9KMZ | pdb_00009kmz

Bat MERSr-CoV NL140422 Nsp1 bound to the Human 40S Ribosomal subunit-State1

PDB DOI: https://doi.org/10.2210/pdb9KMZ/pdb
EM Map EMD-62450: EMDB EMDataResource
NAKB: 9KMZ

Classification: RIBOSOME
Organism(s): Homo sapiens, Middle East respiratory syndrome-related coronavirus
Expression System: Homo sapiens, Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-18 Released: 2025-11-26
Deposition Author(s): Yuan, S., Yan, R., Wu, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Strategic Variations in Sarbecovirus and Merbecovirus Nsp1 Linker Regions for Ribosomal Rotation Defense

Yan, R., Wu, M., Yuan, S.

To be published.

Macromolecule Content

Total Structure Weight: 1,234.22 kDa
Atom Count: 74,738
Modeled Residue Count: 6,566
Deposited Residue Count: 7,452
Unique protein chains: 35
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2	B [auth A]	295	Homo sapiens	Mutation(s): 0 Gene Names: RPSA, LAMBR, LAMR1
UniProt & NIH Common Fund Data Resources
Find proteins for P08865 (Homo sapiens) Explore P08865 Go to UniProtKB: P08865
PHAROS: P08865 GTEx: ENSG00000168028
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08865
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS1	C [auth B]	264	Homo sapiens	Mutation(s): 0 Gene Names: RPS3A, FTE1, MFTL
UniProt & NIH Common Fund Data Resources
Find proteins for P61247 (Homo sapiens) Explore P61247 Go to UniProtKB: P61247
GTEx: ENSG00000145425
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61247
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS5	D [auth C]	293	Homo sapiens	Mutation(s): 0 Gene Names: RPS2, RPS4
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Find proteins for P15880 (Homo sapiens) Explore P15880 Go to UniProtKB: P15880
PHAROS: P15880 GTEx: ENSG00000140988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15880
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3	E [auth D]	243	Homo sapiens	Mutation(s): 0 Gene Names: RPS3, OK/SW-cl.26 EC: 4.2.99.18
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Find proteins for P23396 (Homo sapiens) Explore P23396 Go to UniProtKB: P23396
PHAROS: P23396 GTEx: ENSG00000149273
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23396
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS4, X isoform	F [auth E]	263	Homo sapiens	Mutation(s): 0 Gene Names: RPS4X, CCG2, RPS4, SCAR
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Find proteins for P62701 (Homo sapiens) Explore P62701 Go to UniProtKB: P62701
PHAROS: P62701 GTEx: ENSG00000198034
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62701
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS7	G [auth F]	204	Homo sapiens	Mutation(s): 0 Gene Names: RPS5
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Find proteins for P46782 (Homo sapiens) Explore P46782 Go to UniProtKB: P46782
PHAROS: P46782 GTEx: ENSG00000083845
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46782
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS6	H [auth G]	249	Homo sapiens	Mutation(s): 1 Gene Names: RPS6, OK/SW-cl.2
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Find proteins for P62753 (Homo sapiens) Explore P62753 Go to UniProtKB: P62753
PHAROS: P62753 GTEx: ENSG00000137154
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62753
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS7	I [auth H]	194	Homo sapiens	Mutation(s): 0 Gene Names: RPS7
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Find proteins for P62081 (Homo sapiens) Explore P62081 Go to UniProtKB: P62081
PHAROS: P62081 GTEx: ENSG00000171863
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62081
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS8	J [auth I]	208	Homo sapiens	Mutation(s): 0 Gene Names: RPS8, OK/SW-cl.83
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Find proteins for P62241 (Homo sapiens) Explore P62241 Go to UniProtKB: P62241
PHAROS: P62241 GTEx: ENSG00000142937
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62241
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS4	K [auth J]	194	Homo sapiens	Mutation(s): 0 Gene Names: RPS9
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Find proteins for P46781 (Homo sapiens) Explore P46781 Go to UniProtKB: P46781
PHAROS: P46781 GTEx: ENSG00000170889
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46781
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS10	L [auth K]	165	Homo sapiens	Mutation(s): 0 Gene Names: RPS10
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Find proteins for P46783 (Homo sapiens) Explore P46783 Go to UniProtKB: P46783
