8XXM

Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G

PDB DOI: https://doi.org/10.2210/pdb8XXM/pdb
NAKB: 8XXM
EM Map EMD-38753: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-01-18 Released: 2024-05-01
Deposition Author(s): Ye, X., Huang, Z., Li, Y., Wang, M., Cheng, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.

Ye, X., Huang, Z., Li, Y., Wang, M., Meng, W., Miao, M., Cheng, J.

(2024) Cell Res 34: 522-525

PubMed: 38641729 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-024-00962-z
Primary Citation of Related Structures:
8XXL, 8XXM, 8XXN

Organizational Affiliation

Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 1,313.68 kDa
Atom Count: 76,934
Modelled Residue Count: 6,785
Deposited Residue Count: 8,159
Unique protein chains: 36
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L41	A [auth Ln]	25	Homo sapiens	Mutation(s): 0
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Find proteins for P62945 (Homo sapiens) Explore P62945 Go to UniProtKB: P62945
PHAROS: P62945 GTEx: ENSG00000229117
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62945
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein SA	C [auth SA]	295	Homo sapiens	Mutation(s): 0
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Find proteins for P08865 (Homo sapiens) Explore P08865 Go to UniProtKB: P08865
PHAROS: P08865 GTEx: ENSG00000168028
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UniProt Group	P08865
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3a	D [auth SB]	264	Homo sapiens	Mutation(s): 0
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Find proteins for P61247 (Homo sapiens) Explore P61247 Go to UniProtKB: P61247
GTEx: ENSG00000145425
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61247
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3	E [auth SD]	243	Homo sapiens	Mutation(s): 0 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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UniProt Group	P23396
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4, X isoform	F [auth SE]	263	Homo sapiens	Mutation(s): 0
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Find proteins for P62701 (Homo sapiens) Explore P62701 Go to UniProtKB: P62701
PHAROS: P62701 GTEx: ENSG00000198034
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UniProt Group	P62701
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	G [auth SF]	204	Homo sapiens	Mutation(s): 0
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Find proteins for P46782 (Homo sapiens) Explore P46782 Go to UniProtKB: P46782
PHAROS: P46782 GTEx: ENSG00000083845
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46782
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7	H [auth SH]	194	Homo sapiens	Mutation(s): 0
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Find proteins for P62081 (Homo sapiens) Explore P62081 Go to UniProtKB: P62081
PHAROS: P62081 GTEx: ENSG00000171863
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UniProt Group	P62081
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8	I [auth SI]	208	Homo sapiens	Mutation(s): 0
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Find proteins for P62241 (Homo sapiens) Explore P62241 Go to UniProtKB: P62241
PHAROS: P62241 GTEx: ENSG00000142937
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UniProt Group	P62241
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S10	J [auth SK]	165	Homo sapiens	Mutation(s): 0
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Find proteins for P46783 (Homo sapiens) Explore P46783 Go to UniProtKB: P46783
PHAROS: P46783 GTEx: ENSG00000124614
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UniProt Group	P46783
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11	K [auth SL]	158	Homo sapiens	Mutation(s): 0
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Find proteins for P62280 (Homo sapiens) Explore P62280 Go to UniProtKB: P62280
PHAROS: P62280 GTEx: ENSG00000142534
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62280
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15	L [auth SP]	145	Homo sapiens	Mutation(s): 0
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Find proteins for P62841 (Homo sapiens) Explore P62841 Go to UniProtKB: P62841
PHAROS: P62841 GTEx: ENSG00000115268
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UniProt Group	P62841
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16	M [auth SQ]	146	Homo sapiens	Mutation(s): 0
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Find proteins for P62249 (Homo sapiens) Explore P62249 Go to UniProtKB: P62249
PHAROS: P62249 GTEx: ENSG00000105193
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UniProt Group	P62249
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17	N [auth SR]	135	Homo sapiens	Mutation(s): 0
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Find proteins for P08708 (Homo sapiens) Explore P08708 Go to UniProtKB: P08708
PHAROS: P08708 GTEx: ENSG00000182774
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UniProt Group	P08708
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18	O [auth SS]	152	Homo sapiens	Mutation(s): 0
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Find proteins for P62269 (Homo sapiens) Explore P62269 Go to UniProtKB: P62269
PHAROS: P62269 GTEx: ENSG00000231500
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UniProt Group	P62269
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19	P [auth ST]	145	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P39019 (Homo sapiens) Explore P39019 Go to UniProtKB: P39019
PHAROS: P39019 GTEx: ENSG00000105372
