7ASM

Staphylococcus aureus 50S after 30 minutes incubation at 37C

PDB DOI: https://doi.org/10.2210/pdb7ASM/pdb
NAKB: 7ASM
EM Map EMD-11900: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Staphylococcus aureus
Expression System: Staphylococcus aureus
Mutation(s): No

Deposited: 2020-10-27 Released: 2021-11-17
Deposition Author(s): Cimicata, G., Bashan, A., Yonath, A.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Staphylococcus aureus 50S after 30 minutes incubation a 37C

Cimicata, G., Bashan, A., Yonath, A.

To be published.

Macromolecule Content

Total Structure Weight: 1,322.93 kDa
Atom Count: 86,149
Modelled Residue Count: 5,985
Deposited Residue Count: 6,078
Unique protein chains: 27
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	A [auth N]	114	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZ42 Go to UniProtKB: Q2FZ42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FZ42
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	B [auth E]	206	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW07 Go to UniProtKB: Q2FW07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW07
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	E [auth C]	274	Staphylococcus aureus	Mutation(s): 0 Gene Names: rap, rplB
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P60430 Go to UniProtKB: P60430
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60430
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	F [auth G]	175	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW21 Go to UniProtKB: Q2FW21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW21
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	G [auth H]	145	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW38 Go to UniProtKB: Q2FW38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW38
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	H [auth J]	146	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0F8 Go to UniProtKB: P0A0F8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A0F8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	I [auth K]	137	Staphylococcus aureus	Mutation(s): 0 Gene Names: rplP, rplP_1, BN1321_380075, BTN44_13635, C7P97_04110, CSC83_04395, CSC87_02245, CV021_17950, D1G01_09450, D1G05_10690... rplP, rplP_1, BN1321_380075, BTN44_13635, C7P97_04110, CSC83_04395, CSC87_02245, CV021_17950, D1G01_09450, D1G05_10690, D1G09_02860, D1G21_09920, EF900_08535, EP54_02110, EQ90_01255, ERS072840_01149, ERS140147_00631, HMPREF3211_01568, M1K003_0786, NCTC10654_02415, NCTC10702_03541, NCTC13131_01586, NCTC5664_01669, NCTC6133_03033, NCTC7878_01016, NCTC7988_02322, RK64_11945, SAMEA1708664_00133, SAMEA1708674_02418, SAMEA2445518_02259
UniProt
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW13 Go to UniProtKB: Q2FW13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW13
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	J [auth M]	119	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW22 Go to UniProtKB: Q2FW22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW22
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	K [auth O]	116	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXQ1 Go to UniProtKB: Q2FXQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXQ1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	L [auth P]	102	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXS8 Go to UniProtKB: Q2FXS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXS8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	M [auth R]	89	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW08 Go to UniProtKB: Q2FW08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW08
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	N [auth S]	104	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW17 Go to UniProtKB: Q2FW17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW17
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	O [auth T]	94	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FJE0 (Staphylococcus aureus (strain USA300)) Explore Q2FJE0 Go to UniProtKB: Q2FJE0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FJE0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	P [auth U]	79	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXT0 Go to UniProtKB: Q2FXT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXT0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	Q [auth W]	67	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW14 Go to UniProtKB: Q2FW14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW14
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	R [auth 3]	64	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXQ0 Go to UniProtKB: Q2FXQ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXQ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	S [auth 1]	47	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FYU6 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FYU6 Go to UniProtKB: Q2FYU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FYU6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	T [auth 2]	43	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FUQ0 Go to UniProtKB: Q2FUQ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FUQ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	U [auth 4]	37	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW29 Go to UniProtKB: Q2FW29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW29
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	V [auth D]	215	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW06 Go to UniProtKB: Q2FW06
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW06
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	W [auth F]	158	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW18 Go to UniProtKB: Q2FW18
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW18
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	X [auth I]	122	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW16 Go to UniProtKB: Q2FW16
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW16
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	Y [auth Q]	112	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW11 Go to UniProtKB: Q2FW11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW11
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	Z [auth V]	49	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZ60 Go to UniProtKB: Q2FZ60
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FZ60
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	AA [auth X]	58	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0G2 Go to UniProtKB: P0A0G2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A0G2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	BA [auth Z]	48	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZF1 Go to UniProtKB: Q2FZF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FZF1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	CA [auth L]	120	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FW33 Go to UniProtKB: Q2FW33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FW33
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
23S rRNA	C [auth A]	2,923	Staphylococcus aureus
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5S rRNA	D [auth B]	115	Staphylococcus aureus
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 DA [auth A] MOL2 format, chain DA [auth A]	DA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-17

Deposition Author(s):

Cimicata, G.

Bashan, A.

Yonath, A.

Funding Organization	Location	Grant Number
European Research Council (ERC)		322581

Revision History (Full details and data files)

Version 1.0: 2021-11-17
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

Prepare Data

Validate Data

Deposit Data

Help and Resources

7ASM

Staphylococcus aureus 50S after 30 minutes incubation at 37C

Staphylococcus aureus 50S after 30 minutes incubation a 37C

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

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: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

Sequence Annotations

Entity ID: 20

UniProt

Entity Groups

Sequence Annotations

Entity ID: 21