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1M06
Biol. Unit 1
Info
Asym.Unit (103 KB)
Biol.Unit 1, α-C (5.4 MB)
Biol.Unit 1 (5.4 MB)
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(1)
Title
:
STRUCTURAL STUDIES OF BACTERIOPHAGE ALPHA3 ASSEMBLY, X-RAY CRYSTALLOGRAPHY
Authors
:
R. A. Bernal, S. Hafenstein, N. H. Olson, V. Bowman, P. R. Chipman, T. S. B B. A. Fane, M. G. Rossmann
Date
:
12 Jun 02 (Deposition) - 25 Dec 02 (Release) - 28 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : F,G,J,X
Biol. Unit 1: F,G,J,X (60x)
Keywords
:
Bacteriophage, Three-Dimensional Structure, Virion, Morphogenesis, Phix174, Assembly, Microviridae, Icosahedral Virus, Virus-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. Bernal, S. Hafenstein, N. H. Olson, V. Bowman, P. R. Chipman, T. S. Baker, B. A. Fane, M. G. Rossmann
Structural Studies Of Bacteriophage Alpha3 Assembly
J. Mol. Biol. V. 325 11 2003
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Hetero Components
(1, 600)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
1b: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRb)
1c: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRc)
1d: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRd)
1e: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRe)
1f: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRf)
1g: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRg)
1h: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRh)
1i: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRi)
1j: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
600
OTHER
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE F:212 , ASP F:218 , ARG J:15 , SER J:22 , 3DR X:2 , 3DR X:3 , 3DR X:7
BINDING SITE FOR RESIDUE 3DR X 1
02
AC2
SOFTWARE
LYS F:167 , GLN J:23 , PHE J:24 , 3DR X:1 , 3DR X:3
BINDING SITE FOR RESIDUE 3DR X 2
03
AC3
SOFTWARE
LYS F:167 , LEU J:16 , TRP J:17 , 3DR X:1 , 3DR X:2 , 3DR X:4
BINDING SITE FOR RESIDUE 3DR X 3
04
AC4
SOFTWARE
ARG J:11 , GLY J:13 , ALA J:14 , LEU J:16 , TRP J:17 , 3DR X:3
BINDING SITE FOR RESIDUE 3DR X 4
05
AC5
SOFTWARE
ARG F:217 , SER F:221 , ARG F:234 , SER J:22
BINDING SITE FOR RESIDUE 3DR X 5
06
AC6
SOFTWARE
GLU F:208 , PHE F:212 , SER F:222 , 3DR X:7
BINDING SITE FOR RESIDUE 3DR X 6
07
AC7
SOFTWARE
PHE F:212 , ARG J:15 , TYR J:18 , 3DR X:1 , 3DR X:6
BINDING SITE FOR RESIDUE 3DR X 7
08
AC8
SOFTWARE
THR F:241 , ASP F:242 , PHE F:243 , 3DR X:9 , 3DR X:10
BINDING SITE FOR RESIDUE 3DR X 8
09
AC9
SOFTWARE
ASP F:242 , PHE F:243 , TRP F:244 , 3DR X:8 , 3DR X:10
BINDING SITE FOR RESIDUE 3DR X 9
10
BC1
SOFTWARE
HIS F:240 , THR F:241 , ASP F:242 , 3DR X:8 , 3DR X:9
BINDING SITE FOR RESIDUE 3DR X 10
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1m06f_ (F:)
1b: SCOP_d1m06g_ (G:)
View:
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
ssDNA viruses
(39)
Family
:
Microviridae-like VP
(7)
Protein domain
:
Microvirus capsid proteins
(7)
Bacteriophage alpha3 [TaxId: 10849]
(2)
1a
d1m06f_
F:
1b
d1m06g_
G:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1m06F00 (F:10-431)
2a: CATH_1m06G00 (G:1-187)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
(6)
Homologous Superfamily
:
Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
(6)
Enterobacteria phage alpha3. Organism_taxid: 10849.
(1)
1a
1m06F00
F:10-431
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.20, no name defined]
(133)
Enterobacteria phage alpha3. Organism_taxid: 10849.
(1)
2a
1m06G00
G:1-187
[
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Phage_F_1m06F01 (F:187-429)
1b: PFAM_Phage_F_1m06F02 (F:187-429)
2a: PFAM_Phage_G_1m06G01 (G:1-187)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Phage_F]
(2)
Family
:
Phage_F
(2)
Enterobacteria phage alpha3 (Bacteriophage alpha-3)
(2)
1a
Phage_F-1m06F01
F:187-429
1b
Phage_F-1m06F02
F:187-429
Clan
:
no clan defined [family: Phage_G]
(2)
Family
:
Phage_G
(2)
Enterobacteria phage alpha3 (Bacteriophage alpha-3)
(2)
2a
Phage_G-1m06G01
G:1-187
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Atom Selection
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Protein
Nucleic
Backbone
Sidechain
Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain F
Chain G
Chain J
Chain X
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
Asymmetric Unit 5
Asymmetric Unit 6
Asymmetric Unit 7
Asymmetric Unit 8
Asymmetric Unit 9
Asymmetric Unit 10
Asymmetric Unit 11
Asymmetric Unit 12
Asymmetric Unit 13
Asymmetric Unit 14
Asymmetric Unit 15
Asymmetric Unit 16
Asymmetric Unit 17
Asymmetric Unit 18
Asymmetric Unit 19
Asymmetric Unit 20
Asymmetric Unit 21
Asymmetric Unit 22
Asymmetric Unit 23
Asymmetric Unit 24
Asymmetric Unit 25
Asymmetric Unit 26
Asymmetric Unit 27
Asymmetric Unit 28
Asymmetric Unit 29
Asymmetric Unit 30
Asymmetric Unit 31
Asymmetric Unit 32
Asymmetric Unit 33
Asymmetric Unit 34
Asymmetric Unit 35
Asymmetric Unit 36
Asymmetric Unit 37
Asymmetric Unit 38
Asymmetric Unit 39
Asymmetric Unit 40
Asymmetric Unit 41
Asymmetric Unit 42
Asymmetric Unit 43
Asymmetric Unit 44
Asymmetric Unit 45
Asymmetric Unit 46
Asymmetric Unit 47
Asymmetric Unit 48
Asymmetric Unit 49
Asymmetric Unit 50
Asymmetric Unit 51
Asymmetric Unit 52
Asymmetric Unit 53
Asymmetric Unit 54
Asymmetric Unit 55
Asymmetric Unit 56
Asymmetric Unit 57
Asymmetric Unit 58
Asymmetric Unit 59
Asymmetric Unit 60
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Miscellaneous
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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)
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View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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