3J6B

Structure of the yeast mitochondrial large ribosomal subunit

• PDB DOI: https://doi.org/10.2210/pdb3J6B/pdb
• Entry: 3J6B supersedes: 1VW3, 1VW4
• NAKB: 3J6B
• EM Map EMD-2566: EMDB EMDataResource

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2014-01-22 Released: 2014-04-09 
• Deposition Author(s): Amunts, A., Brown, A., Bai, X.C., Llacer, J.L., Hussain, T., Emsley, P., Long, F., Murshudov, G., Scheres, S.H.W., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the yeast mitochondrial large ribosomal subunit.

Amunts, A., Brown, A., Bai, X.C., Llacer, J.L., Hussain, T., Emsley, P., Long, F., Murshudov, G., Scheres, S.H., Ramakrishnan, V.

(2014) Science 343: 1485-1489

• PubMed: 24675956 
• DOI: https://doi.org/10.1126/science.1249410
• Primary Citation of Related Structures:  
  3J6B


• PubMed Abstract: 
  

  Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 39-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2,040.16 kDa 
• Atom Count: 111,319 
• Modelled Residue Count: 9,445 
• Deposited Residue Count: 11,821 
• Unique protein chains: 39
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein RML2, mitochondrial	B	393	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32611 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32611  Go to UniProtKB:  P32611

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L9, mitochondrial	C	269	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P31334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31334  Go to UniProtKB:  P31334

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein YmL6, mitochondrial	D	286	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P51998 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P51998  Go to UniProtKB:  P51998

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L7, mitochondrial	E	292	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36519  Go to UniProtKB:  P36519

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L6, mitochondrial	F	214	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32904  Go to UniProtKB:  P32904

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L50, mitochondrial	G	139	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53724  Go to UniProtKB:  P53724

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L23, mitochondrial	H	163	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12487 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12487  Go to UniProtKB:  Q12487

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L38, mitochondrial	I	138	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P35996 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35996  Go to UniProtKB:  P35996

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L10, mitochondrial	J	322	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36520 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36520  Go to UniProtKB:  P36520

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L16, mitochondrial	K	232	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38064  Go to UniProtKB:  P38064

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L8, mitochondrial	L	238	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22353 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22353  Go to UniProtKB:  P22353

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein IMG1, mitochondrial	M	169	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25626 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25626  Go to UniProtKB:  P25626

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L49, mitochondrial	N	161	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40858 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40858  Go to UniProtKB:  P40858

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L22, mitochondrial	O	309	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53881 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53881  Go to UniProtKB:  P53881

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L41, mitochondrial	P	263	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32387  Go to UniProtKB:  P32387

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L40, mitochondrial	Q	297	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36534 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36534  Go to UniProtKB:  P36534

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L2, mitochondrial	R	371	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P12687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12687  Go to UniProtKB:  P12687

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L24, mitochondrial	S	258	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36525  Go to UniProtKB:  P36525

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L4, mitochondrial	T	319	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36517 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36517  Go to UniProtKB:  P36517

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L33, mitochondrial	U	86	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20084 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20084  Go to UniProtKB:  P20084

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L36, mitochondrial	V	177	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36531 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36531  Go to UniProtKB:  P36531

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L32, mitochondrial	W	183	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25348  Go to UniProtKB:  P25348

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L39, mitochondrial	X	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36533 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36533  Go to UniProtKB:  P36533

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L34, mitochondrial	Y	105	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04598 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04598  Go to UniProtKB:  Q04598

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial ribosomal protein YNL122C	Z	115	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53921 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53921  Go to UniProtKB:  P53921

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein RTC6, mitochondrial	AA [auth 0]	93	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for O14464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O14464  Go to UniProtKB:  O14464

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L35, mitochondrial	BA [auth 1]	367	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q06678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06678  Go to UniProtKB:  Q06678

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L28, mitochondrial	CA [auth 2]	147	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36527 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36527  Go to UniProtKB:  P36527

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L27, mitochondrial	DA [auth 3]	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36526 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36526  Go to UniProtKB:  P36526

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L51, mitochondrial	EA [auth 4]	140	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q06090 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06090  Go to UniProtKB:  Q06090

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L3, mitochondrial	FA [auth 5]	390	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36516  Go to UniProtKB:  P36516

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L17, mitochondrial	GA [auth 6]	281	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36528 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36528  Go to UniProtKB:  P36528

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein IMG2, mitochondrial	HA [auth 7]	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25642 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25642  Go to UniProtKB:  P25642

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L13, mitochondrial	IA [auth 8]	264	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02204  Go to UniProtKB:  Q02204

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L15, mitochondrial	JA [auth 9]	253	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36523  Go to UniProtKB:  P36523

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L20, mitochondrial	KA [auth a]	195	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22354 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22354  Go to UniProtKB:  P22354

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L25, mitochondrial	LA [auth b]	157	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23369 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23369  Go to UniProtKB:  P23369

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
54S ribosomal protein L31, mitochondrial	MA [auth c]	131	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P14063 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14063  Go to UniProtKB:  P14063

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial homologous recombination protein 1	NA [auth d]	226	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q06630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06630  Go to UniProtKB:  Q06630

Entity ID: 1
Molecule	Chains	Length	Organism	Image
21S ribosomal RNA	A	3,296	Saccharomyces cerevisiae

Entity ID: 41
Molecule	Chains	Length	Organism	Image
E-site tRNA	OA [auth e]	20	Saccharomyces cerevisiae

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	WE [auth W], XE [auth 0]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AB [auth A], AC [auth A], AD [auth A], AE [auth A], BB [auth A], BC [auth A], BD [auth A], BE [auth A], CB [auth A], CC [auth A], CD [auth A], CE [auth A], DB [auth A], DC [auth A], DD [auth A], DE [auth A], EB [auth A], EC [auth A], ED [auth A], EE [auth A], FB [auth A], FC [auth A], FD [auth A], FE [auth A], GB [auth A], GC [auth A], GD [auth A], GE [auth A], HB [auth A], HC [auth A], HD [auth A], HE [auth A], IB [auth A], IC [auth A], ID [auth A], IE [auth A], JB [auth A], JC [auth A], JD [auth A], JE [auth A], KB [auth A], KC [auth A], KD [auth A], KE [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], QA [auth A], QB [auth A], QC [auth A], QD [auth A], QE [auth A], RA [auth A], RB [auth A], RC [auth A], RD [auth A], RE [auth A], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], TA [auth A], TB [auth A], TC [auth A], TD [auth A], TE [auth A], UA [auth A], UB [auth A], UC [auth A], UD [auth A], VA [auth A], VB [auth A], VC [auth A], VD [auth A], VE [auth N], WA [auth A], WB [auth A], WC [auth A], WD [auth A], XA [auth A], XB [auth A], XC [auth A], XD [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	UE [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Amunts, A., Brown, A., Bai, X.C., Llacer, J.L., Hussain, T., Emsley, P., Long, F., Murshudov, G., Scheres, S.H.W., Ramakrishnan, V.
• This entry supersedes: 1VW3, 1VW4

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2014-07-09
  Changes: Other
• Version 1.2: 2014-12-10
  Changes: Other
• Version 1.3: 2014-12-17
  Changes: Other
• Version 1.4: 2018-07-18
  Changes: Data collection
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Derived calculations