9OGY | pdb_00009ogy

Megrivirus E 3' internal ribosome entry site (IRES) RNA core region bound to rabbit ribosome

PDB DOI: https://doi.org/10.2210/pdb9OGY/pdb
NAKB: 9OGY
EM Map EMD-70479: EMDB EMDataResource

Classification: RNA
Organism(s): Oryctolagus cuniculus, Megrivirus E
Mutation(s): No

Deposited: 2025-05-02 Released: 2026-01-14
Deposition Author(s): Sherlock, M.E., Kieft, J.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 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

Megrivirus E 3' internal ribosome entry site (IRES) RNA core region bound to rabbit ribosome

Sherlock, M.E., Kieft, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 1,347.71 kDa
Atom Count: 77,254
Modeled Residue Count: 6,683
Deposited Residue Count: 7,961
Unique protein chains: 34
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
uS2 (SA)	C [auth B]	295	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus) Explore G1TLT8 Go to UniProtKB: G1TLT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TLT8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3a	D [auth C]	264	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus) Explore G1SS70 Go to UniProtKB: G1SS70
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SS70
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	E [auth D]	221	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for O18789 (Bos taurus) Explore O18789 Go to UniProtKB: O18789
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O18789
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S3	F [auth E]	281	Oryctolagus cuniculus	Mutation(s): 0 EC: 4.2.99.18
UniProt
Find proteins for G1TNM3 (Oryctolagus cuniculus) Explore G1TNM3 Go to UniProtKB: G1TNM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TNM3
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4	G [auth F]	263	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus) Explore G1TK17 Go to UniProtKB: G1TK17
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TK17
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S5	H [auth G]	204	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TFM5 (Oryctolagus cuniculus) Explore G1TFM5 Go to UniProtKB: G1TFM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TFM5
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6	I [auth H]	249	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus) Explore G1TM55 Go to UniProtKB: G1TM55
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TM55
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
eS7	J [auth I]	432	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SVB0 (Oryctolagus cuniculus) Explore G1SVB0 Go to UniProtKB: G1SVB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SVB0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8	K [auth J]	208	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus) Explore G1TJW1 Go to UniProtKB: G1TJW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TJW1
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S9 (Predicted)	L [auth K]	194	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus) Explore B7NZS8 Go to UniProtKB: B7NZS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7NZS8
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
S10_plectin domain-containing protein	M [auth L]	149	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1U0Y5 (Oryctolagus cuniculus) Explore G1U0Y5 Go to UniProtKB: G1U0Y5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1U0Y5
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S11	N [auth M]	158	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus) Explore G1TRM4 Go to UniProtKB: G1TRM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TRM4
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S12	O [auth N]	132	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus) Explore G1SFR8 Go to UniProtKB: G1SFR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SFR8
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S13	P [auth O]	151	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus) Explore G1SP51 Go to UniProtKB: G1SP51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SP51
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S14	Q [auth P]	168	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0AAA9WYR1 (Oryctolagus cuniculus) Explore A0AAA9WYR1 Go to UniProtKB: A0AAA9WYR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAA9WYR1
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
uS19	R [auth Q]	145	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus) Explore G1U0Q2 Go to UniProtKB: G1U0Q2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1U0Q2
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S16	S [auth R]	172	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SGX4 (Oryctolagus cuniculus) Explore G1SGX4 Go to UniProtKB: G1SGX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SGX4
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
eS17	T [auth S]	135	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus) Explore G1TU13 Go to UniProtKB: G1TU13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TU13
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
uS13	U [auth T]	152	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus) Explore G1TPG3 Go to UniProtKB: G1TPG3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TPG3
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
eS19	V [auth U]	145	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus) Explore G1TN62 Go to UniProtKB: G1TN62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TN62
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
uS10	W [auth V]	119	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SIZ2 (Oryctolagus cuniculus) Explore G1SIZ2 Go to UniProtKB: G1SIZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SIZ2
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21	X [auth W]	83	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TM82 (Oryctolagus cuniculus) Explore G1TM82 Go to UniProtKB: G1TM82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TM82
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S15a	Y [auth X]	130	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus) Explore G1TG89 Go to UniProtKB: G1TG89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TG89
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Reference Sequence

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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
uS12	Z [auth Y]	143	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus) Explore G1SZ47 Go to UniProtKB: G1SZ47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SZ47
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
eS24	AA [auth Z]	131	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T3D8 (Oryctolagus cuniculus) Explore G1T3D8 Go to UniProtKB: G1T3D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1T3D8
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
eS25	BA [auth a]	124	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus) Explore G1TDB3 Go to UniProtKB: G1TDB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TDB3
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
eS26	CA [auth b]	101	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TFE8 (Oryctolagus cuniculus) Explore G1TFE8 Go to UniProtKB: G1TFE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TFE8
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27	DA [auth c]	84	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus) Explore G1TZ76 Go to UniProtKB: G1TZ76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TZ76
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S28	EA [auth d]	69	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TIB4 (Oryctolagus cuniculus) Explore G1TIB4 Go to UniProtKB: G1TIB4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1TIB4
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
eS29	FA [auth e]	56	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1U7M4 (Oryctolagus cuniculus) Explore G1U7M4 Go to UniProtKB: G1U7M4
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UniProt Group	G1U7M4
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S30	GA [auth f]	133	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus) Explore G1T8A2 Go to UniProtKB: G1T8A2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1T8A2
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
eS31	HA [auth g]	188	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus) Explore G1SK22 Go to UniProtKB: G1SK22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1SK22
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
RACK1	IA [auth h]	317	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SJB4 (Oryctolagus cuniculus) Explore G1SJB4 Go to UniProtKB: G1SJB4
Entity Groups
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UniProt Group	G1SJB4
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Reference Sequence

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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
eL41	JA [auth n]	25	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus) Explore A0A087WNH4 Go to UniProtKB: A0A087WNH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A087WNH4
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
18S ribosomal RNA	A [auth 2]	1,870	Oryctolagus cuniculus
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
Megrivirus E 3' IRES RNA	B [auth A]	270	Megrivirus E
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain KA [auth b] SDF format, chain LA [auth g] MOL2 format, chain KA [auth b] MOL2 format, chain LA [auth g] mmCIF format, chain KA [auth b] mmCIF format, chain LA [auth g]	KA [auth b], LA [auth g]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain KA [auth b] Focus chain LA [auth g] Interactions & Density Focus chain KA [auth b] Focus chain LA [auth g]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-14

Deposition Author(s):

Sherlock, M.E.

Kieft, J.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118070

Revision History (Full details and data files)

Version 1.0: 2026-01-14
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.

9OGY | pdb_00009ogy

Megrivirus E 3' internal ribosome entry site (IRES) RNA core region bound to rabbit ribosome

Literature

Megrivirus E 3' internal ribosome entry site (IRES) RNA core region bound to rabbit ribosome

Biological Assembly 1

Macromolecules

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

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Sequence Annotations

Entity ID: 6

UniProt

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Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

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Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

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Entity ID: 20

UniProt

Entity Groups

Sequence Annotations

Entity ID: 21

UniProt