9T8K | pdb_00009t8k

E. coli 70S ribosome from delta-10 strain, PTC class 0

PDB DOI: https://doi.org/10.2210/pdb9T8K/pdb
NAKB: 9T8K
EM Map EMD-55702: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 2025-11-13 Released: 2026-03-18
Deposition Author(s): Larsson, D.S.D., Selmer, M.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Ribosomal RNA modifications around the peptidyl transfer center stimulate catalytic activity and prevent the formation of alternative structures

Larsson, D.S.D., Liiv, A., Ero, R., Remme, J., Selmer, M.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.03.01.708810

Macromolecule Content

Total Structure Weight: 1,126.6 kDa
Atom Count: 14,213
Modeled Residue Count: 779
Deposited Residue Count: 4,342
Unique protein chains: 9
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	C [auth c]	273	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422 Go to UniProtKB: P60422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60422
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	D [auth d]	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438 Go to UniProtKB: P60438
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60438
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	E [auth e]	201	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723 Go to UniProtKB: P60723
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60723
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	F [auth k]	144	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413 Go to UniProtKB: P02413
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02413
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	G [auth l]	136	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A7ZSK2 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZSK2 Go to UniProtKB: A7ZSK2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7ZSK2
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	H [auth q]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48 Go to UniProtKB: P0AG48
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AG48
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	I [auth r]	110	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175 Go to UniProtKB: P61175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61175
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	J [auth v]	85	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8 Go to UniProtKB: P0A7L8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7L8
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Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	K [auth z]	57	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4 Go to UniProtKB: P0A7N4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7N4
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Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
23S rRNA	A [auth a]	2,904	Escherichia coli
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5S rRNA	B [auth b]	120	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SR0 Query on SR0 Download:Ideal Coordinates CCD File SDF format, chain L [auth a] SDF format, chain M [auth a] MOL2 format, chain L [auth a] MOL2 format, chain M [auth a] mmCIF format, chain L [auth a] mmCIF format, chain M [auth a]	L [auth a], M [auth a]	N~1~-(3-azaniumylpropyl)butane-1,4-diaminium C₇ H₂₂ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-Q		Interactions Focus chain L [auth a] Focus chain M [auth a] Interactions & Density Focus chain L [auth a] Focus chain M [auth a]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AA [auth a] SDF format, chain DA [auth a] SDF format, chain DB [auth a] SDF format, chain EB [auth a] SDF format, chain FA [auth a] SDF format, chain FB [auth a] SDF format, chain GA [auth a] SDF format, chain GB [auth a] SDF format, chain IA [auth a] SDF format, chain IB [auth a] SDF format, chain JB [auth a] SDF format, chain KB [auth a] SDF format, chain LA [auth a] SDF format, chain MB [auth a] SDF format, chain NB [auth a] SDF format, chain Z [auth a] SDF format, chain Y [auth a] SDF format, chain LB [auth a] SDF format, chain HB [auth a] SDF format, chain HA [auth a] SDF