9DYG | pdb_00009dyg

iSAT-PNA-RA20, RA20-B-c class

PDB DOI: https://doi.org/10.2210/pdb9DYG/pdb
EM Map EMD-47303: EMDB EMDataResource
NAKB: 9DYG

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

Deposited: 2024-10-14 Released: 2024-11-13
Deposition Author(s): Sheng, K., Dong, X., Lee, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Domain consolidation in bacterial 50S assembly revealed by anti-sense oligonucleotide probing

Sheng, K., Dong, X., Aiyer, S., Lee, J., Djordjevic-Marquardt, S., Lyumkis, D., Williamson, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 734.52 kDa
Atom Count: 42,760
Modeled Residue Count: 3,071
Deposited Residue Count: 3,257
Unique protein chains: 13
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	B [auth 2]	37	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5 Go to UniProtKB: P0A7P5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7P5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	C [auth D]	204	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	D [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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	E [auth J]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10 Go to UniProtKB: P0AA10
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AA10
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 uL14	F [auth K]	110	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	G [auth N]	120	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44 Go to UniProtKB: P0AG44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AG44
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	H [auth P]	113	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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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	I [auth Q]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3 Go to UniProtKB: P0A7L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7L3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	J [auth R]	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	K [auth S]	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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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	L [auth T]	93	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0 Go to UniProtKB: P0ADZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADZ0
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	M [auth U]	102	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624 Go to UniProtKB: P60624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60624
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	N [auth Y]	63	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for C3SQY2 (Escherichia coli) Explore C3SQY2 Go to UniProtKB: C3SQY2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3SQY2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
23S rRNA	A [auth CA]	1,742	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Sheng, K.

Dong, X.

Lee, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM136412
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM053757

Revision History (Full details and data files)

Version 1.0: 2024-11-13
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.

9DYG | pdb_00009dyg

iSAT-PNA-RA20, RA20-B-c class

Literature

Domain consolidation in bacterial 50S assembly revealed by anti-sense oligonucleotide probing

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

Entity Groups

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: 1

Sequence Annotations

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)