
α-helix	679-701	23
α-helix	712-722	11
α-helix	733-745	13
α-helix	750-756	7
α-helix	760-764	5
α-helix	766-768	3
α-helix	772-794	23
β-strand	799	1	84
β-strand	801-803	3	88
α-helix	804-811	8
α-helix	815-827	13
β-strand	833-835	3	88
β-strand	841-844	4	88
α-helix	851-877	27

Chain d: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-70	6
α-helix	79-83	5
α-helix	92-97	6
β-strand	102-115	14	12
β-strand	120-132	13	12
β-strand	136-144	9	12
α-helix	147-160	14
β-strand	163-164	2	12
β-strand	168	1	13
β-strand	179	1	13
β-strand	184-188	5	14
β-strand	191-197	7	14
β-strand	204-205	2	14
α-helix	208-216	9
β-strand	222-227	6	14
α-helix	233-244	12
α-helix	253-255	3
α-helix	258-259	2
α-helix	265-268	4

44 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
40S ribosomal protein SA	a	protein	295	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	p	protein	264	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S2	d	protein	293	Homo sapiens	P15880 (AlphaFold model)
40S ribosomal protein S26	Q	protein	115	Homo sapiens	P62854 (AlphaFold model)
40S ribosomal protein S4, X isoform	q	protein	263	Homo sapiens	P62701
60S ribosomal protein L41	W	protein	25	Homo sapiens	P62945
40S ribosomal protein S6	r	protein	249	Homo sapiens	P62753
40S ribosomal protein S7	s	protein	194	Homo sapiens	P62081
40S ribosomal protein S8	t	protein	208	Homo sapiens	P62241
40S ribosomal protein S9	c	protein	194	Homo sapiens	P46781
40S ribosomal protein S11	n	protein	158	Homo sapiens	P62280
40S ribosomal protein S13	m	protein	151	Homo sapiens	P62277

42 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>6ZP4_1 40S ribosomal protein SA (chains a)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 2 (p), FASTA

>6ZP4_2 40S ribosomal protein S3a (chains p)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 3 (d), FASTA

>6ZP4_3 40S ribosomal protein S2 (chains d)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 4 (Q), FASTA

>6ZP4_4 40S ribosomal protein S26 (chains Q)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 5 (q), FASTA

>6ZP4_5 40S ribosomal protein S4, X isoform (chains q)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 6 (W), FASTA

>6ZP4_6 60S ribosomal protein L41 (chains W)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 7 (r), FASTA

>6ZP4_7 40S ribosomal protein S6 (chains r)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 8 (s), FASTA

>6ZP4_8 40S ribosomal protein S7 (chains s)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 9 (t), FASTA

>6ZP4_9 40S ribosomal protein S8 (chains t)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 10 (c), FASTA

>6ZP4_10 40S ribosomal protein S9 (chains c)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 11 (n), FASTA

>6ZP4_11 40S ribosomal protein S11 (chains n)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 12 (m), FASTA

>6ZP4_12 40S ribosomal protein S13 (chains m)
MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGV
AQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIES
RIHRLARYYKTKRVLPPNWKYESSTASALVA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
ZN	Zinc ion	Zn	4

Primary citation

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Thoms, M., Buschauer, R., Ameismeier, M. et al. Science (2020) 369:1249-1255. DOI 10.1126/science.abc8665 · PubMed

Other PDB entries of the same protein (UniProt P08865 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
3BCH 2.15 Å, Crystal Structure of the Human Laminin Receptor Precursor
7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)
8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline

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