1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Dong, X.
Gong, Z.
Qin, L.Y.
Ran, M.L.
Zhang, C.L.
Liu, K.
Liu, Z.
Zhang, W.P.
Tang, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H8 N O6 P
185.072
n
PHOSPHOSERINE
PHOSPHONOSERINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Proc. Natl. Acad. Sci. U.S.A.
PNASA6
0040
1091-6490
114
6770
6775
10.1073/pnas.1705718114
28611216
Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch
2017
10.2210/pdb5xk4/pdb
pdb_00005xk4
8656.811
Polyubiquitin-B
UNP residues 1-76
1
man
polymer
no
yes
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKE(SEP)TLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Human
sample
1
76
UBB
9606
Homo sapiens
83333
Escherichia coli K-12
Biological sequence
citation
database_2
pdbx_database_status
pdbx_nmr_spectrometer
repository
Initial release
Database references
Data collection
Database references
Other
1
0
2017-06-28
1
1
2017-07-12
1
2
2023-06-14
_citation.journal_volume
_citation.page_first
_citation.page_last
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_spectrometer.model
China
the Chinese Ministry of Science and Technology
2013CB910200
China
the Chinese Ministry of Science and Technology
2016YFA0501200
China
the National Natural Science Foundation of China
31225007
China
the National Natural Science Foundation of China
81573400
China
he National Natural Science Foundation of China
31500595
China
he National Natural Science Foundation of China
31400735
China
he National Natural Science Foundation of China
31400644
Ubiquitin S65 phosphorylation engenders a pH-sensitive
conformational switch
N
PDBJ
Y
PDBJ
2017-05-05
REL
REL
REL
REL
structures with the lowest energy
800
30
isotropic
1
2D 1H-15N HSQC
isotropic
1
3D CBCA(CO)NH
isotropic
2
3D HNCA
isotropic
2
3D HNCACB
isotropic
2
3D 1H-13C NOESY
isotropic
2
3D 1H-15N NOESY
0.8
mM
[U-98% 13C; U-98% 15N]
150
mM
buffer
7.4
pH
760
mmHg
298
K
simulated annealing
1
closest to the average
0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O
13C 15N pUb
90% H2O/10% D2O
solution
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
structure calculation
X-PLOR NIH
CCPN
chemical shift assignment
CcpNMR
CCPN
peak picking
CcpNMR
600
Bruker
AVANCE III
850
Bruker
AVANCE III
MET
1
n
1
MET
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
PHE
4
n
4
PHE
4
A
VAL
5
n
5
VAL
5
A
LYS
6
n
6
LYS
6
A
THR
7
n
7
THR
7
A
LEU
8
n
8
LEU
8
A
THR
9
n
9
THR
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
GLU
16
n
16
GLU
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
PRO
19
n
19
PRO
19
A
SER
20
n
20
SER
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
ILE
23
n
23
ILE
23
A
GLU
24
n
24
GLU
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
LYS
29
n
29
LYS
29
A
ILE
30
n
30
ILE
30
A
