7SYM | pdb_00007sym

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
EM Map EMD-25533: EMDB EMDataResource
NAKB: 7SYM

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
Modeled 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 G1T168 (Oryctolagus cuniculus) Explore G1T168 Go to UniProtKB: G1T168
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1T168
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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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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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
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: 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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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
Entity Groups
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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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
Entity Groups
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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 A0A5F9D2E6 (Oryctolagus cuniculus) Explore A0A5F9D2E6 Go to UniProtKB: A0A5F9D2E6
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UniProt Group	A0A5F9D2E6
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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% 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 rRNA	A [auth 2]	1,870	Oryctolagus cuniculus
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 36
HCV IRES	JA [auth z]	400	Hepatitis C virus (isolate 1)
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: 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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View more in-depth experimental data

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

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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.

7SYM | pdb_00007sym

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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

Entity Groups

Sequence Annotations

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

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

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Sequence Annotations

Entity ID: 18

UniProt

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Entity ID: 19

UniProt

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Sequence Annotations

Entity ID: 20

UniProt