Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 49-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvw Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 49-mer -A2B2CDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstu 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1717077.63 
• Atom Count: 94121 
• Residue Count: 12106 
• Unique protein chains: 49
• Unique nucleic acid chains: 2

3J7Y

Structure of the large ribosomal subunit from human mitochondria

• DOI: 10.2210/pdb3J7Y/pdb
• EMDataResource: EMD-2762

• Classification: RIBOSOME
• Organism(s): Homo sapiens


• Deposited: 2014-08-26 Released: 2014-10-15 
• Deposition Author(s): Brown, A., Amunts, A., Bai, X.C., Sugimoto, Y., Edwards, P.C., Murshudov, G., Scheres, S.H.W., Ramakrishnan, V.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the large ribosomal subunit from human mitochondria.

Brown, A., Amunts, A., Bai, X.C., Sugimoto, Y., Edwards, P.C., Murshudov, G., Scheres, S.H., Ramakrishnan, V.

(2014) Science 346: 718-722

• PubMed: 25278503 
• DOI: 10.1126/science.1258026


• PubMed Abstract: 
  

Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
uL2	D	305	Homo sapiens	Mutation(s): 0  Gene Names: MRPL2
Find proteins for Q5T653 (Homo sapiens) Go to Gene View: MRPL2 Go to UniProtKB:  Q5T653

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
uL3	E	348	Homo sapiens	Mutation(s): 0  Gene Names: MRPL3 (MRL3, RPML3)
Find proteins for P09001 (Homo sapiens) Go to Gene View: MRPL3 Go to UniProtKB:  P09001

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
uL4	F	311	Homo sapiens	Mutation(s): 0  Gene Names: MRPL4
Find proteins for Q9BYD3 (Homo sapiens) Go to Gene View: MRPL4 Go to UniProtKB:  Q9BYD3

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
bL9	H	267	Homo sapiens	Mutation(s): 0  Gene Names: MRPL9
Find proteins for Q9BYD2 (Homo sapiens) Go to Gene View: MRPL9 Go to UniProtKB:  Q9BYD2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
uL10	I	261	Homo sapiens	Mutation(s): 0  Gene Names: MRPL10 (MRPL8, RPML8)
Find proteins for Q7Z7H8 (Homo sapiens) Go to Gene View: MRPL10 Go to UniProtKB:  Q7Z7H8

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
uL11	J	192	Homo sapiens	Mutation(s): 0  Gene Names: MRPL11
Find proteins for Q9Y3B7 (Homo sapiens) Go to Gene View: MRPL11 Go to UniProtKB:  Q9Y3B7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
uL13	K	178	Homo sapiens	Mutation(s): 0  Gene Names: MRPL13
Find proteins for Q9BYD1 (Homo sapiens) Go to Gene View: MRPL13 Go to UniProtKB:  Q9BYD1

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
uL14	L	145	Homo sapiens	Mutation(s): 0  Gene Names: MRPL14 (MRPL32, RPML32)
Find proteins for Q6P1L8 (Homo sapiens) Go to Gene View: MRPL14 Go to UniProtKB:  Q6P1L8

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
uL15	M	296	Homo sapiens	Mutation(s): 0  Gene Names: MRPL15
Find proteins for Q9P015 (Homo sapiens) Go to Gene View: MRPL15 Go to UniProtKB:  Q9P015

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
uL16	N	251	Homo sapiens	Mutation(s): 0  Gene Names: MRPL16
Find proteins for Q9NX20 (Homo sapiens) Go to Gene View: MRPL16 Go to UniProtKB:  Q9NX20

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
bL17	O	175	Homo sapiens	Mutation(s): 0  Gene Names: MRPL17 (LIP2)
Find proteins for Q9NRX2 (Homo sapiens) Go to Gene View: MRPL17 Go to UniProtKB:  Q9NRX2

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
uL18	P	179	Homo sapiens	Mutation(s): 0  Gene Names: MRPL18
Find proteins for Q9H0U6 (Homo sapiens) Go to Gene View: MRPL18 Go to UniProtKB:  Q9H0U6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
bL19	Q	292	Homo sapiens	Mutation(s): 0  Gene Names: MRPL19 (KIAA0104, MRPL15)
Find proteins for P49406 (Homo sapiens) Go to Gene View: MRPL19 Go to UniProtKB:  P49406

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
bL20	R	149	Homo sapiens	Mutation(s): 0  Gene Names: MRPL20
Find proteins for Q9BYC9 (Homo sapiens) Go to Gene View: MRPL20 Go to UniProtKB:  Q9BYC9