PHAROS: P46783 GTEx: ENSG00000124614
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46783
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17	M [auth L]	158	Homo sapiens	Mutation(s): 0 Gene Names: RPS11
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Find proteins for P62280 (Homo sapiens) Explore P62280 Go to UniProtKB: P62280
PHAROS: P62280 GTEx: ENSG00000142534
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62280
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS12	N [auth M]	132	Homo sapiens	Mutation(s): 0 Gene Names: RPS12
UniProt & NIH Common Fund Data Resources
Find proteins for P25398 (Homo sapiens) Explore P25398 Go to UniProtKB: P25398
PHAROS: P25398 GTEx: ENSG00000112306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25398
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15	O [auth N]	151	Homo sapiens	Mutation(s): 0 Gene Names: RPS13
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Find proteins for P62277 (Homo sapiens) Explore P62277 Go to UniProtKB: P62277
PHAROS: P62277 GTEx: ENSG00000110700
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62277
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS11	P [auth O]	151	Homo sapiens	Mutation(s): 0 Gene Names: RPS14, PRO2640
UniProt & NIH Common Fund Data Resources
Find proteins for P62263 (Homo sapiens) Explore P62263 Go to UniProtKB: P62263
PHAROS: P62263 GTEx: ENSG00000164587
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62263
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS19	Q [auth P]	145	Homo sapiens	Mutation(s): 0 Gene Names: RPS15, RIG
UniProt & NIH Common Fund Data Resources
Find proteins for P62841 (Homo sapiens) Explore P62841 Go to UniProtKB: P62841
PHAROS: P62841 GTEx: ENSG00000115268
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62841
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS9	R [auth Q]	146	Homo sapiens	Mutation(s): 0 Gene Names: RPS16
UniProt & NIH Common Fund Data Resources
Find proteins for P62249 (Homo sapiens) Explore P62249 Go to UniProtKB: P62249
PHAROS: P62249 GTEx: ENSG00000105193
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62249
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS17	S [auth R]	135	Homo sapiens	Mutation(s): 0 Gene Names: RPS17, RPS17L
UniProt & NIH Common Fund Data Resources
Find proteins for P08708 (Homo sapiens) Explore P08708 Go to UniProtKB: P08708
PHAROS: P08708 GTEx: ENSG00000182774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08708
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS13	T [auth S]	152	Homo sapiens	Mutation(s): 0 Gene Names: RPS18, D6S218E
UniProt & NIH Common Fund Data Resources
Find proteins for P62269 (Homo sapiens) Explore P62269 Go to UniProtKB: P62269
PHAROS: P62269 GTEx: ENSG00000231500
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62269
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS19	U [auth T]	145	Homo sapiens	Mutation(s): 0 Gene Names: RPS19
UniProt & NIH Common Fund Data Resources
Find proteins for P39019 (Homo sapiens) Explore P39019 Go to UniProtKB: P39019
PHAROS: P39019 GTEx: ENSG00000105372
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39019
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS10	V [auth U]	119	Homo sapiens	Mutation(s): 0 Gene Names: RPS20
UniProt & NIH Common Fund Data Resources
Find proteins for P60866 (Homo sapiens) Explore P60866 Go to UniProtKB: P60866
PHAROS: P60866 GTEx: ENSG00000008988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60866
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS21	W [auth V]	83	Homo sapiens	Mutation(s): 0 Gene Names: RPS21
UniProt & NIH Common Fund Data Resources
Find proteins for P63220 (Homo sapiens) Explore P63220 Go to UniProtKB: P63220
PHAROS: P63220 GTEx: ENSG00000171858
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63220
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS8	X [auth W]	130	Homo sapiens	Mutation(s): 0 Gene Names: RPS15A, OK/SW-cl.82
UniProt & NIH Common Fund Data Resources
Find proteins for P62244 (Homo sapiens) Explore P62244 Go to UniProtKB: P62244
PHAROS: P62244 GTEx: ENSG00000134419
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62244
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS12	Y [auth X]	143	Homo sapiens	Mutation(s): 0 Gene Names: RPS23
UniProt & NIH Common Fund Data Resources
Find proteins for P62266 (Homo sapiens) Explore P62266 Go to UniProtKB: P62266
PHAROS: P62266 GTEx: ENSG00000186468
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62266