format, chain CA [auth a] MOL2 format, chain AA [auth a] MOL2 format, chain DA [auth a] MOL2 format, chain DB [auth a] MOL2 format, chain EB [auth a] MOL2 format, chain FA [auth a] MOL2 format, chain FB [auth a] MOL2 format, chain GA [auth a] MOL2 format, chain GB [auth a] MOL2 format, chain IA [auth a] MOL2 format, chain IB [auth a] MOL2 format, chain JB [auth a] MOL2 format, chain KB [auth a] MOL2 format, chain LA [auth a] MOL2 format, chain MB [auth a] MOL2 format, chain NB [auth a] MOL2 format, chain Z [auth a] MOL2 format, chain Y [auth a] MOL2 format, chain LB [auth a] MOL2 format, chain HB [auth a] MOL2 format, chain HA [auth a] MOL2 format, chain CA [auth a] mmCIF format, chain AA [auth a] mmCIF format, chain DA [auth a] mmCIF format, chain DB [auth a] mmCIF format, chain EB [auth a] mmCIF format, chain FA [auth a] mmCIF format, chain FB [auth a] mmCIF format, chain GA [auth a] mmCIF format, chain GB [auth a] mmCIF format, chain IA [auth a] mmCIF format, chain IB [auth a] mmCIF format, chain JB [auth a] mmCIF format, chain KB [auth a] mmCIF format, chain LA [auth a] mmCIF format, chain MB [auth a] mmCIF format, chain NB [auth a] mmCIF format, chain Z [auth a] mmCIF format, chain Y [auth a] mmCIF format, chain LB [auth a] mmCIF format, chain HB [auth a] mmCIF format, chain HA [auth a] mmCIF format, chain CA [auth a]	AA [auth a] CA [auth a] DA [auth a] DB [auth a] EB [auth a] AA [auth a], CA [auth a], DA [auth a], DB [auth a], EB [auth a], FA [auth a], FB [auth a], GA [auth a], GB [auth a], HA [auth a], HB [auth a], IA [auth a], IB [auth a], JB [auth a], KB [auth a], LA [auth a], LB [auth a], MB [auth a], NB [auth a], Y [auth a], Z [auth a]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth a] Focus chain CA [auth a] Focus chain DA [auth a] Focus chain DB [auth a] Focus chain EB [auth a] Focus chain FA [auth a] Focus chain FB [auth a] Focus chain GA [auth a] Focus chain GB [auth a] Focus chain HA [auth a] Focus chain HB [auth a] Focus chain IA [auth a] Focus chain IB [auth a] Focus chain JB [auth a] Focus chain KB [auth a] Focus chain LA [auth a] Focus chain LB [auth a] Focus chain MB [auth a] Focus chain NB [auth a] Focus chain Y [auth a] Focus chain Z [auth a] Interactions & Density Focus chain AA [auth a] Focus chain CA [auth a] Focus chain DA [auth a] Focus chain DB [auth a] Focus chain EB [auth a] Focus chain FA [auth a] Focus chain FB [auth a] Focus chain GA [auth a] Focus chain GB [auth a] Focus chain HA [auth a] Focus chain HB [auth a] Focus chain IA [auth a] Focus chain IB [auth a] Focus chain JB [auth a] Focus chain KB [auth a] Focus chain LA [auth a] Focus chain LB [auth a] Focus chain MB [auth a] Focus chain NB [auth a] Focus chain Y [auth a] Focus chain Z [auth a]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth a] SDF format, chain BA [auth a] SDF format, chain BB [auth a] SDF format, chain CB [auth a] SDF format, chain EA [auth a] SDF format, chain JA [auth a] SDF format, chain KA [auth a] SDF format, chain MA [auth a] SDF format, chain N [auth a] SDF format, chain NA [auth a] SDF format, chain O [auth a] SDF format, chain OA [auth a] SDF format, chain OB [auth d] SDF format, chain P [auth a] SDF format, chain PA [auth a] SDF format, chain PB [auth z] SDF format, chain Q [auth a] SDF format, chain QA [auth a] SDF format, chain RA [auth a] SDF format, chain S [auth a] SDF format, chain SA [auth a] SDF format, chain T [auth a] SDF format, chain TA [auth a] SDF format, chain U [auth a] SDF format, chain UA [auth a] SDF format, chain V [auth a] SDF format, chain VA [auth a] SDF format, chain W [auth a] SDF format, chain WA [auth a] SDF format, chain X [auth a] SDF format, chain XA [auth a] SDF format, chain YA [auth a] SDF format, chain ZA [auth a] SDF format, chain R [auth a] MOL2 format, chain AB [auth a] MOL2 format, chain BA [auth a] MOL2 format, chain BB [auth a] MOL2 format, chain CB [auth a] MOL2 format, chain EA [auth a] MOL2 format, chain JA [auth a] MOL2 format, chain KA [auth a] MOL2 format, chain MA [auth a] MOL2 format, chain N [auth a] MOL2 format, chain NA [auth a] MOL2 format, chain O [auth a] MOL2 format, chain OA [auth