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2RDO
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (145 KB)
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(1)
Title
:
50S SUBUNIT WITH EF-G(GDPNP) AND RRF BOUND
Authors
:
N. Gao, A. V. Zavialov, M. Ehrenberg, J. Frank
Date
:
24 Sep 07 (Deposition) - 04 Mar 08 (Release) - 14 Apr 09 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
9.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,0,1,2,3,4,7,8,9
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,0,1,2,3,4,7,8,9 (1x)
Keywords
:
Elongation Factor G, Ef-G, Rrf, Ribosome Recycling Factor, Gdpnp, 50S Subunit, Cryo-Em, Real-Space Refinement, Ribonucleoprotein, Ribosomal Protein, Rna-Binding, Rrna- Binding, Methylation, Antibiotic Resistance, Repressor, Transcription, Transcription Regulation, Transcription Termination, Translation Regulation, Trna-Binding, Phosphoprotein, Metal-Binding, Zinc, Cytoplasm, Gtp-Binding, Nucleotide-Binding, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Gao, A. V. Zavialov, M. Ehrenberg, J. Frank
Specific Interaction Between Ef-G And Rrf And Its Implication For Gtp-Dependent Ribosome Splitting Into Subunits.
J. Mol. Biol. V. 374 1345 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_RL22_ECOLI_001 (R8C, chain S, )
2: VAR_RL4_ECOLI_001 (K63E, chain E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_RL22_ECOLI_001
*
R
8
C
RL22_ECOLI
---
---
S
R
8
C
2
UniProt
VAR_RL4_ECOLI_001
*
K
63
E
RL4_ECOLI
---
---
E
K
63
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(28, 28)
Info
All PROSITE Patterns/Profiles
01: RIBOSOMAL_L34 (2:2-21)
02: RIBOSOMAL_L35 (3:4-30)
03: RIBOSOMAL_L24 (U:7-24)
04: RIBOSOMAL_L36 (4:11-37)
05: RIBOSOMAL_L9 (H:13-40)
06: RIBOSOMAL_L33 (1:20-39)
07: RIBOSOMAL_L30 (Y:22-54)
08: RIBOSOMAL_L17 (N:34-56)
09: RIBOSOMAL_L27 (W:33-47)
10: RIBOSOMAL_L31 (Z:35-56)
11: RIBOSOMAL_L29 (X:39-53)
12: G_TR_1 (7:64-66)
13: RIBOSOMAL_L20 (Q:53-69)
14: RIBOSOMAL_L5 (F:56-72)
15: RIBOSOMAL_L16_1 (M:58-69)
16: RIBOSOMAL_L14 (K:60-86)
17: RIBOSOMAL_L21 (R:72-94)
18: RIBOSOMAL_L16_2 (M:81-92)
19: RIBOSOMAL_L23 (T:81-96)
20: RIBOSOMAL_L22 (S:83-107)
21: RIBOSOMAL_L19 (P:85-100)
22: RIBOSOMAL_L3 (D:101-124)
23: RIBOSOMAL_L13 (J:105-127)
24: RIBOSOMAL_L15 (L:109-139)
25: RIBOSOMAL_L1 (9:120-138)
26: RIBOSOMAL_L11 (I:126-141)
27: RIBOSOMAL_L6_1 (G:153-161)
28: RIBOSOMAL_L2 (C:217-228)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_L34
PS00784
Ribosomal protein L34 signature.
RL34_ECOLI
2-21
1
2:2-21
2
RIBOSOMAL_L35
PS00936
Ribosomal protein L35 signature.
RL35_ECOLI
5-31
1
3:4-30
3
RIBOSOMAL_L24
PS01108
Ribosomal protein L24 signature.
RL24_ECOLI
8-25
1
U:7-24
4
RIBOSOMAL_L36
PS00828
Ribosomal protein L36 signature.
RL36_ECOLI
11-37
1
4:11-37
5
RIBOSOMAL_L9
PS00651
Ribosomal protein L9 signature.