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
bL21	S	205	Homo sapiens	Mutation(s): 0  Gene Names: MRPL21
Find proteins for Q7Z2W9 (Homo sapiens) Go to Gene View: MRPL21 Go to UniProtKB:  Q7Z2W9

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
uL22	T	212	Homo sapiens	Mutation(s): 0  Gene Names: MRPL22 (MRPL25, RPML25)
Find proteins for Q9NWU5 (Homo sapiens) Go to Gene View: MRPL22 Go to UniProtKB:  Q9NWU5

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
uL23	U	153	Homo sapiens	Mutation(s): 0  Gene Names: MRPL23 (L23MRP, RPL23L)
Find proteins for Q16540 (Homo sapiens) Go to Gene View: MRPL23 Go to UniProtKB:  Q16540

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
uL24	V	216	Homo sapiens	Mutation(s): 0  Gene Names: MRPL24
Find proteins for Q96A35 (Homo sapiens) Go to Gene View: MRPL24 Go to UniProtKB:  Q96A35

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
bL27	W	148	Homo sapiens	Mutation(s): 0  Gene Names: MRPL27
Find proteins for Q9P0M9 (Homo sapiens) Go to Gene View: MRPL27 Go to UniProtKB:  Q9P0M9

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
bL28	X	256	Homo sapiens	Mutation(s): 0  Gene Names: MRPL28 (MAAT1)
Find proteins for Q13084 (Homo sapiens) Go to Gene View: MRPL28 Go to UniProtKB:  Q13084

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
uL29	Y	250	Homo sapiens	Mutation(s): 0  Gene Names: MRPL47 (NCM1)
Find proteins for Q9HD33 (Homo sapiens) Go to Gene View: MRPL47 Go to UniProtKB:  Q9HD33

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
uL30	Z	161	Homo sapiens	Mutation(s): 0  Gene Names: MRPL30 (MRPL28, RPML28)
Find proteins for Q8TCC3 (Homo sapiens) Go to Gene View: MRPL30 Go to UniProtKB:  Q8TCC3

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
bL32	0	188	Homo sapiens	Mutation(s): 0  Gene Names: MRPL32
Find proteins for Q9BYC8 (Homo sapiens) Go to Gene View: MRPL32 Go to UniProtKB:  Q9BYC8

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
bL33	1	65	Homo sapiens	Mutation(s): 0  Gene Names: MRPL33 (C2orf1)
Find proteins for O75394 (Homo sapiens) Go to Gene View: MRPL33 Go to UniProtKB:  O75394

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
bL34	2	92	Homo sapiens	Mutation(s): 0  Gene Names: MRPL34
Find proteins for Q9BQ48 (Homo sapiens) Go to Gene View: MRPL34 Go to UniProtKB:  Q9BQ48

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
bL35	3	188	Homo sapiens	Mutation(s): 0  Gene Names: MRPL35
Find proteins for Q9NZE8 (Homo sapiens) Go to Gene View: MRPL35 Go to UniProtKB:  Q9NZE8

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
bL36	4	103	Homo sapiens	Mutation(s): 0  Gene Names: MRPL36 (BRIP1)
Find proteins for Q9P0J6 (Homo sapiens) Go to Gene View: MRPL36 Go to UniProtKB:  Q9P0J6

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
mL37	5	423	Homo sapiens	Mutation(s): 0  Gene Names: MRPL37 (MRPL2, RPML2)
Find proteins for Q9BZE1 (Homo sapiens) Go to Gene View: MRPL37 Go to UniProtKB:  Q9BZE1

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
mL38	6	380	Homo sapiens	Mutation(s): 0  Gene Names: MRPL38
Find proteins for Q96DV4 (Homo sapiens) Go to Gene View: MRPL38 Go to UniProtKB:  Q96DV4

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
mL39	7	338	Homo sapiens	Mutation(s): 0  Gene Names: MRPL39 (C21orf92, MRPL5, RPML5)
Find proteins for Q9NYK5 (Homo sapiens) Go to Gene View: MRPL39 Go to UniProtKB:  Q9NYK5

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
mL40	8	206	Homo sapiens	Mutation(s): 0  Gene Names: MRPL40 (NLVCF, URIM)
Find proteins for Q9NQ50 (Homo sapiens) Go to Gene View: MRPL40 Go to UniProtKB:  Q9NQ50

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
mL41	9	137	Homo sapiens	Mutation(s): 0  Gene Names: MRPL41 (BMRP, MRPL27, RPML27)
Find proteins for Q8IXM3 (Homo sapiens) Go to Gene View: MRPL41 Go to UniProtKB:  Q8IXM3

