8KIE | pdb_00008kie

Structure of YchF with 50S ribosomal subunit (local map)

PDB DOI: https://doi.org/10.2210/pdb8KIE/pdb
NAKB: 8KIE
EM Map EMD-37258: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-08-23 Released: 2024-08-28
Deposition Author(s): Yu, T., Li, X., Zeng, F.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Guangdong Basic and Applied Basic Research Foundation, Shenzhen Science and Technology Program

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure basis of translation regulation by YchF bound to ribosome

Li, X., Yu, T., Li, Q., Zeng, F.

To be published.

Macromolecule Content

Total Structure Weight: 1,010.77 kDa
Atom Count: 12,424
Modeled Residue Count: 961
Deposited Residue Count: 3,521
Unique protein chains: 3
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-binding ATPase YchF	A [auth y]	379	Escherichia coli	Mutation(s): 1 Gene Names: ychF
UniProt
Find proteins for P0ABU2 (Escherichia coli (strain K12)) Explore P0ABU2 Go to UniProtKB: P0ABU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABU2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	C [auth j]	123	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3 Go to UniProtKB: P0ADY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADY3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	D [auth o]	115	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6 Go to UniProtKB: P0A7K6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7K6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
23S rRNA (partial)	B [auth a]	2,904	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth a] SDF format, chain Y [auth a] SDF format, chain X [auth a] SDF format, chain W [auth a] SDF format, chain V [auth a] SDF format, chain U [auth a] SDF format, chain T [auth a] SDF format, chain S [auth a] SDF format, chain R [auth a] SDF format, chain Q [auth a] SDF format, chain P [auth a] SDF format, chain O [auth a] SDF format, chain N [auth a] SDF format, chain M [auth a] SDF format, chain L [auth a] SDF format, chain K [auth a] SDF format, chain J [auth a] SDF format, chain I [auth a] SDF format, chain HA [auth a] SDF format, chain H [auth a] SDF format, chain GA [auth a] SDF format, chain G [auth a] SDF format, chain FA [auth a] SDF format, chain F [auth a] SDF format, chain EA [auth a] SDF format, chain E [auth a] SDF format, chain DA [auth a] SDF format, chain CA [auth a] SDF format, chain BA [auth a] SDF format, chain AA [auth a] MOL2 format, chain Z [auth a] MOL2 format, chain Y [auth a] MOL2 format, chain X [auth a] MOL2 format, chain W [auth a] MOL2 format, chain V [auth a] MOL2 format, chain U [auth a] MOL2 format, chain T [auth a] MOL2 format, chain S [auth a] MOL2 format, chain R [auth a] MOL2 format, chain Q [auth a] MOL2 format, chain P [auth a] MOL2 format, chain O [auth a] MOL2 format, chain N [auth a] MOL2 format, chain M [auth a] MOL2 format, chain L [auth a] MOL2 format, chain K [auth a] MOL2 format, chain J [auth a] MOL2 format, chain I [auth a] MOL2 format, chain HA [auth a] MOL2 format, chain H [auth a] MOL2 format, chain GA [auth a] MOL2 format, chain G [auth a] MOL2 format, chain FA [auth a] MOL2 format, chain F [auth a] MOL2 format, chain EA [auth a] MOL2 format, chain E [auth a] MOL2 format, chain DA [auth a] MOL2 format, chain CA [auth a] MOL2 format, chain BA [auth a] MOL2 format, chain AA [auth a] mmCIF format, chain Z [auth a] mmCIF format, chain Y [auth a] mmCIF format, chain X [auth a] mmCIF format, chain W [auth a] mmCIF format, chain V [auth a] mmCIF format, chain U [auth a] mmCIF format, chain T [auth a] mmCIF format, chain S [auth a] mmCIF format, chain R [auth a] mmCIF format, chain Q [auth a] mmCIF format, chain P [auth a] mmCIF format, chain O [auth a] mmCIF format, chain N [auth a] mmCIF format, chain M [auth a] mmCIF format, chain L [auth a] mmCIF format, chain K [auth a] mmCIF format, chain J [auth a] mmCIF format, chain I [auth a] mmCIF format, chain HA [auth a] mmCIF format, chain H [auth a] mmCIF format, chain GA [auth a] mmCIF format, chain G [auth a] mmCIF format, chain FA [auth a] mmCIF format, chain F [auth a] mmCIF format, chain EA [auth a] mmCIF format, chain E [auth a] mmCIF format, chain DA [auth a] mmCIF format, chain CA [auth a] mmCIF format, chain BA [auth a] mmCIF format, chain AA [auth a]	AA [auth a] BA [auth a] CA [auth a] DA [auth a] E [auth a] AA [auth a], BA [auth a], CA [auth a], DA [auth a], E [auth a], EA [auth a], F [auth a], FA [auth a], G [auth a], GA [auth a], H [auth a], HA [auth a], I [auth a], J [auth a], K [auth a], L [auth a], M [auth a], N [auth a], O [auth a], P [auth a], Q [auth a], R [auth a], S [auth a], T [auth a], U [auth a], V [auth a], W [auth a], X [auth a], Y [auth a], Z [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth a] Focus chain BA [auth a] Focus chain CA [auth a] Focus chain DA [auth a] Focus chain E [auth a] Focus chain EA [auth a] Focus chain F [auth a] Focus chain FA [auth a] Focus chain G [auth a] Focus chain GA [auth a] Focus chain H [auth a] Focus chain HA [auth a] Focus chain I [auth a] Focus chain J [auth a] Focus chain K [auth a] Focus chain L [auth a] Focus chain M [auth a] Focus chain N [auth a] Focus chain O [auth a] Focus chain P [auth a] Focus chain Q [auth a] Focus chain R [auth a] Focus chain S [auth a] Focus chain T [auth a] Focus chain U [auth a] Focus chain V [auth a] Focus chain W [auth a] Focus chain X [auth a] Focus chain Y [auth a] Focus chain Z [auth a] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth a] Focus chain CA [auth a] Focus chain DA [auth a] Focus chain E [auth a] Focus chain EA [auth a] Focus chain F [auth a] Focus chain FA [auth a] Focus chain G [auth a] Focus chain GA [auth a] Focus chain H [auth a] Focus chain HA [auth a] Focus chain I [auth a] Focus chain J [auth a] Focus chain K [auth a] Focus chain L [auth a] Focus chain M [auth a] Focus chain N [auth a] Focus chain O [auth a] Focus chain P [auth a] Focus chain Q [auth a] Focus chain R [auth a] Focus chain S [auth a] Focus chain T [auth a] Focus chain U [auth a] Focus chain V [auth a] Focus chain W [auth a] Focus chain X [auth a] Focus chain Y [auth a] Focus chain Z [auth a]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Yu, T.

Li, X.

Zeng, F.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171200
Guangdong Basic and Applied Basic Research Foundation	China	2021A1515010805
Shenzhen Science and Technology Program	China	JCYJ20220530115210023