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1NVU
Asym. Unit
Info
Asym.Unit (150 KB)
Biol.Unit 1 (144 KB)
Biol.Unit 2 (568 KB)
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(1)
Title
:
STRUCTURAL EVIDENCE FOR FEEDBACK ACTIVATION BY RASGTP OF THE RAS-SPECIFIC NUCLEOTIDE EXCHANGE FACTOR SOS
Authors
:
S. M. Margarit, H. Sondermann, B. E. Hall, B. Nagar, A. Hoelz, M. Pirruccello, D. Bar-Sagi, J. Kuriyan
Date
:
04 Feb 03 (Deposition) - 01 Apr 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : Q,R,S
Biol. Unit 1: Q,R,S (1x)
Biol. Unit 2: Q,R,S (4x)
Keywords
:
Proto-Oncogene, Gtp Binding, Guanine Nucleotide Release Factor, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. M. Margarit, H. Sondermann, B. E. Hall, B. Nagar, A. Hoelz, M. Pirruccello, D. Bar-Sagi, J. Kuriyan
Structural Evidence For Feedback Activation By Rasgtp Of The Ras-Specific Nucleotide Exchange Factor Sos
Cell(Cambridge, Mass. ) V. 112 685 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
2a: MAGNESIUM ION (MGa)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GTP
1
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
PO4
5
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER Q:17 , THR Q:35 , GTP Q:1001 , HOH Q:1008 , HOH Q:1011
BINDING SITE FOR RESIDUE MG Q 1002
2
AC2
SOFTWARE
GLY R:13 , VAL R:14 , GLY R:15 , LYS R:16 , SER R:17 , GLY R:59 , GLU R:62 , HOH R:1074
BINDING SITE FOR RESIDUE PO4 R 1003
3
AC3
SOFTWARE
HOH S:127 , HOH S:363 , ARG S:625 , HIS S:695 , HIS S:699 , HIS S:700
BINDING SITE FOR RESIDUE PO4 S 1047
4
AC4
SOFTWARE
GLU R:63 , SER R:127 , ARG R:128 , GLN R:131 , HOH R:1028 , HOH S:372 , HOH S:384 , LYS S:814 , GLU S:815 , ARG S:826
BINDING SITE FOR RESIDUE PO4 S 1048
5
AC5
SOFTWARE
HOH S:115 , ARG S:660 , TYR S:709 , GLU S:716 , HIS S:951
BINDING SITE FOR RESIDUE PO4 S 1049
6
AC6
SOFTWARE
GLU Q:153 , ASP Q:154 , TYR Q:157 , ARG Q:161
BINDING SITE FOR RESIDUE PO4 Q 1007
7
AC7
SOFTWARE
GLY Q:12 , GLY Q:13 , VAL Q:14 , GLY Q:15 , LYS Q:16 , SER Q:17 , ALA Q:18 , PHE Q:28 , VAL Q:29 , ASP Q:30 , TYR Q:32 , PRO Q:34 , THR Q:35 , GLY Q:60 , GLU Q:62 , ASN Q:116 , LYS Q:117 , ASP Q:119 , LEU Q:120 , SER Q:145 , ALA Q:146 , LYS Q:147 , MG Q:1002 , HOH Q:1008 , HOH Q:1011 , HOH Q:1019
BINDING SITE FOR RESIDUE GTP Q 1001
[
close Site info
]
SAPs(SNPs)/Variants
(29, 46)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_026106 (G12A, chain Q/R, )
02: VAR_045975 (G12C, chain Q/R, )
03: VAR_068816 (G12D, chain Q/R, )
04: VAR_045976 (G12E, chain Q/R, )
05: VAR_006837 (G12S, chain Q/R, )
06: VAR_006836 (G12V, chain Q/R, )
07: VAR_026107 (G13C, chain Q/R, )
08: VAR_026108 (G13D, chain Q/R, )
09: VAR_068817 (G13R, chain Q/R, )
10: VAR_045977 (Q22K, chain Q/R, )
11: VAR_045978 (T58I, chain Q/R, )
12: VAR_045979 (Q61K, chain Q/R, )
13: VAR_006838 (Q61L, chain Q/R, )
14: VAR_045980 (E63K, chain Q/R, )
15: VAR_045981 (K117R, chain Q/R, )
16: VAR_045982 (A146T, chain Q/R, )
