6ZON: SARS-CoV-2 Nsp1

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1. Determined by electron microscopy at 3.0 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 48
Atoms: 109,201
Mol. weight: 1894.02 kDa
Ligands: ZN
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6ZON contains 412 α-helices and 411 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 a: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	1
β-strand	38-41	4	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	81-83	3
α-helix	84-94	11
β-strand	97-100	4	2
β-strand	121-124	4	2
α-helix	131-137	7
β-strand	144-148	5	2
β-strand	159-162	4	2
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-201	3
α-helix	207-214	8

Chain A: 42 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
α-helix	24-36	13
α-helix	45-47	3
α-helix	49-61	13
α-helix	64-77	14
α-helix	84-114	31
α-helix	126-132	7
α-helix	137-141	5
α-helix	142-146	5
α-helix	147-163	17
α-helix	168-170	3
α-helix	171-188	18
α-helix	191-210	20
α-helix	218-219	2
α-helix	223-242	20
α-helix	246-262	17
α-helix	269-285	17
α-helix	289-305	17
α-helix	313-326	14
α-helix	337-342	6
α-helix	353-357	5
α-helix	367-376	10
α-helix	379-381	3
α-helix	390-391	2
α-helix	392-396	5
α-helix	400-406	7
α-helix	408-415	8
α-helix	422-424	3
α-helix	428-446	19
β-strand	447-451	5	95
α-helix	452-458	7
α-helix	464-476	13
β-strand	482-485	4	95
β-strand	490-493	4	95
α-helix	516-519	4
α-helix	522-537	16
α-helix	540-554	15
α-helix	556-560	5
α-helix	564-574	11
α-helix	575-579	5
α-helix	580-597	18
α-helix	603-634	32
α-helix	636-639	4
α-helix	643-682	40
α-helix	708-724	17

Chain b: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34	1	124
β-strand	41	1	125
β-strand	46	1	125
β-strand	52	1	124
α-helix	64-75	12
α-helix	79-80	2
β-strand	84	1	125
α-helix	94-96	3
α-helix	98-110	13
α-helix	115-129	15
β-strand	137-138	2	126
β-strand	150-151	2	126
α-helix	163-166	4
β-strand	171-172	2	127
β-strand	176	1	128
β-strand	181	1	128
β-strand	185-186	2	127
β-strand	209-210	2	120
α-helix	211-212	2
β-strand	223-226	4	62

Chain B: 8 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	189	1	77
α-helix	192-194	3
α-helix	200-210	11
β-strand	219-221	3	78
β-strand	224-225	2	79
β-strand	228-229	2	79
β-strand	233	1	77
β-strand	234-236	3	78
α-helix	240-248	9
β-strand	254	1	80
β-strand	260	1	80
α-helix	290-293	4
β-strand	306-310	5	81
β-strand	315-317	3	81
β-strand	342	1	82
β-strand	349	1	82
β-strand	350	1	83
β-strand	353	1	84
β-strand	356	1	84
β-strand	357-359	3	83
β-strand	369-371	3	83
β-strand	378-381	4	85
β-strand	388-391	4	85
β-strand	404-407	4	85
β-strand	414-418	5	85
β-strand	437-439	3	86
β-strand	448-450	3	86
β-strand	480-483	4	87
α-helix	490	1
β-strand	491-497	7	87
β-strand	502-509	8	87
β-strand	515-516	2	88
β-strand	519	1	89
β-strand	526	1	89
β-strand	527-530	4	88
β-strand	543-547	5	88
β-strand	556-560	5	88
β-strand	569-570	2	90
β-strand	577-581	5	90
β-strand	588-592	5	90
β-strand	613-614	2	91
β-strand	625-626	2	91
β-strand	635-636	2	91
β-strand	638	1	92
β-strand	645	1	92
β-strand	658-659	2	93
β-strand	665-667	3	93
β-strand	681-682	2	94
β-strand	684-685	2	93
β-strand	693-694	2	94
β-strand	702-704	3	81
α-helix	705-706	2
α-helix	715-720	6
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	94-99	6
α-helix	102-106	5
β-strand	109	1	67
α-helix	110-116	7
α-helix	123-131	9
β-strand	135-137	3	68
β-strand	141	1	68
β-strand	148	1	67
α-helix	149-150	2
α-helix	154-156	3
β-strand	157-159	3	68
α-helix	172-178	7