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UniProt Group	P39019
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S20	Q [auth SU]	119	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60866 (Homo sapiens) Explore P60866 Go to UniProtKB: P60866
PHAROS: P60866 GTEx: ENSG00000008988
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UniProt Group	P60866
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21	R [auth SV]	83	Homo sapiens	Mutation(s): 0
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Find proteins for P63220 (Homo sapiens) Explore P63220 Go to UniProtKB: P63220
PHAROS: P63220 GTEx: ENSG00000171858
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UniProt Group	P63220
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23	S [auth SX]	143	Homo sapiens	Mutation(s): 0
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Find proteins for P62266 (Homo sapiens) Explore P62266 Go to UniProtKB: P62266
PHAROS: P62266 GTEx: ENSG00000186468
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UniProt Group	P62266
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S26	T [auth Sa]	115	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62854 (Homo sapiens) Explore P62854 Go to UniProtKB: P62854
PHAROS: P62854 GTEx: ENSG00000197728
Entity Groups
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UniProt Group	P62854
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28	U [auth Sc]	69	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62857 (Homo sapiens) Explore P62857 Go to UniProtKB: P62857
PHAROS: P62857 GTEx: ENSG00000233927
Entity Groups
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UniProt Group	P62857
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S29	V [auth Sd]	56	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62273 (Homo sapiens) Explore P62273 Go to UniProtKB: P62273
PHAROS: P62273 GTEx: ENSG00000213741
Entity Groups
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UniProt Group	P62273
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor of activated protein C kinase 1	W [auth Sg]	317	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63244
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	X [auth SC]	293	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15880 (Homo sapiens) Explore P15880 Go to UniProtKB: P15880
PHAROS: P15880 GTEx: ENSG00000140988
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UniProt Group	P15880
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6	Y [auth SG]	249	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62753 (Homo sapiens) Explore P62753 Go to UniProtKB: P62753
PHAROS: P62753 GTEx: ENSG00000137154
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UniProt Group	P62753
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9	Z [auth SJ]	194	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P46781 (Homo sapiens) Explore P46781 Go to UniProtKB: P46781
PHAROS: P46781 GTEx: ENSG00000170889
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UniProt Group	P46781
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S12	AA [auth SM]	132	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25398 (Homo sapiens) Explore P25398 Go to UniProtKB: P25398
PHAROS: P25398 GTEx: ENSG00000112306
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UniProt Group	P25398
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	BA [auth SN]	151	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62277 (Homo sapiens) Explore P62277 Go to UniProtKB: P62277
PHAROS: P62277 GTEx: ENSG00000110700
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UniProt Group	P62277
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14	CA [auth SO]	151	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62263 (Homo sapiens) Explore P62263 Go to UniProtKB: P62263
PHAROS: P62263 GTEx: ENSG00000164587
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UniProt Group	P62263
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15a	DA [auth SW]	130	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62244 (Homo sapiens) Explore P62244 Go to UniProtKB: P62244
PHAROS: P62244 GTEx: ENSG00000134419
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UniProt Group	P62244
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24	EA [auth SY]	133	Homo sapiens	Mutation(s): 0
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Find proteins for P62847 (Homo sapiens) Explore P62847 Go to UniProtKB: P62847
PHAROS: P62847 GTEx: ENSG00000138326
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UniProt Group	P62847
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25	FA [auth SZ]	125	Homo sapiens	Mutation(s): 0
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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UniProt Group	P62851
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27	GA [auth Sb]	84	Homo sapiens	Mutation(s): 0
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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UniProt Group	P42677
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S30	HA [auth Se]	59	Homo sapiens	Mutation(s): 0
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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UniProt Group	P62861
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S27a	IA [auth Sf]	156	Homo sapiens	Mutation(s): 0
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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UniProt Group	P62979
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 4	JA [auth CD]	469	Homo sapiens	Mutation(s): 0
