5OOL

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/nsmb.3464
  • Primary Citation of Related Structures:  

  • 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 ba ...

    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.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L2, mitochondrial
D
305Homo sapiensMutation(s): 0 
Gene Names: MRPL2
Find proteins for Q5T653 (Homo sapiens)
Go to Gene View: MRPL2
Go to UniProtKB:  Q5T653
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L3, mitochondrial
E
348Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L4, mitochondrial
F
311Homo sapiensMutation(s): 0 
Gene Names: MRPL4
Find proteins for Q9BYD3 (Homo sapiens)
Go to Gene View: MRPL4
Go to UniProtKB:  Q9BYD3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L9, mitochondrial
H
267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
Find proteins for Q9BYD2 (Homo sapiens)
Go to Gene View: MRPL9
Go to UniProtKB:  Q9BYD2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L10, mitochondrial
I
261Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L11, mitochondrial
J
192Homo sapiensMutation(s): 0 
Gene Names: MRPL11
Find proteins for Q9Y3B7 (Homo sapiens)
Go to Gene View: MRPL11
Go to UniProtKB:  Q9Y3B7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L13, mitochondrial
K
178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
Find proteins for Q9BYD1 (Homo sapiens)
Go to Gene View: MRPL13
Go to UniProtKB:  Q9BYD1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L14, mitochondrial
L
145Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L15, mitochondrial
M
296Homo sapiensMutation(s): 0 
Gene Names: MRPL15
Find proteins for Q9P015 (Homo sapiens)
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Go to UniProtKB:  Q9P015
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L16, mitochondrial
N
251Homo sapiensMutation(s): 0 
Gene Names: MRPL16
Find proteins for Q9NX20 (Homo sapiens)
Go to Gene View: MRPL16
Go to UniProtKB:  Q9NX20
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L17, mitochondrial
O
175Homo sapiensMutation(s): 0 
Gene Names: MRPL17 (LIP2)
Find proteins for Q9NRX2 (Homo sapiens)
Go to Gene View: MRPL17
Go to UniProtKB:  Q9NRX2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L18, mitochondrial
P
180Homo sapiensMutation(s): 0 
Gene Names: MRPL18
Find proteins for Q9H0U6 (Homo sapiens)
Go to Gene View: MRPL18
Go to UniProtKB:  Q9H0U6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L19, mitochondrial
Q
292Homo sapiensMutation(s): 0 
Gene Names: MRPL19 (KIAA0104, MRPL15)
Find proteins for P49406 (Homo sapiens)
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Go to UniProtKB:  P49406
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L20, mitochondrial
R
149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
Find proteins for Q9BYC9 (Homo sapiens)
Go to Gene View: MRPL20
Go to UniProtKB:  Q9BYC9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L21, mitochondrial
S
205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
Find proteins for Q7Z2W9 (Homo sapiens)
Go to Gene View: MRPL21
Go to UniProtKB:  Q7Z2W9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L22, mitochondrial
T
206Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L23, mitochondrial
U
153Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L24, mitochondrial
V
216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
Find proteins for Q96A35 (Homo sapiens)
Go to Gene View: MRPL24
Go to UniProtKB:  Q96A35
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L27, mitochondrial
W
148Homo sapiensMutation(s): 0 
Gene Names: MRPL27
Find proteins for Q9P0M9 (Homo sapiens)
Go to Gene View: MRPL27
Go to UniProtKB:  Q9P0M9
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L28, mitochondrial
X
256Homo sapiensMutation(s): 0 
Gene Names: MRPL28 (MAAT1)
Find proteins for Q13084 (Homo sapiens)
Go to Gene View: MRPL28
Go to UniProtKB:  Q13084
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L47, mitochondrial
Y
250Homo sapiensMutation(s): 0 
Gene Names: MRPL47 (NCM1)
Find proteins for Q9HD33 (Homo sapiens)
Go to Gene View: MRPL47
Go to UniProtKB:  Q9HD33
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L30, mitochondrial
Z
161Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L32, mitochondrial
0
188Homo sapiensMutation(s): 0 
Gene Names: MRPL32
Find proteins for Q9BYC8 (Homo sapiens)
Go to Gene View: MRPL32
Go to UniProtKB:  Q9BYC8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L33, mitochondrial
1
65Homo sapiensMutation(s): 0 
Gene Names: MRPL33 (C2orf1)
Find proteins for O75394 (Homo sapiens)
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Go to UniProtKB:  O75394
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L34, mitochondrial
2
92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
Find proteins for Q9BQ48 (Homo sapiens)
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Go to UniProtKB:  Q9BQ48
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L35, mitochondrial
3
188Homo sapiensMutation(s): 0 
Gene Names: MRPL35
Find proteins for Q9NZE8 (Homo sapiens)
Go to Gene View: MRPL35
Go to UniProtKB:  Q9NZE8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L36, mitochondrial