RL9_ECOLI
13-40
1
H:13-40
6
RIBOSOMAL_L33
PS00582
Ribosomal protein L33 signature.
RL33_ECOLI
21-40
1
1:20-39
7
RIBOSOMAL_L30
PS00634
Ribosomal protein L30 signature.
RL30_ECOLI
23-55
1
Y:22-54
8
RIBOSOMAL_L17
PS01167
Ribosomal protein L17 signature.
RL17_ECOLI
34-56
1
N:34-56
9
RIBOSOMAL_L27
PS00831
Ribosomal protein L27 signature.
RL27_ECOLI
34-48
1
W:33-47
10
RIBOSOMAL_L31
PS01143
Ribosomal protein L31 signature.
RL31_ECOLI
35-56
1
Z:35-56
11
RIBOSOMAL_L29
PS00579
Ribosomal protein L29 signature.
RL29_ECOLI
39-53
1
X:39-53
12
G_TR_1
PS00301
Translational (tr)-type guanine nucleotide-binding (G) domain signature.
EFG_ECOLI
51-66
1
7:64-66
13
RIBOSOMAL_L20
PS00937
Ribosomal protein L20 signature.
RL20_ECOLI
54-70
1
Q:53-69
14
RIBOSOMAL_L5
PS00358
Ribosomal protein L5 signature.
RL5_ECOLI
57-73
1
F:56-72
15
RIBOSOMAL_L16_1
PS00586
Ribosomal protein L16 signature 1.
RL16_ECOLI
58-69
1
M:58-69
16
RIBOSOMAL_L14
PS00049
Ribosomal protein L14 signature.
RL14_ECOLI
60-86
1
K:60-86
17
RIBOSOMAL_L21
PS01169
Ribosomal protein L21 signature.
RL21_ECOLI
72-94
1
R:72-94
18
RIBOSOMAL_L16_2
PS00701
Ribosomal protein L16 signature 2.
RL16_ECOLI
81-92
1
M:81-92
19
RIBOSOMAL_L23
PS00050
Ribosomal protein L23 signature.
RL23_ECOLI
81-96
1
T:81-96
20
RIBOSOMAL_L22
PS00464
Ribosomal protein L22 signature.
RL22_ECOLI
83-107
1
S:83-107
21
RIBOSOMAL_L19
PS01015
Ribosomal protein L19 signature.
RL19_ECOLI
86-101
1
P:85-100
22
RIBOSOMAL_L3
PS00474
Ribosomal protein L3 signature.
RL3_ECOLI
101-124
1
D:101-124
23
RIBOSOMAL_L13
PS00783
Ribosomal protein L13 signature.
RL13_ECOLI
105-127
1
J:105-127
24
RIBOSOMAL_L15
PS00475
Ribosomal protein L15 signature.
RL15_ECOLI
109-139
1
L:109-139
25
RIBOSOMAL_L1
PS01199
Ribosomal protein L1 signature.
RL1_ECOLI
121-139
1
9:120-138
26
RIBOSOMAL_L11
PS00359
Ribosomal protein L11 signature.
RL11_ECOLI
127-142
1
I:126-141
27
RIBOSOMAL_L6_1
PS00525
Ribosomal protein L6 signature 1.
RL6_ECOLI
154-162
1
G:153-161
28
RIBOSOMAL_L2
PS00467
Ribosomal protein L2 signature.