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Find proteins for Q53EL6 (Homo sapiens) Explore Q53EL6 Go to UniProtKB: Q53EL6
PHAROS: Q53EL6 GTEx: ENSG00000150593
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UniProt Group	Q53EL6
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit G	KA [auth 3G]	320	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75821 (Homo sapiens) Explore O75821 Go to UniProtKB: O75821
PHAROS: O75821 GTEx: ENSG00000130811
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UniProt Group	O75821
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Entity ID: 2
Molecule	Chains	Length	Organism	Image
18S rRNA	B [auth S2]	1,869	Homo sapiens
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Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain HB [auth Sa] SDF format, chain IB [auth Sd] SDF format, chain KB [auth Sf] MOL2 format, chain HB [auth Sa] MOL2 format, chain IB [auth Sd] MOL2 format, chain KB [auth Sf] mmCIF format, chain HB [auth Sa] mmCIF format, chain IB [auth Sd] mmCIF format, chain KB [auth Sf]	HB [auth Sa], IB [auth Sd], KB [auth Sf]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HB [auth Sa] Focus chain IB [auth Sd] Focus chain KB [auth Sf] Interactions & Density Focus chain HB [auth Sa] Focus chain IB [auth Sd] Focus chain KB [auth Sf]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth S2] SDF format, chain BB [auth S2] SDF format, chain CB [auth S2] SDF format, chain DB [auth S2] SDF format, chain EB [auth S2] SDF format, chain FB [auth S2] SDF format, chain GB [auth S2] SDF format, chain JB [auth SG] SDF format, chain LA [auth S2] SDF format, chain MA [auth S2] SDF format, chain NA [auth S2] SDF format, chain OA [auth S2] SDF format, chain PA [auth S2] SDF format, chain QA [auth S2] SDF format, chain RA [auth S2] SDF format, chain SA [auth S2] SDF format, chain TA [auth S2] SDF format, chain UA [auth S2] SDF format, chain VA [auth S2] SDF format, chain WA [auth S2] SDF format, chain XA [auth S2] SDF format, chain YA [auth S2] SDF format, chain ZA [auth S2] MOL2 format, chain AB [auth S2] MOL2 format, chain BB [auth S2] MOL2 format, chain CB [auth S2] MOL2 format, chain DB [auth S2] MOL2 format, chain EB [auth S2] MOL2 format, chain FB [auth S2] MOL2 format, chain GB [auth S2] MOL2 format, chain JB [auth SG] MOL2 format, chain LA [auth S2] MOL2 format, chain MA [auth S2] MOL2 format, chain NA [auth S2] MOL2 format, chain OA [auth S2] MOL2 format, chain PA [auth S2] MOL2 format, chain QA [auth S2] MOL2 format, chain RA [auth S2] MOL2 format, chain SA [auth S2] MOL2 format, chain TA [auth S2] MOL2 format, chain UA [auth S2] MOL2 format, chain VA [auth S2] MOL2 format, chain WA [auth S2] MOL2 format, chain XA [auth S2] MOL2 format, chain YA [auth S2] MOL2 format, chain ZA [auth S2] mmCIF format, chain AB [auth S2] mmCIF format, chain BB [auth S2] mmCIF format, chain CB [auth S2] mmCIF format, chain DB [auth S2] mmCIF format, chain EB [auth S2] mmCIF format, chain FB [auth S2] mmCIF format, chain GB [auth S2] mmCIF format, chain JB [auth SG] mmCIF format, chain LA [auth S2] mmCIF format, chain MA [auth S2] mmCIF format, chain NA [auth S2] mmCIF format, chain OA [auth S2] mmCIF format, chain PA [auth S2] mmCIF format, chain QA [auth S2] mmCIF format, chain RA [auth S2] mmCIF format, chain SA [auth S2] mmCIF format, chain TA [auth S2] mmCIF format, chain UA [auth S2] mmCIF format, chain VA [auth S2] mmCIF format, chain WA [auth S2] mmCIF format, chain XA [auth S2] mmCIF format, chain YA [auth S2] mmCIF format, chain ZA [auth S2]	AB [auth S2] BB [auth S2] CB [auth S2] DB [auth S2] EB [auth S2] AB [auth S2], BB [auth S2], CB [auth S2], DB [auth S2], EB [auth S2], FB [auth S2], GB [auth S2], JB [auth SG], LA [auth S2], MA [auth S2], NA [auth S2], OA [auth S2], PA [auth S2], QA [auth S2], RA [auth S2], SA [auth S2], TA [auth S2], UA [auth S2], VA [auth S2], WA [auth S2], XA [auth S2], YA [auth S2], ZA [auth S2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth S2] Focus chain BB [auth S2] Focus chain CB [auth S2] Focus chain DB [auth S2] Focus chain EB [auth S2] Focus chain FB [auth S2] Focus chain GB [auth S2] Focus chain JB [auth SG] Focus chain LA [auth S2] Focus chain MA [auth S2] Focus chain NA [auth S2] Focus chain OA [auth S2] Focus chain PA [auth S2] Focus chain QA [auth S2] Focus chain RA [auth S2] Focus chain SA [auth S2] Focus chain TA [auth S2] Focus chain UA [auth S2] Focus chain VA [auth S2] Focus chain WA [auth S2] Focus chain XA [auth S2] Focus chain YA [auth S2] Focus chain ZA [auth S2] Interactions & Density Focus chain AB [auth S2] Focus chain BB [auth S2] Focus chain CB [auth S2] Focus chain DB [auth S2] Focus chain EB [auth S2] Focus chain FB [auth S2] Focus chain GB [auth S2] Focus chain JB [auth SG] Focus chain LA [auth S2] Focus chain MA [auth S2] Focus chain NA [auth S2] Focus chain OA [auth S2] Focus chain PA [auth S2] Focus chain QA [auth S2] Focus chain RA [auth S2] Focus chain SA [auth S2] Focus chain TA [auth S2] Focus chain UA [auth S2] Focus chain VA [auth S2] Focus chain WA [auth S2] Focus chain XA [auth S2] Focus chain YA [auth S2] Focus chain ZA [auth S2]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-05-01
Type: Initial release
Version 1.1: 2024-07-10
Changes: Data collection, Database references

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.

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Validate Data

Deposit Data

Help and Resources

8XXM

Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G

Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.

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