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 1.4 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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L2, mitochondrial
D
305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
Find proteins for Q5T653 (Homo sapiens)
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PHAROS  Q5T653
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L4, mitochondrial
F
311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
Find proteins for Q9BYD3 (Homo sapiens)
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PHAROS  Q9BYD3
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L10, mitochondrial
I
261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
Find proteins for Q7Z7H8 (Homo sapiens)
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PHAROS  Q7Z7H8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L11, mitochondrial
J
192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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PHAROS  Q9Y3B7
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L13, mitochondrial
K
178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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PHAROS  Q9BYD1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L14, mitochondrial
L
145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
Find proteins for Q6P1L8 (Homo sapiens)
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PHAROS  Q6P1L8
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L15, mitochondrial
M
296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
Find proteins for Q9P015 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L16, mitochondrial
N
251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L17, mitochondrial
O
175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L18, mitochondrial
P
180Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L19, mitochondrial
Q
292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L20, mitochondrial
R
149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L21, mitochondrial
S
205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L23, mitochondrial
U
153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
Find proteins for Q16540 (Homo sapiens)
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PHAROS  Q16540
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L24, mitochondrial
V
216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
Find proteins for Q96A35 (Homo sapiens)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L27, mitochondrial
W
148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
Find proteins for Q9P0M9 (Homo sapiens)
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PHAROS  Q9P0M9
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L28, mitochondrial
X
256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
Find proteins for Q13084 (Homo sapiens)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L47, mitochondrial
Y
250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L30, mitochondrial
Z
161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L32, mitochondrial
0
188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L33, mitochondrial
1
65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
Find proteins for O75394 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L34, mitochondrial
2
92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L35, mitochondrial
3
188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
Find proteins for Q9NZE8 (Homo sapiens)
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PHAROS  Q9NZE8
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L36, mitochondrial
4
103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
Find proteins for Q9P0J6 (Homo sapiens)
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PHAROS  Q9P0J6
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L37, mitochondrial
5
423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
Find proteins for Q9BZE1 (Homo sapiens)
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PHAROS  Q9BZE1
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L38, mitochondrial
6
380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
Find proteins for Q96DV4 (Homo sapiens)
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PHAROS  Q96DV4
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L39, mitochondrial
7
338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
Find proteins for Q9NYK5 (Homo sapiens)
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PHAROS  Q9NYK5
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L40, mitochondrial
8
206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
Find proteins for Q9NQ50 (Homo sapiens)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L41, mitochondrial
9
137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
Find proteins for Q8IXM3 (Homo sapiens)
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PHAROS  Q8IXM3
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L42, mitochondrial
a
142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
Find proteins for Q9Y6G3 (Homo sapiens)
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PHAROS  Q9Y6G3
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L43, mitochondrial
b
215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens)
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PHAROS  Q8N983
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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)
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PHAROS  Q9H9J2
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L46, mitochondrial
e
279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L48, mitochondrial
f
212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
Find proteins for Q96GC5 (Homo sapiens)
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PHAROS  Q96GC5
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L49, mitochondrial
g
166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
Find proteins for Q13405 (Homo sapiens)
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PHAROS  Q13405
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L51, mitochondrial
i
128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L53, mitochondrial
k
112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L54, mitochondrial
l
138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L55, mitochondrial
m
128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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PHAROS  Q7Z7F7
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein 63, mitochondrial
o
102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-tRNA hydrolase ICT1, mitochondrial
p
206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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PHAROS  Q14197
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Growth arrest and DNA damage-inducible proteins-interacting protein 1
q
222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
Find proteins for Q8TAE8 (Homo sapiens)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein S30, mitochondrial
s
439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Unknown protein or protein extension
t
28Homo sapiensMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial assembly of ribosomal large subunit protein 1
u
234Homo sapiensMutation(s): 0 
Gene Names: MALSU1C7orf30
Find proteins for Q96EH3 (Homo sapiens)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein, mitochondrial
w
156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
Find proteins for O14561 (Homo sapiens)
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PHAROS  O14561
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L22, mitochondrial
T
206Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
Find proteins for Q9NWU5 (Homo sapiens)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L45, mitochondrial
d
306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
Find proteins for Q9BRJ2 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L3, mitochondrial
E
348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
Find proteins for P09001 (Homo sapiens)
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PHAROS  P09001
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L50, mitochondrial
h
158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
Find proteins for Q8N5N7 (Homo sapiens)
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PHAROS  Q8N5N7
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L52, mitochondrial
j
123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
Find proteins for Q86TS9 (Homo sapiens)
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PHAROS  Q86TS9
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein S18a, mitochondrial
r
196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
Find proteins for Q9NVS2 (Homo sapiens)
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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)
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PHAROS  L0R8F8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L9, mitochondrial
H
267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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PHAROS  Q9BYD2
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1559Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
mitochondrial tRNAValB69Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS

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v
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

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0, 4, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, D, M, T, W, g
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other