5XYU

Small subunit of Mycobacterium smegmatis ribosome

PDB DOI: https://doi.org/10.2210/pdb5XYU/pdb
NAKB: 5XYU
EM Map EMD-6790: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Mycolicibacterium smegmatis MC2 155
Mutation(s): No

Deposited: 2017-07-10 Released: 2017-09-27
Deposition Author(s): Li, Z., Zhang, Y., Zheng, L., Ge, X., Sanyal, S., Gao, N.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.

Li, Z., Ge, X., Zhang, Y., Zheng, L., Sanyal, S., Gao, N.

(2018) Protein Cell 9: 384-388

PubMed: 28875450 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-017-0456-9
Primary Citation of Related Structures:
5XYM, 5XYU

Organizational Affiliation

State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.

Macromolecule Content

Total Structure Weight: 764.83 kDa
Atom Count: 45,157
Modelled Residue Count: 3,345
Deposited Residue Count: 3,933
Unique protein chains: 19
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	B [auth C]	275	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD7 Go to UniProtKB: A0QSD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QSD7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	C [auth D]	201	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSL7 Go to UniProtKB: A0QSL7
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UniProt Group	A0QSL7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	D [auth E]	214	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG6 Go to UniProtKB: A0QSG6
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QSG6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	E [auth F]	90	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R7F9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R7F9 Go to UniProtKB: A0R7F9
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R7F9
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	F [auth G]	156	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS97 Go to UniProtKB: A0QS97
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QS97
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	G [auth H]	132	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG3 Go to UniProtKB: A0QSG3
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UniProt Group	A0QSG3
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	H [auth I]	150	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSP9 Go to UniProtKB: A0QSP9
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QSP9
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	I [auth J]	101	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD0 Go to UniProtKB: A0QSD0
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UniProt Group	A0QSD0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	J [auth K]	138	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSL6 Go to UniProtKB: A0QSL6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QSL6
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	K [auth L]	124	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS96 Go to UniProtKB: A0QS96
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QS96
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	L [auth M]	124	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSL5 Go to UniProtKB: A0QSL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QSL5
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	M [auth N]	61	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSG2 Go to UniProtKB: A0QSG2
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UniProt Group	A0QSG2
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	N [auth O]	89	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QVQ3 Go to UniProtKB: A0QVQ3
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UniProt Group	A0QVQ3
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	O [auth P]	156	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QV37 Go to UniProtKB: A0QV37
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UniProt Group	A0QV37
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	P [auth Q]	98	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSE0 Go to UniProtKB: A0QSE0
Entity Groups
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UniProt Group	A0QSE0
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18 2	Q [auth R]	84	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R7F7 Go to UniProtKB: A0R7F7
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UniProt Group	A0R7F7
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	R [auth S]	93	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QSD5 Go to UniProtKB: A0QSD5
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UniProt Group	A0QSD5
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	S [auth T]	86	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R102 Go to UniProtKB: A0R102
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UniProt Group	A0R102
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved domain protein	T [auth U]	33	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QR10 Go to UniProtKB: A0QR10
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QR10
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Reference Sequence

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S RNA	A	1,528	Mycolicibacterium smegmatis MC2 155
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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 AA [auth A] SDF format, chain AB [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth A] SDF format, chain DA [auth A] SDF format, chain DB [auth A] SDF format, chain EA [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 HA [auth A] SDF format, chain HB [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth A] SDF format, chain KA [auth A] SDF format, chain KB [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth A] SDF format, chain MA [auth A] SDF format, chain MB [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth A] SDF format, chain OA [auth A] SDF format, chain OB [auth A] SDF format, chain PA [auth A] SDF format, chain PB [auth C] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [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 Y [auth A] SDF format, chain YA [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain EA [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 HA [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [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 Y [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth A]	AA [auth A] AB [auth A] BA [auth A] BB [auth A] CA [auth A] AA [auth A], AB [auth A], BA [auth A], BB [auth A], CA [auth A], CB [auth A], DA [auth A], DB [auth A], EA [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], JA [auth A], JB [auth A], KA [auth A], KB [auth A], LA [auth A], LB [auth A], MA [auth A], MB [auth A], NA [auth A], NB [auth A], OA [auth A], OB [auth A], PA [auth A], PB [auth C], QA [auth A], RA [auth A], SA [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], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain EA [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 JA [auth A] Focus chain JB [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [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 Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain EA [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 JA [auth A] Focus chain JB [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [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 Y [auth A] Focus chain YA [auth A] Focus chain Z [auth A] Focus chain ZA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2018-04-11
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Advisory, Derived calculations
Version 1.3: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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Help and Resources

5XYU

Small subunit of Mycobacterium smegmatis ribosome

Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.

Entity ID: 2

UniProt

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Entity ID: 3

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Entity ID: 15

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Entity ID: 19

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Entity ID: 20