Chain C: 42 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	52-55	4
α-helix	57-61	5
α-helix	64-72	9
α-helix	77-81	5
α-helix	83-91	9
α-helix	92-94	3
α-helix	97-99	3
α-helix	104-120	17
α-helix	136-148	13
α-helix	326-333	8
α-helix	347-359	13
α-helix	368-383	16
α-helix	395-414	20
β-strand	419	1	96
β-strand	421	1	97
β-strand	439	1	96
β-strand	442	1	97
α-helix	444-459	16
α-helix	469-472	4
α-helix	473-475	3
α-helix	476-489	14
β-strand	490	1	98
β-strand	493	1	98
α-helix	496-508	13
α-helix	545-557	13
α-helix	563-578	16
α-helix	583-592	10
α-helix	594-597	4
α-helix	603-621	19
α-helix	626-632	7
α-helix	634-638	5
α-helix	642-645	4
α-helix	663-666	4
α-helix	670-672	3
α-helix	673-675	3
α-helix	679-688	10
α-helix	695-701	7
α-helix	712-720	9
α-helix	733-736	4
α-helix	738-746	9
α-helix	749-753	5
α-helix	760-764	5
α-helix	766-768	3
α-helix	772-795	24
α-helix	796-798	3
β-strand	801-803	3	95
α-helix	804-810	7
α-helix	815-827	13
β-strand	833-834	2	95
β-strand	835	1	99
β-strand	841-844	4	95
α-helix	851-877	27

Chain d: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	65-70	6
α-helix	79-82	4
α-helix	92-97	6
β-strand	102-116	15	14
β-strand	119-132	14	14
β-strand	136-137	2	15
β-strand	138-144	7	14
α-helix	147-159	13
β-strand	163-164	2	15
β-strand	168	1	16
β-strand	179	1	16
β-strand	184-188	5	17
β-strand	191-196	6	17
β-strand	204-205	2	17
α-helix	208-217	10
β-strand	222-227	6	17
α-helix	233-245	13
α-helix	246-248	3
α-helix	258-259	2
α-helix	265-268	4

Chain D: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	55-58	4
β-strand	81-82	2	113
α-helix	83	1
β-strand	173-175	3	117
α-helix	176-179	4
α-helix	189-190	2
β-strand	191-197	7	117
β-strand	198-199	2	118
β-strand	201-202	2	119
α-helix	205-208	4
β-strand	216	1	119
α-helix	235-239	5
β-strand	245-248	4	117
α-helix	249-255	7
β-strand	265-272	8	117
β-strand	275-279	5	117
α-helix	312-326	15
β-strand	328-329	2	119
β-strand	335-336	2	118
β-strand	339	1	117
β-strand	357-364	8	117
β-strand	370-374	5	117
β-strand	379-381	3	119
β-strand	390-398	9	119
α-helix	420-423	4
α-helix	433-442	10
β-strand	446-454	9	119
β-strand	463-465	3	119
β-strand	471	1	119
α-helix	484-497	14
β-strand	504-510	7	117
β-strand	516-520	5	117
α-helix	522-523	2

39 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

36 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>6ZON_1 40S ribosomal protein SA (chains a)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 2 (p), FASTA

>6ZON_2 40S ribosomal protein S3a (chains p)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 3 (d), FASTA

>6ZON_3 40S ribosomal protein S2 (chains d)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 4 (Q), FASTA

>6ZON_4 40S ribosomal protein S26 (chains Q)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 5 (q), FASTA

>6ZON_5 40S ribosomal protein S4, X isoform (chains q)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 6 (W), FASTA

>6ZON_6 60S ribosomal protein L41 (chains W)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 7 (r), FASTA

>6ZON_7 40S ribosomal protein S6 (chains r)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 8 (s), FASTA

>6ZON_8 40S ribosomal protein S7 (chains s)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 9 (t), FASTA

>6ZON_9 40S ribosomal protein S8 (chains t)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 10 (c), FASTA

>6ZON_10 40S ribosomal protein S9 (chains c)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 11 (n), FASTA

>6ZON_11 40S ribosomal protein S11 (chains n)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 12 (m), FASTA

>6ZON_12 40S ribosomal protein S13 (chains m)
MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGV
AQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIES
RIHRLARYYKTKRVLPPNWKYESSTASALVA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

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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