4
103Homo sapiensMutation(s): 0 
Gene Names: MRPL36 (BRIP1)
Find proteins for Q9P0J6 (Homo sapiens)
Go to Gene View: MRPL36
Go to UniProtKB:  Q9P0J6
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L37, mitochondrial
5
423Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L38, mitochondrial
6
380Homo sapiensMutation(s): 0 
Gene Names: MRPL38
Find proteins for Q96DV4 (Homo sapiens)
Go to Gene View: MRPL38
Go to UniProtKB:  Q96DV4
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L39, mitochondrial
7
338Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L40, mitochondrial
8
206Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L41, mitochondrial
9
137Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L42, mitochondrial
a
142Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L43, mitochondrial
b
215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens)
Go to Gene View: MRPL43
Go to UniProtKB:  Q8N983
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L44, mitochondrial
c
332Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L45, mitochondrial
d
306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
Find proteins for Q9BRJ2 (Homo sapiens)
Go to Gene View: MRPL45
Go to UniProtKB:  Q9BRJ2
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L46, mitochondrial
e
279Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L48, mitochondrial
f
212Homo sapiensMutation(s): 0 
Gene Names: MRPL48
Find proteins for Q96GC5 (Homo sapiens)
Go to Gene View: MRPL48
Go to UniProtKB:  Q96GC5
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L49, mitochondrial
g
166Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L50, mitochondrial
h
158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
Find proteins for Q8N5N7 (Homo sapiens)
Go to Gene View: MRPL50
Go to UniProtKB:  Q8N5N7
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L51, mitochondrial
i
128Homo sapiensMutation(s): 0 
Gene Names: MRPL51 (MRP64)
Find proteins for Q4U2R6 (Homo sapiens)
Go to Gene View: MRPL51
Go to UniProtKB:  Q4U2R6
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L52, mitochondrial
j
123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
Find proteins for Q86TS9 (Homo sapiens)
Go to Gene View: MRPL52
Go to UniProtKB:  Q86TS9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L53, mitochondrial
k
112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens)
Go to Gene View: MRPL53
Go to UniProtKB:  Q96EL3
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L54, mitochondrial
l
138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
Find proteins for Q6P161 (Homo sapiens)
Go to Gene View: MRPL54
Go to UniProtKB:  Q6P161
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L55, mitochondrial
m
128Homo sapiensMutation(s): 0 
Gene Names: MRPL55
Find proteins for Q7Z7F7 (Homo sapiens)
Go to Gene View: MRPL55
Go to UniProtKB:  Q7Z7F7
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein 63, mitochondrial
o
102Homo sapiensMutation(s): 0 
Gene Names: MRPL57 (MRP63)
Find proteins for Q9BQC6 (Homo sapiens)
Go to Gene View: MRPL57
Go to UniProtKB:  Q9BQC6
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-tRNA hydrolase ICT1, mitochondrial
p
206Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Growth arrest and DNA damage-inducible proteins-interacting protein 1
q
222Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein S18a, mitochondrial
r
196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
Find proteins for Q9NVS2 (Homo sapiens)
Go to Gene View: MRPS18A
Go to UniProtKB:  Q9NVS2
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein S30, mitochondrial
s
439Homo sapiensMutation(s): 0 
Gene Names: MRPS30 (PDCD9)
Find proteins for Q9NP92 (Homo sapiens)
Go to Gene View: MRPS30
Go to UniProtKB:  Q9NP92
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Unknown protein or protein extension
t
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial assembly of ribosomal large subunit protein 1
u
234Homo sapiensMutation(s): 0 
Gene Names: MALSU1 (C7orf30)
Find proteins for Q96EH3 (Homo sapiens)
Go to Gene View: MALSU1
Go to UniProtKB:  Q96EH3
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
MIEF1 upstream open reading frame protein
v
70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
Find proteins for L0R8F8 (Homo sapiens)
Go to Gene View: MIEF1
Go to UniProtKB:  L0R8F8
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein, mitochondrial
w
156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
Find proteins for O14561 (Homo sapiens)
Go to Gene View: NDUFAB1
Go to UniProtKB:  O14561
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1559Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
mitochondrial tRNAValB69Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
0, 4, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PNS
Query on PNS

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Download CCD File 
v
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, D, g, M, T, W
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
t
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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