RL2_ECOLI
218-229
1
C:217-228
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(31, 33)
Info
All SCOP Domains
01a: SCOP_d2rdoi1 (I:73-141)
02a: SCOP_d2rdox1 (X:1-63)
03a: SCOP_d2rdoq1 (Q:1-117)
04a: SCOP_d2rdow1 (W:1-84)
05a: SCOP_d2rdor1 (R:1-103)
06a: SCOP_d2rdoc2 (C:61-124)
07a: SCOP_d2rdod1 (D:1-209)
08a: SCOP_d2rdok1 (K:2-122)
09a: SCOP_d2rdov1 (V:1-94)
10a: SCOP_d2rdoc1 (C:125-269)
11a: SCOP_d2rdou1 (U:1-102)
12a: SCOP_d2rdom1 (M:1-136)
13a: SCOP_d2rdoz1 (Z:1-70)
14a: SCOP_d2rdo31 (3:1-64)
15a: SCOP_d2rdoh2 (H:1-58)
16a: SCOP_d2rdon1 (N:1-127)
17a: SCOP_d2rdoi2 (I:1-72)
18a: SCOP_d2rdos1 (S:1-110)
19a: SCOP_d2rdoy1 (Y:1-58)
20a: SCOP_d2rdog1 (G:1-81)
20b: SCOP_d2rdog2 (G:82-176)
21a: SCOP_d2rdoh1 (H:59-149)
22a: SCOP_d2rdot1 (T:1-99)
23a: SCOP_d2rdof1 (F:1-178)
24a: SCOP_d2rdo81 (8:1-185)
25a: SCOP_d2rdoo1 (O:1-117)
26a: SCOP_d2rdoj1 (J:1-140)
27a: SCOP_d2rdoe1 (E:1-201)
28a: SCOP_d2rdol1 (L:2-144)
29a: SCOP_d2rdo11 (1:3-52)
29b: SCOP_d2rdop1 (P:1-114)
30a: SCOP_d2rdo41 (4:1-38)
31a: SCOP_d2rdo01 (0:1-56)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Ribosomal protein L11, C-terminal domain
(96)
Family
:
Ribosomal protein L11, C-terminal domain
(96)
Protein domain
:
Ribosomal protein L11, C-terminal domain
(96)
Escherichia coli [TaxId: 562]
(29)
01a
d2rdoi1
I:73-141
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
Ribosomal protein L29 (L29p)
(89)
Family
:
Ribosomal protein L29 (L29p)
(89)
Protein domain
:
Ribosomal protein L29 (L29p)
(89)
Escherichia coli [TaxId: 562]
(30)
02a
d2rdox1
X:1-63
Fold
:
PABP domain-like
(63)
Superfamily
:
Ribosomal protein L20
(51)
Family
:
Ribosomal protein L20
(51)
Protein domain
:
Ribosomal protein L20
(51)
Escherichia coli [TaxId: 562]
(29)
03a
d2rdoq1
Q:1-117
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Ribosomal L27 protein-like
(52)
Family
:
Ribosomal L27 protein
(42)
Protein domain
:
Ribosomal protein L27
(42)
Escherichia coli [TaxId: 562]
(29)
04a
d2rdow1
W:1-84
Fold
:
L21p-like
(48)
Superfamily
:
L21p-like
(48)
Family
:
Ribosomal protein L21p
(48)
Protein domain
:
Ribosomal protein L21p
(48)
Escherichia coli [TaxId: 562]
(27)
05a
d2rdor1
R:1-103
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Cold shock DNA-binding domain-like
(310)
Protein domain
:
N-terminal domain of ribosomal protein L2
(79)
Escherichia coli [TaxId: 562]
(27)
06a
d2rdoc2
C:61-124
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
Ribosomal protein L3
(107)
Protein domain
:
Ribosomal protein L3
(107)
Escherichia coli [TaxId: 562]
(29)
07a
d2rdod1
D:1-209
Fold
:
Ribosomal protein L14
(91)
Superfamily
:
Ribosomal protein L14
(91)
Family
:
Ribosomal protein L14
(91)
Protein domain
:
Ribosomal protein L14
(91)
Escherichia coli [TaxId: 562]
(29)
08a
d2rdok1
K:2-122
Fold
:
Ribosomal protein L25-like
(72)
Superfamily
:
Ribosomal protein L25-like
(72)
Family
:
Ribosomal protein L25-like
(54)
