6DZI

Cryo-EM Structure of Mycobacterium smegmatis 70S C(minus) ribosome 70S-MPY complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Zinc depletion induces ribosome hibernation in mycobacteria.

Li, Y.Sharma, M.R.Koripella, R.K.Yang, Y.Kaushal, P.S.Lin, Q.Wade, J.T.Gray, T.A.Derbyshire, K.M.Agrawal, R.K.Ojha, A.K.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 8191-8196


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CONSERVED PROTEIN DOMAIN
j
32N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
k
208Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsC
Find proteins for A0QSD7 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
l
200Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsD
Find proteins for A0QSL7 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
m
180Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsE
Find proteins for A0QSG6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
n
96Mycobacterium smegmatisMutation(s): 0 
Gene Names: rpsF
Find proteins for A0A0D6J3X3 (Mycobacterium smegmatis)
Go to UniProtKB:  A0A0D6J3X3
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
p
155Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsG
Find proteins for A0QS97 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS97
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
q
131Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsH
Find proteins for A0QSG3 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
4
126Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsI
Find proteins for A0QSP9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSP9
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
s
99Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for A0QSD0 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
t
115Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsK
Find proteins for A0QSL6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL6
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
u
122Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsL
Find proteins for A0QS96 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS96
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
v
116Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsM
Find proteins for A0QSL5 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
x
88Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsO
Find proteins for A0QVQ3 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QVQ3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
z
113Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsP
Find proteins for A0QV37 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV37
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
5
94Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for A0QSE0 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSE0
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
6
82Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsS
Find proteins for A0QSD5 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
7
85Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsT
Find proteins for A0R102 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R102
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
8
228Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsB
Find proteins for A0QVB8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QVB8
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18 1
r
84Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsR1 (rpsR2)
Find proteins for A0R549 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R549
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promoting factor
Y
103Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: hpf
Find proteins for A0QTK6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QTK6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
9
100Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsN
Find proteins for A0R550 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R550
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
275Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplB
Find proteins for A0QSD4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD4
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
214Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplC
Find proteins for A0QSD1 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD1
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
209Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplD
Find proteins for A0QSD2 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
182Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplE
Find proteins for A0QSG1 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG1
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
176Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplF
Find proteins for A0QSG4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG4
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
151Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplI
Find proteins for A0R7F6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7F6
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
126Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplJ
Find proteins for A0QS62 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS62
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
133Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplK
Find proteins for A0QS45 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS45
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
146Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplM
Find proteins for A0QSP8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSP8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
122Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplN
Find proteins for A0QSF9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSF9
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
145Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplO
Find proteins for I7G436 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  I7G436
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplP
Find proteins for A0QSD8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD8
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
118Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplQ
Find proteins for A0QSL9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL9
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
126Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplR
Find proteins for I7FGD9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  I7FGD9
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
113Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplS
Find proteins for A0QV42 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV42
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
124Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplT
Find proteins for A0QYU6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYU6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
100Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplU
Find proteins for A0R151 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R151
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
114Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplV
Find proteins for A0QSD6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD6
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
97Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplW
Find proteins for A0QSD3 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD3
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
105Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplX
Find proteins for A0QSG0 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG0
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
192Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0R3D2 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3D2
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
79Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmA
Find proteins for A0R150 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R150
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
64Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmC
Find proteins for A0QSD9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD9
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
59Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmD
Find proteins for A0QSG7 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG7
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
54Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmF
Find proteins for A0R3I9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3I9
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 2
c
53Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmG2
Find proteins for A0R551 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R551
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmH
Find proteins for A0R7K0 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7K0
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
63Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmI
Find proteins for A0QYU7 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYU7
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
37Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0QSL4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL4
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
g
82Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmE
Find proteins for A0R554 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R554
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
y
77N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
3
23Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Find proteins for A0QTP4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QTP4
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAh1511Mycolicibacterium smegmatis MC2 155
Entity ID: 23
MoleculeChainsLengthOrganism
23 S rRNA (3119-MER)A3119Mycolicibacterium smegmatis MC2 155
Entity ID: 24
MoleculeChainsLengthOrganism
5S RNA (118-MER)B118Mycolicibacterium smegmatis MC2 155
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM061576
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI107595
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI097191

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release