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS24	Z [auth Y]	130	Homo sapiens	Mutation(s): 0 Gene Names: RPS24
UniProt & NIH Common Fund Data Resources
Find proteins for P62847 (Homo sapiens) Explore P62847 Go to UniProtKB: P62847
PHAROS: P62847 GTEx: ENSG00000138326
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62847
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS25	AA [auth Z]	125	Homo sapiens	Mutation(s): 0 Gene Names: RPS25
UniProt & NIH Common Fund Data Resources
Find proteins for P62851 (Homo sapiens) Explore P62851 Go to UniProtKB: P62851
PHAROS: P62851 GTEx: ENSG00000118181
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62851
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS26	BA [auth a]	101	Homo sapiens	Mutation(s): 0 Gene Names: RPS26
UniProt & NIH Common Fund Data Resources
Find proteins for P62854 (Homo sapiens) Explore P62854 Go to UniProtKB: P62854
PHAROS: P62854 GTEx: ENSG00000197728
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62854
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS27	CA [auth b]	82	Homo sapiens	Mutation(s): 0 Gene Names: RPS27, MPS1
UniProt & NIH Common Fund Data Resources
Find proteins for P42677 (Homo sapiens) Explore P42677 Go to UniProtKB: P42677
PHAROS: P42677 GTEx: ENSG00000177954
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42677
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS28	DA [auth c]	62	Homo sapiens	Mutation(s): 0 Gene Names: RPS28
UniProt & NIH Common Fund Data Resources
Find proteins for P62857 (Homo sapiens) Explore P62857 Go to UniProtKB: P62857
PHAROS: P62857 GTEx: ENSG00000233927
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62857
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14	EA [auth d]	55	Homo sapiens	Mutation(s): 0 Gene Names: RPS29
UniProt & NIH Common Fund Data Resources
Find proteins for P62273 (Homo sapiens) Explore P62273 Go to UniProtKB: P62273
PHAROS: P62273 GTEx: ENSG00000213741
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62273
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS30	FA [auth e]	56	Homo sapiens	Mutation(s): 0 Gene Names: FAU
UniProt & NIH Common Fund Data Resources
Find proteins for P62861 (Homo sapiens) Explore P62861 Go to UniProtKB: P62861
PHAROS: P62861 GTEx: ENSG00000149806
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62861
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS31	GA [auth f]	74	Homo sapiens	Mutation(s): 0 Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979 Go to UniProtKB: P62979
PHAROS: P62979 GTEx: ENSG00000143947
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62979
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein RACK1	HA [auth g]	315	Homo sapiens	Mutation(s): 0 Gene Names: RACK1, GNB2L1, HLC7, PIG21
UniProt & NIH Common Fund Data Resources
Find proteins for P63244 (Homo sapiens) Explore P63244 Go to UniProtKB: P63244
PHAROS: P63244 GTEx: ENSG00000204628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63244
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS32	IA [auth h]	25	Homo sapiens	Mutation(s): 0 Gene Names: RPL41
UniProt & NIH Common Fund Data Resources
Find proteins for P62945 (Homo sapiens) Explore P62945 Go to UniProtKB: P62945
PHAROS: P62945 GTEx: ENSG00000229117
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62945
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1ab polyprotein	JA [auth n]	196	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: orf1ab
UniProt
Find proteins for A0A2R4KP83 (Middle East respiratory syndrome-related coronavirus) Explore A0A2R4KP83 Go to UniProtKB: A0A2R4KP83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2R4KP83
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
18S ribosomal RNA	A [auth 2]	1,869	Homo sapiens
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Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Yuan, S.

Yan, R.

Wu, M.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-11-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9KMZ | pdb_00009kmz

Bat MERSr-CoV NL140422 Nsp1 bound to the Human 40S Ribosomal subunit-State1

Literature

Strategic Variations in Sarbecovirus and Merbecovirus Nsp1 Linker Regions for Ribosomal Rotation Defense

Biological Assembly 1

Macromolecules

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

UniProt & NIH Common Fund Data Resources

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19

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Entity ID: 20

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