7SYM

Structure of the HCV IRES bound to the 40S ribosomal subunit, head opening. Structure 7(delta dII)

PDB DOI: https://doi.org/10.2210/pdb7SYM/pdb
NAKB: 7SYM
EM Map EMD-25533: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Oryctolagus cuniculus, Hepatitis C virus (isolate 1)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-25 Released: 2022-07-13
Deposition Author(s): Brown, Z.P., Abaeva, I.S., De, S., Hellen, C.U.T., Pestova, T.V., Frank, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Comprehensive structural overview of the HCV IRES-mediated translation initiation pathway

Brown, Z.P., Abaeva, I.S., De, S., Hellen, C.U.T., Pestova, T.V., Frank, J.

To be published.

Macromolecule Content

Total Structure Weight: 1,389.78 kDa
Atom Count: 78,761
Modelled Residue Count: 6,750
Deposited Residue Count: 8,091
Unique protein chains: 34
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein SA	B	295	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus) Explore G1TLT8 Go to UniProtKB: G1TLT8
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UniProt Group	G1TLT8
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3a	C	264	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus) Explore G1SS70 Go to UniProtKB: G1SS70
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UniProt Group	G1SS70
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	D	221	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SV32 (Oryctolagus cuniculus) Explore G1SV32 Go to UniProtKB: G1SV32
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1SV32
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
uS3	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
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UniProt Group	G1TNM3
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4	F	263	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TA47 (Oryctolagus cuniculus) Explore G1TA47 Go to UniProtKB: G1TA47
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1TA47
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
uS7	G	204	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TFM5 (Oryctolagus cuniculus) Explore G1TFM5 Go to UniProtKB: G1TFM5
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UniProt Group	G1TFM5
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
eS6	H	249	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A5K1UJS7 (Oryctolagus cuniculus) Explore A0A5K1UJS7 Go to UniProtKB: A0A5K1UJS7
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UniProt Group	A0A5K1UJS7
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7	I	432	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SVB0 (Oryctolagus cuniculus) Explore G1SVB0 Go to UniProtKB: G1SVB0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1SVB0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
eS8	J	208	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus) Explore G1TJW1 Go to UniProtKB: G1TJW1
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UniProt Group	G1TJW1
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
uS4	K	194	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus) Explore B7NZS8 Go to UniProtKB: B7NZS8
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7NZS8
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
eS10	L	149	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TPV3 (Oryctolagus cuniculus) Explore G1TPV3 Go to UniProtKB: G1TPV3
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1TPV3
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
uS17	M	158	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus) Explore G1TRM4 Go to UniProtKB: G1TRM4
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UniProt Group	G1TRM4
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
eS12	N	132	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus) Explore G1SFR8 Go to UniProtKB: G1SFR8
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UniProt Group	G1SFR8
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
uS15	O	151	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus) Explore G1SP51 Go to UniProtKB: G1SP51
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UniProt Group	G1SP51
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
uS11	P	168	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus) Explore G1T1F0 Go to UniProtKB: G1T1F0
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UniProt Group	G1T1F0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
uS19	Q	145	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus) Explore G1U0Q2 Go to UniProtKB: G1U0Q2
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UniProt Group	G1U0Q2
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
uS9	R	172	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SGX4 (Oryctolagus cuniculus) Explore G1SGX4 Go to UniProtKB: G1SGX4
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UniProt Group	G1SGX4
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
eS17	S	135	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus) Explore G1TU13 Go to UniProtKB: G1TU13
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1TU13
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
uS13	T	152	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus) Explore G1TPG3 Go to UniProtKB: G1TPG3
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1TPG3
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
eS19	U	145	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus) Explore G1TN62 Go to UniProtKB: G1TN62
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1TN62
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
uS10	V	119	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SIZ2 (Oryctolagus cuniculus) Explore G1SIZ2 Go to UniProtKB: G1SIZ2
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1SIZ2
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21	W	83	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TM82 (Oryctolagus cuniculus) Explore G1TM82 Go to UniProtKB: G1TM82
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UniProt Group	G1TM82
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
uS8	X	130	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus) Explore G1TG89 Go to UniProtKB: G1TG89
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UniProt Group	G1TG89
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
uS12	Y	143	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus) Explore G1SZ47 Go to UniProtKB: G1SZ47
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UniProt Group	G1SZ47
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24	Z	131	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1T3D8 (Oryctolagus cuniculus) Explore G1T3D8 Go to UniProtKB: G1T3D8
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UniProt Group	G1T3D8
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25	AA [auth a]	124	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus) Explore G1TDB3 Go to UniProtKB: G1TDB3
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UniProt Group	G1TDB3
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
eS26 (S26)	BA [auth b]	101	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TFE8 (Oryctolagus cuniculus) Explore G1TFE8 Go to UniProtKB: G1TFE8
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UniProt Group	G1TFE8
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
eS27	CA [auth c]	84	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus) Explore G1TZ76 Go to UniProtKB: G1TZ76
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UniProt Group	G1TZ76
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
eS28	DA [auth d]	69	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1TIB4 (Oryctolagus cuniculus) Explore G1TIB4 Go to UniProtKB: G1TIB4
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UniProt Group	G1TIB4
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
eS29	EA [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: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
eS30	FA [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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UniProt Group	G1T8A2
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27a	GA [auth g]	188	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus) Explore G1SK22 Go to UniProtKB: G1SK22
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UniProt Group	G1SK22
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
RACK1	HA [auth h]	317	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for G1SJB4 (Oryctolagus cuniculus) Explore G1SJB4 Go to UniProtKB: G1SJB4
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UniProt Group	G1SJB4
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60s ribosomal protein l41	IA [auth n]	25	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus) Explore A0A087WNH4 Go to UniProtKB: A0A087WNH4
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A087WNH4
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Entity ID: 1
Molecule	Chains	Length	Organism	Image
18S rRNA	A [auth 2]	1,870	Oryctolagus cuniculus
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Entity ID: 36
Molecule	Chains	Length	Organism	Image
HCV IRES	JA [auth z]	400	Hepatitis C virus (isolate 1)
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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 LA [auth g] SDF format, chain KA [auth b] MOL2 format, chain LA [auth g] MOL2 format, chain KA [auth b] mmCIF format, chain LA [auth g] mmCIF format, chain KA [auth b]	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: 4.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.1-4122
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM139453
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM122602
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI123406
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM55440

Revision History (Full details and data files)

Version 1.0: 2022-07-13
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Refinement description

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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Help and Resources

7SYM

Structure of the HCV IRES bound to the 40S ribosomal subunit, head opening. Structure 7(delta dII)

Comprehensive structural overview of the HCV IRES-mediated translation initiation pathway

Entity ID: 2

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Entity ID: 20