11HV | pdb_000011hv

Rabbit 60S ribosomal subunit with eEF2 domain IV open

PDB DOI: https://doi.org/10.2210/pdb11HV/pdb
EM Map EMD-75704: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2026-02-25 Released: 2026-09-02
Deposition Author(s): Seraj, Z., Zottig, X., Huang, C.H., Loveland, A.B., Diggs, S., Sholi, E., Grigorieff, N., Korostelev, A.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles

Seraj, Z., Zottig, X., Huang, C.H., Loveland, A.B., Diggs, S., Sholi, E., Grigorieff, N., Korostelev, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 4,257.04 kDa
Atom Count: 147,582
Modeled Residue Count: 11,979
Deposited Residue Count: 18,645
Unique protein chains: 46
Unique nucleic acid chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 2	A [auth v]	858	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8	D [auth L8]	248	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus) Explore G1TT27 Go to UniProtKB: G1TT27
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UniProt Group	G1TT27
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	E [auth L3]	394	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus) Explore G1TL06 Go to UniProtKB: G1TL06
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UniProt Group	G1TL06
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4	F [auth L4]	362	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	A0A5F9DCT1
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	G [auth L5]	293	Oryctolagus cuniculus	Mutation(s): 0
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Find proteins for P19949 (Oryctolagus cuniculus) Explore P19949 Go to UniProtKB: P19949
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UniProt Group	P19949
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL6	H [auth L6]	251	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SKF7
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7	I [auth L7]	225	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SV32
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL8	J [auth aa]	266	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9	K [auth L9]	190	Oryctolagus cuniculus	Mutation(s): 0
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Find proteins for G1SWI6 (Oryctolagus cuniculus) Explore G1SWI6 Go to UniProtKB: G1SWI6
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UniProt Group	G1SWI6
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L10	L [auth 10]	213	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	B7NZQ2
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11	M [auth 11]	170	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1TUB8
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL13	N [auth 13]	261	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14	O [auth 14]	138	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SZ12
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L15	P [auth 15]	203	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1T0C1
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	Q [auth bb]	199	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1TVS8
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17	R [auth 17]	153	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SCJ6
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19	S [auth 19]	180	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL20	T [auth 20]	176	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21	U [auth 21]	159	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus) Explore G1SHQ2 Go to UniProtKB: G1SHQ2
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UniProt Group	G1SHQ2
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL22	V [auth 22]	99	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L24	W [auth 24]	63	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus) Explore G1SE28 Go to UniProtKB: G1SE28
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UniProt Group	G1SE28
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	X [auth cc]	118	Oryctolagus cuniculus	Mutation(s): 0
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Find proteins for G1SE76 (Oryctolagus cuniculus) Explore G1SE76 Go to UniProtKB: G1SE76
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UniProt Group	G1SE76
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26	Y [auth 26]	134	Oryctolagus cuniculus	Mutation(s): 0
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Find proteins for G1SQH0 (Oryctolagus cuniculus) Explore G1SQH0 Go to UniProtKB: G1SQH0
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UniProt Group	G1SQH0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27	Z [auth 27]	135	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1TXF6
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27a	AA [auth dd]	147	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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UniProt Group	G1SNY0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL29	BA [auth 29]	245	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SGR6
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	CA [auth 30]	98	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus) Explore G1TDL2 Go to UniProtKB: G1TDL2
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UniProt Group	G1TDL2
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31	DA [auth 31]	107	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SHG0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL32	EA [auth 32]	128	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL33	FA [auth ee]	109	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SF08
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34	GA [auth 34]	114	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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UniProt Group	G1TXG5
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35	HA [auth 35]	122	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1SIT5
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36	IA [auth 36]	102	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1TTQ5
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37	JA [auth 37]	86	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	U3KPD5
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL38	KA [auth 38]	69	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	LA [auth 39]	50	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	G1TTN1
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL40	MA [auth 40]	52	Oryctolagus cuniculus	Mutation(s): 0
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UniProt Group	P0DXC2
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
eL42	NA [auth 42]	104	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A5F9D391 (Oryctolagus cuniculus) Explore A0A5F9D391 Go to UniProtKB: A0A5F9D391
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UniProt Group	A0A5F9D391
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37a	OA [auth ff]	91	Oryctolagus cuniculus	Mutation(s): 0
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Find proteins for G1SY53 (Oryctolagus cuniculus) Explore G1SY53 Go to UniProtKB: G1SY53
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UniProt Group	G1SY53
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	PA [auth gg]	124	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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UniProt Group	G1U7L1
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S acidic ribosomal protein P0	QA [auth s]	196	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SPK4 (Oryctolagus cuniculus) Explore G1SPK4 Go to UniProtKB: G1SPK4
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UniProt Group	G1SPK4
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
uL11	RA [auth t]	153	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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UniProt Group	G1SMR7
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferation-associated protein 2G4	SA [auth EB]	375	Oryctolagus cuniculus	Mutation(s): 0
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PHAROS: Q9UQ80 GTEx: ENSG00000170515
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UniProt Group	Q9UQ80
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10a	TA [auth u]	206	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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UniProt Group	G1SKZ8
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL18	UA [auth Q]	187	Oryctolagus cuniculus	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	XA [auth 25]	139	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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UniProt Group	G1T6D1
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5.8S rRNA	B [auth 58]	156	Oryctolagus cuniculus
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Molecule	Chains	Length	Organism
Entity ID: 3
5S rRNA	C [auth 5]	120	Oryctolagus cuniculus
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Molecule	Chains	Length	Organism
Entity ID: 48
ES27L	VA [auth ES]	5,070	Oryctolagus cuniculus
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Molecule	Chains	Length	Organism
Entity ID: 49
28S rRNA	WA [auth 28]	4,807	Oryctolagus cuniculus
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain YA [auth v] MOL2 format, chain YA [auth v] mmCIF format, chain YA [auth v]	YA [auth v]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain YA [auth v] Interactions & Density Focus chain YA [auth v]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth 37] SDF format, chain ZA [auth 34] SDF format, chain BB [auth ff] MOL2 format, chain AB [auth 37] MOL2 format, chain ZA [auth 34] MOL2 format, chain BB [auth ff] mmCIF format, chain AB [auth 37] mmCIF format, chain ZA [auth 34] mmCIF format, chain BB [auth ff]	AB [auth 37], BB [auth ff], ZA [auth 34]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth 37] Focus chain BB [auth ff] Focus chain ZA [auth 34] Interactions & Density Focus chain AB [auth 37] Focus chain BB [auth ff] Focus chain ZA [auth 34]