3J9M

Structure of the human mitochondrial ribosome (class 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ribosome. The structure of the human mitochondrial ribosome.

Amunts, A.Brown, A.Toots, J.Scheres, S.H.Ramakrishnan, V.

(2015) Science 348: 95-98

  • DOI: 10.1126/science.aaa1193
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-pa ...

    The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
uL2m
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: 4
MoleculeChainsSequence LengthOrganismDetails
uL3m
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: 5
MoleculeChainsSequence LengthOrganismDetails
uL4m
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: 6
MoleculeChainsSequence LengthOrganismDetails
bL9m
H
267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
Find proteins for Q9BYD2 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uL10m
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
uL11m
J
192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
Find proteins for Q9Y3B7 (Homo sapiens)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
uL13m
K
178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
Find proteins for Q9BYD1 (Homo sapiens)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uL14m
L
145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
Find proteins for Q6P1L8 (Homo sapiens)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL15m
M
296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
uL16m
N
251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
bL17m
O
175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
bL19m
Q
292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
Find proteins for P49406 (Homo sapiens)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
bL20m
R
149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
bL21m
S
205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
uL22m
T
212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
uL23m
U
153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
Find proteins for Q16540 (Homo sapiens)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
uL24m
V
216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
bL27m
W
148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
Find proteins for Q9P0M9 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
bL28m
X
256Homo sapiensMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL29m
Y
250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
Find proteins for Q9HD33 (Homo sapiens)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uL30m
Z
161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
Find proteins for Q8TCC3 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
bL32m
0
188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
Find proteins for Q9BYC8 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
bL34m
2
92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
Find proteins for Q9BQ48 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
bL35m
3
188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
Find proteins for Q9NZE8 (Homo sapiens)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
bL36m
4
103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
Find proteins for Q9P0J6 (Homo sapiens)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
mL37
5
423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
Find proteins for Q9BZE1 (Homo sapiens)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
mL38
6
380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
Find proteins for Q96DV4 (Homo sapiens)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
mL39
7
338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
Find proteins for Q9NYK5 (Homo sapiens)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
mL40
8
206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
Find proteins for Q9NQ50 (Homo sapiens)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
mL41
9
137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
Find proteins for Q8IXM3 (Homo sapiens)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
mL42
a
142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
Find proteins for Q9Y6G3 (Homo sapiens)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
mL43
b
155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
mL44
c
332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
Find proteins for Q9H9J2 (Homo sapiens)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
mL45
d
306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
mL46
e
279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
mL48
f
194Homo 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
mL49
g
166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
mL50
h
158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
mL51
i
128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
mL52
j
123Homo sapiensMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
mL53
k
112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
mL54
l
138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
bL31m
m
128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
Find proteins for Q7Z7F7 (Homo sapiens)
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
mL63
o
102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
Find proteins for Q9BQC6 (Homo sapiens)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
mL62 (ICT1)
p
206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
Find proteins for Q14197 (Homo sapiens)
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PHAROS  Q14197
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
mL64 (CRIF1)
q
222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
Find proteins for Q8TAE8 (Homo sapiens)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
mL66 (bS18a)
r
196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
mL65 (mS30)
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/protein extension
t
28Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
uS2m
AB
296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
Find proteins for Q9Y399 (Homo sapiens)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
uS3m
AC
167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
Find proteins for Q96EL2 (Homo sapiens)
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
uS5m
AD
430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
bS6m
AE
125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
Find proteins for P82932 (Homo sapiens)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
uS7m
AF
242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
uS9m
AG
396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
Find proteins for P82933 (Homo sapiens)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
uS10m
AH
201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
Find proteins for P82664 (Homo sapiens)
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
uS11m
AI
194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
Find proteins for P82912 (Homo sapiens)
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
uS12m
AJ
138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
Find proteins for O15235 (Homo sapiens)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS14m
AK
128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
Find proteins for O60783 (Homo sapiens)
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PHAROS  O60783
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uS15m
AL
257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
Find proteins for P82914 (Homo sapiens)
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PHAROS  P82914
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
bS16m
AM
137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
Find proteins for Q9Y3D3 (Homo sapiens)
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PHAROS  Q9Y3D3
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
uS17m
AN
130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
Find proteins for Q9Y2R5 (Homo sapiens)
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
mS40 (bS18b)
AO
258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
Find proteins for Q9Y676 (Homo sapiens)
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PHAROS  Q9Y676
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
bS18m (bS18c)
AP
142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
Find proteins for Q9Y3D5 (Homo sapiens)
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PHAROS  Q9Y3D5
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
bS21m
AQ
87Homo sapiensMutation(s): 0 
Gene Names: MRPS21RPMS21MDS016
Find proteins for P82921 (Homo sapiens)
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PHAROS  P82921
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
mS22
AR
360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
Find proteins for P82650 (Homo sapiens)
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PHAROS  P82650
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
mS23
AS
190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
Find proteins for Q9Y3D9 (Homo sapiens)
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PHAROS  Q9Y3D9
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
mS25
AT
173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
Find proteins for P82663 (Homo sapiens)
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PHAROS  P82663
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
mS26
AU
205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
Find proteins for Q9BYN8 (Homo sapiens)
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PHAROS  Q9BYN8
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
mS27
AV
414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
Find proteins for Q92552 (Homo sapiens)
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PHAROS  Q92552
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
bS1m
AW
187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
Find proteins for Q9Y2Q9 (Homo sapiens)
Go to UniProtKB:  Q9Y2Q9
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PHAROS  Q9Y2Q9
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
mS29
AX
398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
Find proteins for P51398 (Homo sapiens)
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PHAROS  P51398
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
mS31
AY
395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
Find proteins for Q92665 (Homo sapiens)
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PHAROS  Q92665
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
mS33
AZ
106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
Find proteins for Q9Y291 (Homo sapiens)
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PHAROS  Q9Y291
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
mS34
A0
218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82930 (Homo sapiens)
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PHAROS  P82930
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
mS35
A1
323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
Find proteins for P82673 (Homo sapiens)
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PHAROS  P82673
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
mS37
A2
118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
Find proteins for Q96BP2 (Homo sapiens)
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PHAROS  Q96BP2
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
mS38
A3
199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
Find proteins for Q9NWT8 (Homo sapiens)
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PHAROS  Q9NWT8
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
mS39
A4
579Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
Find proteins for Q96EY7 (Homo sapiens)
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PHAROS  Q96EY7
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
uL18m
P
179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
Find proteins for A8K9D2 (Homo sapiens)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
bL33m
1
65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
Find proteins for O75394 (Homo sapiens)
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PHAROS  O75394
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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1559Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
mt-tRNAValB73Homo sapiens
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Entity ID: 54
MoleculeChainsLengthOrganism
E-site tRNAu2Homo sapiens

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Entity ID: 55
MoleculeChainsLengthOrganism
12S rRNAAA954Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download CCD File 
AX
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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0, 4, AB, AO, AP, AT, r
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection