3J7Y

Structure of the large ribosomal subunit from human mitochondria


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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

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

  • 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 c ...

    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
MoleculeChainsSequence LengthOrganismDetails
uL2
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
uL3
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
uL4
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
bL9
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
uL10
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
uL11
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
uL13
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
uL14
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
uL15
M
296Homo sapiensMutation(s): 0 
Gene Names: MRPL15
Find proteins for Q9P015 (Homo sapiens)
Go to Gene View: MRPL15
Go to UniProtKB:  Q9P015
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
uL16
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
bL17
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
uL18
P
179Homo 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
bL19
Q
292Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
bL20
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
bL21
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
uL22
T
212Homo 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
uL23
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
uL24
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
bL27
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
bL28
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
uL29
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
uL30
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
bL32
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
bL33
1
65Homo sapiensMutation(s): 0 
Gene Names: MRPL33 (C2orf1)
Find proteins for O75394 (Homo sapiens)
Go to Gene View: MRPL33
Go to UniProtKB:  O75394
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
bL34
2
92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
Find proteins for Q9BQ48 (Homo sapiens)
Go to Gene View: MRPL34
Go to UniProtKB:  Q9BQ48
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
bL35
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
bL36
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
mL37
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
mL38
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
mL39
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
mL40
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
mL41
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
mL42
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
mL43
b
155Homo 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
mL44
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
mL45
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
mL46
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
mL48
f
211Homo 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
mL49
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
mL50
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
mL51
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
mL52
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
mL53
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
mL63
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: 47
MoleculeChainsSequence LengthOrganismDetails
ICT1
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: 48
MoleculeChainsSequence LengthOrganismDetails
CRIF1
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: 49
MoleculeChainsSequence LengthOrganismDetails
bS18a
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: 50
MoleculeChainsSequence LengthOrganismDetails
mS30
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: 51
MoleculeChainsSequence LengthOrganismDetails
unknown protein
t
127N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1559Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
mt-tRNAValB73Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
f, t
L-PEPTIDE LINKINGC4 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 NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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