17: VAR_045983 (A146V, chain Q/R, )
18: VAR_066051 (L569V, chain S, )
19: VAR_066052 (F623I, chain S, )
20: VAR_030437 (P655L, chain S, )
21: VAR_030438 (Y702H, chain S, )
22: VAR_066053 (A708T, chain S, )
23: VAR_030439 (W729L, chain S, )
24: VAR_030440 (I733F, chain S, )
25: VAR_066054 (I784T, chain S, )
26: VAR_030441 (E846K, chain S, )
27: VAR_066055 (P894R, chain S, )
28: VAR_030442 (Q977R, chain S, )
29: VAR_066056 (N1011S, chain S, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_026106
G
12
A
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
12
A
02
UniProt
VAR_045975
G
12
C
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
12
C
03
UniProt
VAR_068816
G
12
D
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
12
D
04
UniProt
VAR_045976
G
12
E
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
12
E
05
UniProt
VAR_006837
G
12
S
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
12
S
06
UniProt
VAR_006836
G
12
V
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
12
V
07
UniProt
VAR_026107
G
13
C
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
13
C
08
UniProt
VAR_026108
G
13
D
RASH_HUMAN
Disease (CSTLO)
---
Q/R
G
13
D
09
UniProt
VAR_068817
G
13
R
RASH_HUMAN
Disease (SFM)
---
Q/R
G
13
R
10
UniProt
VAR_045977
Q
22
K
RASH_HUMAN
Disease (CMEMS)
---
Q/R
Q
22
K
11
UniProt
VAR_045978
T
58
I
RASH_HUMAN
Disease (CSTLO)
---
Q/R
T
58
I
12
UniProt
VAR_045979
Q
61
K
RASH_HUMAN
Unclassified
28933406
Q/R
Q
61
K
13
UniProt
VAR_006838
Q
61
L
RASH_HUMAN
Unclassified
---
Q/R
Q
61
L
14
UniProt
VAR_045980
E
63
K
RASH_HUMAN
Disease (CMEMS)
---
Q/R
E
63
K
15
UniProt
VAR_045981
K
117
R
RASH_HUMAN
Disease (CSTLO)
---
Q/R
K
117
R
16
UniProt
VAR_045982
A
146
T
RASH_HUMAN
Disease (CSTLO)
---
Q/R
A
146
T
17
UniProt
VAR_045983
A
146
V
RASH_HUMAN
Disease (CSTLO)
---
Q/R
A
146
V
18
UniProt
VAR_066051
L
569
V
SOS1_HUMAN
Polymorphism
---
S
L
569
V
19
UniProt
VAR_066052
F
623
I
SOS1_HUMAN
Disease (NS4)
---
S
F
623
I
20
UniProt
VAR_030437
P
655
L
SOS1_HUMAN
Polymorphism
56219475
S
P
655
L
21
UniProt
VAR_030438
Y
702
H
SOS1_HUMAN
Disease (NS4)
---
S
Y
702
H
22
UniProt
VAR_066053
A
708
T
SOS1_HUMAN
Polymorphism
140811086
S
A
708
T
23
UniProt
VAR_030439
W
729
L
SOS1_HUMAN
Disease (NS4)
---
S
W
729
L
24
UniProt
VAR_030440
I
733
F
SOS1_HUMAN
Disease (NS4)
---
S
I
733
F
25
UniProt
VAR_066054
I
784
T
SOS1_HUMAN
Unclassified
---
S
I
784
T
26
UniProt
VAR_030441
E
846
K
SOS1_HUMAN
Disease (NS4)
---
S
E
846
K
27
UniProt
VAR_066055
P
894
R
SOS1_HUMAN
Disease (NS4)
---
S
P
894
R
28
UniProt
VAR_030442
Q
977
R
SOS1_HUMAN
Polymorphism
---
S
Q
977
R
29
UniProt
VAR_066056
N
1011
S
SOS1_HUMAN
Polymorphism
8192671
S
N
1011
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 5)
Info
All PROSITE Patterns/Profiles
1: RAS (Q:1-166,R:1-166)
2: RASGEF_NTER (S:597-741)
3: RASGEF_CAT (S:780-1019)
4: RASGEF (S:927-960)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAS
PS51421
small GTPase Ras family profile.