a] MOL2 format, chain OB [auth d] MOL2 format, chain P [auth a] MOL2 format, chain PA [auth a] MOL2 format, chain PB [auth z] MOL2 format, chain Q [auth a] MOL2 format, chain QA [auth a] MOL2 format, chain RA [auth a] MOL2 format, chain S [auth a] MOL2 format, chain SA [auth a] MOL2 format, chain T [auth a] MOL2 format, chain TA [auth a] MOL2 format, chain U [auth a] MOL2 format, chain UA [auth a] MOL2 format, chain V [auth a] MOL2 format, chain VA [auth a] MOL2 format, chain W [auth a] MOL2 format, chain WA [auth a] MOL2 format, chain X [auth a] MOL2 format, chain XA [auth a] MOL2 format, chain YA [auth a] MOL2 format, chain ZA [auth a] MOL2 format, chain R [auth a] mmCIF format, chain AB [auth a] mmCIF format, chain BA [auth a] mmCIF format, chain BB [auth a] mmCIF format, chain CB [auth a] mmCIF format, chain EA [auth a] mmCIF format, chain JA [auth a] mmCIF format, chain KA [auth a] mmCIF format, chain MA [auth a] mmCIF format, chain N [auth a] mmCIF format, chain NA [auth a] mmCIF format, chain O [auth a] mmCIF format, chain OA [auth a] mmCIF format, chain OB [auth d] mmCIF format, chain P [auth a] mmCIF format, chain PA [auth a] mmCIF format, chain PB [auth z] mmCIF format, chain Q [auth a] mmCIF format, chain QA [auth a] mmCIF format, chain RA [auth a] mmCIF format, chain S [auth a] mmCIF format, chain SA [auth a] mmCIF format, chain T [auth a] mmCIF format, chain TA [auth a] mmCIF format, chain U [auth a] mmCIF format, chain UA [auth a] mmCIF format, chain V [auth a] mmCIF format, chain VA [auth a] mmCIF format, chain W [auth a] mmCIF format, chain WA [auth a] mmCIF format, chain X [auth a] mmCIF format, chain XA [auth a] mmCIF format, chain YA [auth a] mmCIF format, chain ZA [auth a] mmCIF format, chain R [auth a]	AB [auth a] BA [auth a] BB [auth a] CB [auth a] EA [auth a] AB [auth a], BA [auth a], BB [auth a], CB [auth a], EA [auth a], JA [auth a], KA [auth a], MA [auth a], N [auth a], NA [auth a], O [auth a], OA [auth a], OB [auth d], P [auth a], PA [auth a], PB [auth z], Q [auth a], QA [auth a], R [auth a], RA [auth a], S [auth a], SA [auth a], T [auth a], TA [auth a], U [auth a], UA [auth a], V [auth a], VA [auth a], W [auth a], WA [auth a], X [auth a], XA [auth a], YA [auth a], ZA [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth a] Focus chain BA [auth a] Focus chain BB [auth a] Focus chain CB [auth a] Focus chain EA [auth a] Focus chain JA [auth a] Focus chain KA [auth a] Focus chain MA [auth a] Focus chain N [auth a] Focus chain NA [auth a] Focus chain O [auth a] Focus chain OA [auth a] Focus chain OB [auth d] Focus chain P [auth a] Focus chain PA [auth a] Focus chain PB [auth z] Focus chain Q [auth a] Focus chain QA [auth a] Focus chain R [auth a] Focus chain RA [auth a] Focus chain S [auth a] Focus chain SA [auth a] Focus chain T [auth a] Focus chain TA [auth a] Focus chain U [auth a] Focus chain UA [auth a] Focus chain V [auth a] Focus chain VA [auth a] Focus chain W [auth a] Focus chain WA [auth a] Focus chain X [auth a] Focus chain XA [auth a] Focus chain YA [auth a] Focus chain ZA [auth a] Interactions & Density Focus chain AB [auth a] Focus chain BA [auth a] Focus chain BB [auth a] Focus chain CB [auth a] Focus chain EA [auth a] Focus chain JA [auth a] Focus chain KA [auth a] Focus chain MA [auth a] Focus chain N [auth a] Focus chain NA [auth a] Focus chain O [auth a] Focus chain OA [auth a] Focus chain OB [auth d] Focus chain P [auth a] Focus chain PA [auth a] Focus chain PB [auth z] Focus chain Q [auth a] Focus chain QA [auth a] Focus chain R [auth a] Focus chain RA [auth a] Focus chain S [auth a] Focus chain SA [auth a] Focus chain T [auth a] Focus chain TA [auth a] Focus chain U [auth a] Focus chain UA [auth a] Focus chain V [auth a] Focus chain VA [auth a] Focus chain W [auth a] Focus chain WA [auth a] Focus chain X [auth a] Focus chain XA [auth a] Focus chain YA [auth a] Focus chain ZA [auth a]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEQ Query on MEQ	D [auth d]	L-PEPTIDE LINKING	C₆ H₁₂ N₂ O₃		GLN
4D4 Query on 4D4	G [auth l]	L-PEPTIDE LINKING	C₆ H₁₄ N₄ O₃		ARG
MS6 Query on MS6	G [auth l]	L-PEPTIDE LINKING	C₅ H₁₁ N O S₂		MET