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
mL42	a	142	Homo sapiens	Mutation(s): 0  Gene Names: MRPL42 (MRPL31, MRPS32, RPML31)
Find proteins for Q9Y6G3 (Homo sapiens) Go to Gene View: MRPL42 Go to UniProtKB:  Q9Y6G3

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
mL43	b	155	Homo sapiens	Mutation(s): 0  Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens) Go to Gene View: MRPL43 Go to UniProtKB:  Q8N983

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
mL44	c	332	Homo sapiens	Mutation(s): 0  Gene Names: MRPL44 EC: 3.1.26.-
Find proteins for Q9H9J2 (Homo sapiens) Go to Gene View: MRPL44 Go to UniProtKB:  Q9H9J2

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
mL45	d	306	Homo sapiens	Mutation(s): 0  Gene Names: MRPL45
Find proteins for Q9BRJ2 (Homo sapiens) Go to Gene View: MRPL45 Go to UniProtKB:  Q9BRJ2

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
mL46	e	279	Homo sapiens	Mutation(s): 0  Gene Names: MRPL46 (C15orf4, LIECG2)
Find proteins for Q9H2W6 (Homo sapiens) Go to Gene View: MRPL46 Go to UniProtKB:  Q9H2W6

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
mL48	f	211	Homo sapiens	Mutation(s): 0  Gene Names: MRPL48
Find proteins for Q96GC5 (Homo sapiens) Go to Gene View: MRPL48 Go to UniProtKB:  Q96GC5

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
mL49	g	166	Homo sapiens	Mutation(s): 0  Gene Names: MRPL49 (C11orf4, NOF1)
Find proteins for Q13405 (Homo sapiens) Go to Gene View: MRPL49 Go to UniProtKB:  Q13405

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
mL50	h	158	Homo sapiens	Mutation(s): 0  Gene Names: MRPL50
Find proteins for Q8N5N7 (Homo sapiens) Go to Gene View: MRPL50 Go to UniProtKB:  Q8N5N7

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
mL51	i	128	Homo sapiens	Mutation(s): 0  Gene Names: MRPL51 (MRP64)
Find proteins for Q4U2R6 (Homo sapiens) Go to Gene View: MRPL51 Go to UniProtKB:  Q4U2R6

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
mL52	j	123	Homo sapiens	Mutation(s): 0  Gene Names: MRPL52
Find proteins for Q86TS9 (Homo sapiens) Go to Gene View: MRPL52 Go to UniProtKB:  Q86TS9

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
mL53	k	112	Homo sapiens	Mutation(s): 0  Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens) Go to Gene View: MRPL53 Go to UniProtKB:  Q96EL3

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
mL63	o	102	Homo sapiens	Mutation(s): 0  Gene Names: MRPL57 (MRP63)
Find proteins for Q9BQC6 (Homo sapiens) Go to Gene View: MRPL57 Go to UniProtKB:  Q9BQC6

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
ICT1	p	206	Homo sapiens	Mutation(s): 0  Gene Names: MRPL58 (DS1, ICT1) EC: 3.1.1.29
Find proteins for Q14197 (Homo sapiens) Go to Gene View: MRPL58 Go to UniProtKB:  Q14197

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
CRIF1	q	222	Homo sapiens	Mutation(s): 0  Gene Names: GADD45GIP1 (MRPL59, PLINP1, PRG6)
Find proteins for Q8TAE8 (Homo sapiens) Go to Gene View: GADD45GIP1 Go to UniProtKB:  Q8TAE8

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
bS18a	r	196	Homo sapiens	Mutation(s): 0  Gene Names: MRPS18A
Find proteins for Q9NVS2 (Homo sapiens) Go to Gene View: MRPS18A Go to UniProtKB:  Q9NVS2

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
mS30	s	439	Homo sapiens	Mutation(s): 0  Gene Names: MRPS30 (PDCD9)
Find proteins for Q9NP92 (Homo sapiens) Go to Gene View: MRPS30 Go to UniProtKB:  Q9NP92

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
unknown protein	t	127	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Length	Organism
16S rRNA	A	1559	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism
mt-tRNAVal	B	73	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	0, 4, r	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
A	A	ADENOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG	A, E	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	f, t	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-26 
• Released Date: 2014-10-15 
• Deposition Author(s): Brown, A., Amunts, A., Bai, X.C., Sugimoto, Y., Edwards, P.C., Murshudov, G., Scheres, S.H.W., Ramakrishnan, V.

Revision History 

• Version 1.0: 2014-10-15
  Type: Initial release
• Version 1.1: 2014-11-19
  Type: Database references
• Version 1.2: 2018-07-18
  Type: Data collection