Protein domain
:
Ribosomal protein L25
(32)
Escherichia coli [TaxId: 562]
(32)
09a
d2rdov1
V:1-94
Fold
:
SH3-like barrel
(1035)
Superfamily
:
Translation proteins SH3-like domain
(251)
Family
:
C-terminal domain of ribosomal protein L2
(79)
Protein domain
:
C-terminal domain of ribosomal protein L2
(79)
Escherichia coli [TaxId: 562]
(27)
10a
d2rdoc1
C:125-269
Family
:
Ribosomal proteins L24p and L21e
(132)
Protein domain
:
Ribosomal proteins L24 (L24p)
(92)
Escherichia coli [TaxId: 562]
(30)
11a
d2rdou1
U:1-102
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
Ribosomal protein L16p/L10e
(100)
Family
:
Ribosomal protein L16p
(41)
Protein domain
:
Ribosomal protein L16p
(41)
Escherichia coli [TaxId: 562]
(29)
12a
d2rdom1
M:1-136
Fold
:
L28p-like
(42)
Superfamily
:
L28p-like
(42)
Family
:
Ribosomal protein L31p
(16)
Protein domain
:
Ribosomal protein L31p
(16)
Escherichia coli [TaxId: 562]
(9)
13a
d2rdoz1
Z:1-70
Fold
:
L35p-like
(42)
Superfamily
:
L35p-like
(42)
Family
:
Ribosomal protein L35p
(42)
Protein domain
:
Ribosomal protein L35p
(42)
Escherichia coli [TaxId: 562]
(27)
14a
d2rdo31
3:1-64
Fold
:
MbtH/L9 domain-like
(48)
Superfamily
:
L9 N-domain-like
(45)
Family
:
Ribosomal protein L9 N-domain
(43)
Protein domain
:
Ribosomal protein L9 N-domain
(43)
Escherichia coli [TaxId: 562]
(29)
15a
d2rdoh2
H:1-58
Fold
:
Prokaryotic ribosomal protein L17
(45)
Superfamily
:
Prokaryotic ribosomal protein L17
(45)
Family
:
Prokaryotic ribosomal protein L17
(45)
Protein domain
:
Prokaryotic ribosomal protein L17
(45)
Escherichia coli [TaxId: 562]
(27)
16a
d2rdon1
N:1-127
Fold
:
Ribosomal L11/L12e N-terminal domain
(53)
Superfamily
:
Ribosomal L11/L12e N-terminal domain
(53)
Family
:
Ribosomal L11/L12e N-terminal domain
(53)
Protein domain
:
Ribosomal protein L11, N-terminal domain
(52)
Escherichia coli [TaxId: 562]
(29)
17a
d2rdoi2
I:1-72
Fold
:
Ribosomal protein L22
(105)
Superfamily
:
Ribosomal protein L22
(105)
Family
:
Ribosomal protein L22
(105)
Protein domain
:
Ribosomal protein L22
(105)
Escherichia coli [TaxId: 562]
(29)
18a
d2rdos1
S:1-110
Fold
:
Ribosomal protein L30p/L7e
(86)
Superfamily
:
Ribosomal protein L30p/L7e
(86)
Family
:
Ribosomal protein L30p/L7e
(86)
Protein domain
:
Prokaryotic ribosomal protein L30
(46)
Escherichia coli [TaxId: 562]
(29)
19a
d2rdoy1
Y:1-58
Fold
:
Ribosomal protein L6
(90)
Superfamily
:
Ribosomal protein L6
(90)
Family
:
Ribosomal protein L6
(90)
Protein domain
:
Ribosomal protein L6
(90)
Escherichia coli [TaxId: 562]
(27)
20a
d2rdog1
G:1-81
20b
d2rdog2
G:82-176
Fold
:
Ribosomal protein L9 C-domain
(39)
Superfamily
:
Ribosomal protein L9 C-domain
(39)
Family
:
Ribosomal protein L9 C-domain
(39)
Protein domain
:
Ribosomal protein L9 C-domain
(39)
Escherichia coli [TaxId: 562]
(29)
21a
d2rdoh1
H:59-149
Fold
:
Ribosomal proteins S24e, L23 and L15e
(151)
Superfamily
:
Ribosomal proteins S24e, L23 and L15e