RASH_HUMAN
1-188
2
Q:1-166
R:1-166
2
RASGEF_NTER
PS50212
Ras guanine-nucleotide exchange factors N-terminal domain profile.
SOS1_HUMAN
597-741
1
S:597-741
3
RASGEF_CAT
PS50009
Ras guanine-nucleotide exchange factors catalytic domain profile.
SOS1_HUMAN
780-1019
1
S:780-1019
4
RASGEF
PS00720
Ras Guanine-nucleotide exchange factors domain signature.
SOS1_HUMAN
927-960
1
S:927-960
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.5b (Q:1-37 | R:1-37)
Exon 1.6c (Q:38-97 | R:38-97)
Exon 1.7a (Q:97-150 | R:97-150)
Exon 1.9d (Q:151-166 | R:151-166)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.5b
2: Boundary 1.5b/1.6c
3: Boundary 1.6c/1.7a
4: Boundary 1.7a/1.9d
5: Boundary 1.9d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3
ENST00000397596
3
ENSE00001529352
chr11:
535339-535257
83
RASH_HUMAN
-
0
0
-
-
1.5b
ENST00000397596
5b
ENSE00002189675
chr11:
534375-534212
164
RASH_HUMAN
1-37
37
2
Q:1-37
R:1-37
37
37
1.6c
ENST00000397596
6c
ENSE00001728710
chr11:
533944-533766
179
RASH_HUMAN
38-97
60
2
Q:38-97
R:38-97
60
60
1.7a
ENST00000397596
7a
ENSE00001206466
chr11:
533612-533453
160
RASH_HUMAN
97-150
54
2
Q:97-150
R:97-150
54
54
1.9d
ENST00000397596
9d
ENSE00001628271
chr11:
532755-532242
514
RASH_HUMAN
151-189
39
2
Q:151-166
R:151-166
16
16
[
close EXON info
]
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1nvus_ (S:)
2a: SCOP_d1nvuq_ (Q:)
2b: SCOP_d1nvur_ (R:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ras GEF
(11)
Superfamily
:
Ras GEF
(11)
Family
:
Ras GEF
(11)
Protein domain
:
Son of sevenless protein homolog 1 (sos-1)
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d1nvus_
S:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
cH-p21 Ras protein
(104)
Human (Homo sapiens) [TaxId: 9606]
(104)
2a
d1nvuq_
Q:
2b
d1nvur_
R:
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1nvuQ00 (Q:1-166)
1b: CATH_1nvuR00 (R:1-166)
2a: CATH_1nvuS02 (S:759-930,S:974-1043)
3a: CATH_1nvuS01 (S:568-741,S:931-973)
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Architectures
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
1nvuQ00
Q:1-166
1b
1nvuR00
R:1-166
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Son of Sevenless (SoS) protein; Chain S, domain 2
(8)
Homologous Superfamily
:
Son of sevenless (Sos) protein Chain
(8)
Human (Homo sapiens)
(8)
2a
1nvuS02
S:759-930,S:974-1043
Architecture
:
Up-down Bundle
(3216)
Topology
:
Son of sevenless (SoS) protein; Chain S, domain 1
(8)
Homologous Superfamily
:
Son of sevenless (SoS) protein Chain: S domain 1
(8)
Human (Homo sapiens)
(8)
3a
1nvuS01
S:568-741,S:931-973
[
close CATH info
]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_Ras_1nvuR01 (R:5-165)
1b: PFAM_Ras_1nvuR02 (R:5-165)
2a: PFAM_RasGEF_1nvuS01 (S:777-963)
3a: PFAM_RasGEF_N_1nvuS02 (S:600-717)
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Clans
(
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(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-1nvuR01
R:5-165
1b
Ras-1nvuR02
R:5-165
Clan
:
no clan defined [family: RasGEF]
(8)
Family
:
RasGEF
(8)
Homo sapiens (Human)
(8)
2a
RasGEF-1nvuS01
S:777-963
Clan
:
no clan defined [family: RasGEF_N]
(7)
Family
:
RasGEF_N
(7)
Homo sapiens (Human)
(7)
3a
RasGEF_N-1nvuS02
S:600-717
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