9J9H | pdb_00009j9h

High-resolution cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to RACK1 and E-tRNA

PDB DOI: https://doi.org/10.2210/pdb9J9H/pdb
NAKB: 9J9H
EM Map EMD-61272: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Plasmodium falciparum 3D7
Mutation(s): No

Deposited: 2024-08-22 Released: 2025-06-04
Deposition Author(s): Yan, X.F., Gao, Y.G.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Antimalarial drug artemisinin stabilizes PfRACK1 binding to the ribosome.

Go, K.D., Yan, X.F., Wirjanata, G., Ero, R., Pazicky, S., Dziekan, J., Tjia, S., Lescar, J., Bozdech, Z., Gao, Y.G.

(2025) Structure 33: 1386

PubMed: 40480224 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2025.05.008
Primary Citation Related Structures:
9J9H, 9J9I

PubMed Abstract:
Artemisinin and its derivatives represent the core agents in artemisinin combination therapies that are the current frontline treatment for P. falciparum and P. vivax malaria infections. Artemisinins are known to bind a wide array of proteins that disrupt the parasite's cellular physiology. Here, we show that artemisinins' cytotoxic activity involves structural alteration of key P. falciparum macromolecular complexes, including the ribosome, proteasome, and T-complex. The structural analysis revealed that, following artemisinin treatment, a larger population of Pf80S ribosomes binds PfRACK1. Unlike in most eukaryotes, PfRACK1 does not interact with the C-terminal tail of the r-protein uS3 that in Plasmodium is truncated. This likely suggests an evolved role of uS3 in facilitating RACK1-mediated translational regulation, which would potentially benefit the parasite under certain conditions. Stabilization of RACK1 ribosome interaction likely contributes to artemisinins' mode of action.

Organizational Affiliation

School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.

Macromolecule Content

Total Structure Weight: 3,452.22 kDa
Atom Count: 200,146
Modeled Residue Count: 16,273
Deposited Residue Count: 18,783
Unique protein chains: 75
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24, putative	B [auth 0]	162	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6	C [auth q]	306	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27	F [auth 1]	146	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5, putative	G [auth r]	195	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor for activated c kinase	H [auth AR]	323	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for Q8IBA0 (Plasmodium falciparum (isolate 3D7)) Explore Q8IBA0 Go to UniProtKB: Q8IBA0
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UniProt Group	Q8IBA0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	J [auth 2]	127	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7	K [auth s]	194	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2	L [auth D]	260	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35, putative	M [auth 3]	124	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15A, putative	N [auth t]	130	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	O [auth E]	386	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	P [auth 4]	67	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for C6S3J6 (Plasmodium falciparum (isolate 3D7)) Explore C6S3J6 Go to UniProtKB: C6S3J6
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UniProt Group	C6S3J6
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8	Q [auth u]	218	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4	R [auth F]	411	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7, putative	S [auth 5]	257	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16, putative	T [auth v]	144	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11a, putative	U [auth G]	173	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30e, putative	V [auth 6]	108	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S20e, putative	W [auth w]	118	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6, putative	X [auth H]	190	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31	Y [auth 7]	120	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S10, putative	Z [auth x]	137	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6, putative	AA [auth I]	221	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for A0A5K1K8V8 (Plasmodium falciparum (isolate 3D7)) Explore A0A5K1K8V8 Go to UniProtKB: A0A5K1K8V8
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UniProt Group	A0A5K1K8V8
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	BA [auth 8]	131	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11	CA [auth y]	151	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for A0A5K1K925 (Plasmodium falciparum (isolate 3D7)) Explore A0A5K1K925 Go to UniProtKB: A0A5K1K925
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UniProt Group	A0A5K1K925
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7a	DA [auth J]	283	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35ae, putative	EA [auth 9]	140	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23, putative	FA [auth z]	145	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13, putative	GA [auth K]	202	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34	HA [auth a]	150	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS12	IA [auth AA]	141	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for O97249 (Plasmodium falciparum (isolate 3D7)) Explore O97249 Go to UniProtKB: O97249
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UniProt Group	O97249
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13	JA [auth L]	215	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36	KA [auth b]	112	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18, putative	LA [auth AB]	156	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23, putative	MA [auth M]	139	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L37	NA [auth c]	92	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S29, putative	OA [auth AC]	54	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14, putative	PA [auth N]	165	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	QA [auth d]	87	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15	RA [auth AD]	151	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27a, putative	SA [auth O]	148	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	TA [auth e]	51	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11, putative	UA [auth AE]	161	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L15	VA [auth P]	205	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-60S ribosomal protein L40	WA [auth f]	128	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17, putative	XA [auth AF]	137	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10, putative	YA [auth Q]	219	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L41	ZA [auth g]	39	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7)) Explore C6S3G4 Go to UniProtKB: C6S3G4
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UniProt Group	C6S3G4
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19	AB [auth AG]	145	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5, putative	BB [auth R]	294	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL43	CB [auth h]	96	Plasmodium falciparum 3D7	Mutation(s): 0
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Find proteins for O96184 (Plasmodium falciparum (isolate 3D7)) Explore O96184 Go to UniProtKB: O96184
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UniProt Group	O96184
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19	DB [auth AH]	170	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18-2, putative	EB [auth S]	187	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL42	FB [auth i]	104	Plasmodium falciparum 3D7	Mutation(s): 0
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Find proteins for O97231 (Plasmodium falciparum (isolate 3D7)) Explore O97231 Go to UniProtKB: O97231
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UniProt Group	O97231
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21	GB [auth AI]	82	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19	HB [auth T]	182	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24	JB [auth AJ]	133	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18a	KB [auth U]	184	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS1	LB [auth k]	262	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for O97313 (Plasmodium falciparum (isolate 3D7)) Explore O97313 Go to UniProtKB: O97313
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UniProt Group	O97313
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25	MB [auth AK]	105	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21	NB [auth V]	161	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2	OB [auth l]	263	Plasmodium falciparum 3D7	Mutation(s): 0
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Find proteins for Q8IJD4 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJD4 Go to UniProtKB: Q8IJD4
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UniProt Group	Q8IJD4
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S26	PB [auth AL]	107	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17, putative	QB [auth W]	203	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3	RB [auth m]	221	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27	SB [auth AM]	82	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL22	TB [auth X]	139	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9, putative	UB [auth n]	189	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28e, putative	VB [auth AN]	67	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23	WB [auth Y]	190	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4	XB [auth o]	261	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS30	YB [auth AO]	58	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for O96269 (Plasmodium falciparum (isolate 3D7)) Explore O96269 Go to UniProtKB: O96269
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UniProt Group	O96269
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Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26, putative	ZB [auth Z]	126	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	AC [auth p]	272	Plasmodium falciparum 3D7	Mutation(s): 0
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Entity ID: 80
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S27a, putative	BC [auth AP]	149	Plasmodium falciparum 3D7	Mutation(s): 0
UniProt
Find proteins for Q8IM64 (Plasmodium falciparum (isolate 3D7)) Explore Q8IM64 Go to UniProtKB: Q8IM64
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UniProt Group	Q8IM64
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