9KMT | pdb_00009kmt

Bat SARSr-CoV RaTG15 Nsp1 bound to the Human 40S Ribosomal subunit-State1

• PDB DOI: https://doi.org/10.2210/pdb9KMT/pdb
• NAKB: 9KMT
• EM Map EMD-62444: EMDB EMDataResource

• Classification: RIBOSOME
• Organism(s): Homo sapiens, SARS bat 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

Yan, R., Wu, M., Yuan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 35-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,232.13 kDa 
• Atom Count: 74,832 
• Modeled Residue Count: 6,576 
• Deposited Residue Count: 7,436 
• Unique protein chains: 35
• Unique nucleic acid chains: 1

Macromolecules

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 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 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
UniProt & NIH Common Fund Data Resources
Find proteins for P15880 (Homo sapiens) Explore P15880  Go to UniProtKB:  P15880
PHAROS:  P15880 GTEx:  ENSG00000140988

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
UniProt & NIH Common Fund Data Resources
Find proteins for P23396 (Homo sapiens) Explore P23396  Go to UniProtKB:  P23396
PHAROS:  P23396 GTEx:  ENSG00000149273

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
UniProt & NIH Common Fund Data Resources
Find proteins for P62701 (Homo sapiens) Explore P62701  Go to UniProtKB:  P62701
PHAROS:  P62701 GTEx:  ENSG00000198034

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
UniProt & NIH Common Fund Data Resources
Find proteins for P46782 (Homo sapiens) Explore P46782  Go to UniProtKB:  P46782
PHAROS:  P46782 GTEx:  ENSG00000083845

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
UniProt & NIH Common Fund Data Resources
Find proteins for P62753 (Homo sapiens) Explore P62753  Go to UniProtKB:  P62753
PHAROS:  P62753 GTEx:  ENSG00000137154

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
UniProt & NIH Common Fund Data Resources
Find proteins for P62081 (Homo sapiens) Explore P62081  Go to UniProtKB:  P62081
PHAROS:  P62081 GTEx:  ENSG00000171863

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
UniProt & NIH Common Fund Data Resources
Find proteins for P62241 (Homo sapiens) Explore P62241  Go to UniProtKB:  P62241
PHAROS:  P62241 GTEx:  ENSG00000142937

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
UniProt & NIH Common Fund Data Resources
Find proteins for P46781 (Homo sapiens) Explore P46781  Go to UniProtKB:  P46781
PHAROS:  P46781 GTEx:  ENSG00000170889

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
UniProt & NIH Common Fund Data Resources
Find proteins for P46783 (Homo sapiens) Explore P46783  Go to UniProtKB:  P46783
PHAROS:  P46783 GTEx:  ENSG00000124614

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
UniProt & NIH Common Fund Data Resources
Find proteins for P62280 (Homo sapiens) Explore P62280  Go to UniProtKB:  P62280
PHAROS:  P62280 GTEx:  ENSG00000142534

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 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
UniProt & NIH Common Fund Data Resources
Find proteins for P62277 (Homo sapiens) Explore P62277  Go to UniProtKB:  P62277
PHAROS:  P62277 GTEx:  ENSG00000110700

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 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 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 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 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 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 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 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 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 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 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 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

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

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

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 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 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

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

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 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 ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1ab polyprotein	JA [auth n]	180	SARS bat coronavirus	Mutation(s): 0  Gene Names: ORF1ab

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Yuan, S., Yan, R., Wu, M.

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

Revision History  

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