(151)
Family
:
L23p
(105)
Protein domain
:
Ribosomal protein L23
(105)
Escherichia coli [TaxId: 562]
(28)
22a
d2rdot1
T:1-99
Fold
:
RL5-like
(90)
Superfamily
:
RL5-like
(90)
Family
:
Ribosomal protein L5
(82)
Protein domain
:
Ribosomal protein L5
(82)
Escherichia coli [TaxId: 562]
(29)
23a
d2rdof1
F:1-178
Fold
:
RRF/tRNA synthetase additional domain-like
(47)
Superfamily
:
Ribosome recycling factor, RRF
(28)
Family
:
Ribosome recycling factor, RRF
(22)
Protein domain
:
Ribosome recycling factor, RRF
(20)
Escherichia coli [TaxId: 562]
(5)
24a
d2rdo81
8:1-185
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Translational machinery components
(160)
Family
:
Ribosomal protein L18 and S11
(153)
Protein domain
:
Ribosomal protein L18 (L18p)
(83)
Escherichia coli [TaxId: 562]
(29)
25a
d2rdoo1
O:1-117
Fold
:
Ribosomal protein L13
(90)
Superfamily
:
Ribosomal protein L13
(90)
Family
:
Ribosomal protein L13
(90)
Protein domain
:
Ribosomal protein L13
(90)
Escherichia coli [TaxId: 562]
(29)
26a
d2rdoj1
J:1-140
Fold
:
Ribosomal protein L4
(89)
Superfamily
:
Ribosomal protein L4
(89)
Family
:
Ribosomal protein L4
(89)
Protein domain
:
Ribosomal protein L4
(89)
Escherichia coli [TaxId: 562]
(29)
27a
d2rdoe1
E:1-201
Fold
:
Ribosomal proteins L15p and L18e
(126)
Superfamily
:
Ribosomal proteins L15p and L18e
(126)
Family
:
Ribosomal proteins L15p and L18e
(126)
Protein domain
:
Ribosomal protein L15 (L15p)
(86)
Escherichia coli [TaxId: 562]
(29)
28a
d2rdol1
L:2-144
Class
:
Low resolution protein structures
(283)
Fold
:
Ribosome and ribosomal fragments
(154)
Superfamily
:
Ribosome and ribosomal fragments
(154)
Family
:
Ribosome complexes
(103)
Protein domain
:
70S ribosome functional complex
(103)
Escherichia coli [TaxId: 562]
(72)
29a
d2rdo11
1:3-52
29b
d2rdop1
P:1-114
Class
:
Small proteins
(3458)
Fold
:
Ribosomal protein L36
(43)
Superfamily
:
Ribosomal protein L36
(43)
Family
:
Ribosomal protein L36
(43)
Protein domain
:
Ribosomal protein L36
(43)
Escherichia coli [TaxId: 562]
(27)
30a
d2rdo41
4:1-38
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Zn-binding ribosomal proteins
(209)
Family
:
Ribosomal protein L32p
(44)
Protein domain
:
Ribosomal protein L32p
(44)
Escherichia coli [TaxId: 562]
(27)
31a
d2rdo01
0:1-56
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
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Chain 0
Chain 1
Chain 2
Chain 3
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Chain 7
Chain 8
Chain 9
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
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by Rainbow (Group)
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(e.g.: "#3cb371" or "60,179,113")
Stereo
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Asym.Unit (149 KB)
Header - Asym.Unit
Biol.Unit 1 (145 KB)
Header - Biol.Unit 1
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