Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 54-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzAB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 1797380.75 
• Atom Count: 98998 
• Residue Count: 12785 
• Unique protein chains: 54
• Unique nucleic acid chains: 2

5OOL

Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA

• DOI: 10.2210/pdb5OOL/pdb
• EMDataResource: EMD-3842

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


• Deposited: 2017-08-08 Released: 2017-09-13 
• Deposition Author(s): Brown, A., Rathore, S., Kimanius, D., Aibara, S., Bai, X.C., Rorbach, J., Amunts, A., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of the human mitochondrial ribosome in native states of assembly.

Brown, A., Rathore, S., Kimanius, D., Aibara, S., Bai, X.C., Rorbach, J., Amunts, A., Ramakrishnan, V.

(2017) Nat. Struct. Mol. Biol. 24: 866-869

• PubMed: 28892042 
• DOI: 10.1038/nsmb.3464
• Primary Citation of Related Structures:  
  5OOM


• PubMed Abstract: 
  

Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
39S ribosomal protein L2, mitochondrial	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
39S ribosomal protein L3, mitochondrial	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
39S ribosomal protein L4, mitochondrial	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
39S ribosomal protein L9, mitochondrial	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
39S ribosomal protein L10, mitochondrial	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
39S ribosomal protein L11, mitochondrial	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
39S ribosomal protein L13, mitochondrial	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
39S ribosomal protein L14, mitochondrial	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
39S ribosomal protein L15, mitochondrial	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
39S ribosomal protein L16, mitochondrial	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
39S ribosomal protein L17, mitochondrial	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
39S ribosomal protein L18, mitochondrial	P	180	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
39S ribosomal protein L19, mitochondrial	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
39S ribosomal protein L20, mitochondrial	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
39S ribosomal protein L21, mitochondrial	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
39S ribosomal protein L22, mitochondrial	T	206	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
39S ribosomal protein L23, mitochondrial	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
39S ribosomal protein L24, mitochondrial	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
39S ribosomal protein L27, mitochondrial	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
39S ribosomal protein L28, mitochondrial	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
39S ribosomal protein L47, mitochondrial	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
39S ribosomal protein L30, mitochondrial	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
39S ribosomal protein L32, mitochondrial	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
39S ribosomal protein L33, mitochondrial	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
39S ribosomal protein L34, mitochondrial	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
39S ribosomal protein L35, mitochondrial	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
39S ribosomal protein L36, mitochondrial	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
39S ribosomal protein L37, mitochondrial	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
39S ribosomal protein L38, mitochondrial	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
39S ribosomal protein L39, mitochondrial	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
39S ribosomal protein L40, mitochondrial	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
39S ribosomal protein L41, mitochondrial	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
39S ribosomal protein L42, mitochondrial	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
39S ribosomal protein L43, mitochondrial	b	215	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
39S ribosomal protein L44, mitochondrial	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
39S ribosomal protein L45, mitochondrial	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
39S ribosomal protein L46, mitochondrial	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
39S ribosomal protein L48, mitochondrial	f	212	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
39S ribosomal protein L49, mitochondrial	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
39S ribosomal protein L50, mitochondrial	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
39S ribosomal protein L51, mitochondrial	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
39S ribosomal protein L52, mitochondrial	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
39S ribosomal protein L53, mitochondrial	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
39S ribosomal protein L54, mitochondrial	l	138	Homo sapiens	Mutation(s): 0  Gene Names: MRPL54
Find proteins for Q6P161 (Homo sapiens) Go to Gene View: MRPL54 Go to UniProtKB:  Q6P161

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
39S ribosomal protein L55, mitochondrial	m	128	Homo sapiens	Mutation(s): 0  Gene Names: MRPL55
Find proteins for Q7Z7F7 (Homo sapiens) Go to Gene View: MRPL55 Go to UniProtKB:  Q7Z7F7

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
Ribosomal protein 63, mitochondrial	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: 49
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-tRNA hydrolase ICT1, mitochondrial	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: 50
Molecule	Chains	Sequence Length	Organism	Details
Growth arrest and DNA damage-inducible proteins-interacting protein 1	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: 51
Molecule	Chains	Sequence Length	Organism	Details
39S ribosomal protein S18a, mitochondrial	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: 52
Molecule	Chains	Sequence Length	Organism	Details
39S ribosomal protein S30, mitochondrial	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: 53
Molecule	Chains	Sequence Length	Organism	Details
Unknown protein or protein extension	t	28	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details
Mitochondrial assembly of ribosomal large subunit protein 1	u	234	Homo sapiens	Mutation(s): 0  Gene Names: MALSU1 (C7orf30)
Find proteins for Q96EH3 (Homo sapiens) Go to Gene View: MALSU1 Go to UniProtKB:  Q96EH3

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details
MIEF1 upstream open reading frame protein	v	70	Homo sapiens	Mutation(s): 0  Gene Names: MIEF1
Find proteins for L0R8F8 (Homo sapiens) Go to Gene View: MIEF1 Go to UniProtKB:  L0R8F8

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
Acyl carrier protein, mitochondrial	w	156	Homo sapiens	Mutation(s): 0  Gene Names: NDUFAB1
Find proteins for O14561 (Homo sapiens) Go to Gene View: NDUFAB1 Go to UniProtKB:  O14561

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

Entity ID: 2
Molecule	Chains	Length	Organism
mitochondrial tRNAVal	B	69	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	0, 4, I	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
PNS	v	4'-PHOSPHOPANTETHEINE C11 H23 N2 O7 P S JDMUPRLRUUMCTL-VIFPVBQESA-N
MG	A, D, g, M, T, W	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-08-08 
• Released Date: 2017-09-13 
• Deposition Author(s): Brown, A., Rathore, S., Kimanius, D., Aibara, S., Bai, X.C., Rorbach, J., Amunts, A., Ramakrishnan, V.

Revision History 

• Version 1.0: 2017-09-13
  Type: Initial release
• Version 1.1: 2017-09-20
  Type: Database references
• Version 1.2: 2017-10-18
  Type: Database references
• Version 1.3: 2019-02-20
  Type: Advisory, Data collection, Derived calculations