GLN
31
n
31
GLN
31
A
ASP
32
n
32
ASP
32
A
LYS
33
n
33
LYS
33
A
GLU
34
n
34
GLU
34
A
GLY
35
n
35
GLY
35
A
ILE
36
n
36
ILE
36
A
PRO
37
n
37
PRO
37
A
PRO
38
n
38
PRO
38
A
ASP
39
n
39
ASP
39
A
GLN
40
n
40
GLN
40
A
GLN
41
n
41
GLN
41
A
ARG
42
n
42
ARG
42
A
LEU
43
n
43
LEU
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
ALA
46
n
46
ALA
46
A
GLY
47
n
47
GLY
47
A
LYS
48
n
48
LYS
48
A
GLN
49
n
49
GLN
49
A
LEU
50
n
50
LEU
50
A
GLU
51
n
51
GLU
51
A
ASP
52
n
52
ASP
52
A
GLY
53
n
53
GLY
53
A
ARG
54
n
54
ARG
54
A
THR
55
n
55
THR
55
A
LEU
56
n
56
LEU
56
A
SER
57
n
57
SER
57
A
ASP
58
n
58
ASP
58
A
TYR
59
n
59
TYR
59
A
ASN
60
n
60
ASN
60
A
ILE
61
n
61
ILE
61
A
GLN
62
n
62
GLN
62
A
LYS
63
n
63
LYS
63
A
GLU
64
n
64
GLU
64
A
SEP
65
n
65
SEP
65
A
THR
66
n
66
THR
66
A
LEU
67
n
67
LEU
67
A
HIS
68
n
68
HIS
68
A
LEU
69
n
69
LEU
69
A
VAL
70
n
70
VAL
70
A
LEU
71
n
71
LEU
71
A
ARG
72
n
72
ARG
72
A
LEU
73
n
73
LEU
73
A
ARG
74
n
74
ARG
74
A
GLY
75
n
75
GLY
75
A
GLY
76
n
76
GLY
76
A
author_defined_assembly
1
monomeric
none
0
0
5260
A
SEP
65
modified residue
A
SEP
65
SER
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LEU
15
A
O
LEU
15
A
N
ILE
3
A
N
ILE
3
A
N
LYS
6
A
N
LYS
6
A
O
LEU
69
A
O
LEU
69
A
O
ARG
72
A
O
ARG
72
A
N
ARG
42
A
N
ARG
42
A
N
PHE
45
A
N
PHE
45
A
O
LYS
48
A
O
LYS
48
2
A
A
O
H
ILE
LYS
61
63
1.59
11
A
A
HG1
H
THR
LEU
66
67
1.34
21
A
A
HE
HE
ARG
ARG
42
74
1.31
21
A
A
O
H
ILE
LYS
61
63
1.57
1
A
PRO
38
-43.31
-12.37
1
A
ASP
52
-62.34
20.00
1
A
GLN
62
-69.78
48.05
1
A
SEP
65
-128.32
-146.60
2
A
PRO
37
-46.83
156.89
2
A
ASP
52
-61.36
14.69
2
A
GLN
62
-68.77
47.61
2
A
SEP
65
-128.33
-147.22
2
A
LEU
67
-79.53
43.34
3
A
ASP
52
-62.56
18.82
3
A
GLN
62
-69.97
47.55
3
A
SEP
65
-128.42
-146.88
4
A
PRO
37
-47.18
155.01
4
A
ASP
52
-63.41
26.93
4
A
GLN
62
-70.07
47.54
4
A
SEP
65
-128.47
-146.73
4
A
LEU
67
-79.06
45.49
5
A
ASP
52
-62.17
17.29
5
A
GLN
62
-70.17
45.16
5
A
SEP
65
-128.19
-147.35
5
A
LEU
67
-79.93
43.80
6
A
THR
9
-69.10
0.64
6
A
ASP
52
-62.84
31.56
6
A
GLN
62
-69.14
48.33
6
A
SEP
65
-128.20
-146.66
7
A
PRO
37
-47.65
154.68
7
A
ASP
52
-63.05
21.20
7
A
GLN
62
-70.68
46.84
7
A
SEP
65
-127.58
-148.68
7
A
LEU
67
-79.89
40.63
8
A
ASP
52
-62.95
17.99
8
A
GLN
62
-70.62
45.68
8
A
SEP
65
-127.27
-148.18
8
A
LEU
67
-81.17
37.77
9
A
ASP
52
-62.82
19.35
9
A
GLN
62
-69.30
47.12
9
A
SEP
65
-128.47
-147.41
9
A
LEU
67
-79.96
36.44
10
A
PRO
38
-42.99
-14.31
10
A
ASP
52
-62.53
22.23
10
A
GLN
62
-72.84
44.75
10
A
SEP
65
-127.61
-147.60
10
A
LEU
67
-81.18
38.09
11
A
PRO
37
-46.71
156.66
11
A
ASP
52
-61.59
27.85
11
A
GLN
62
-71.25
45.33
11
A
SEP
65
-128.76
-147.50
12
A
PRO
37
-46.44
157.53
12
A
ASP
52
-61.53
16.39
12
A
GLN
62
-71.11
45.14
12
A
SEP
65
-128.19
-148.10
12
A
LEU
67
-80.89
40.41
13
A
PRO
37
-45.80
157.76
13
A
ASP
52
-62.50
15.88
13
A
GLN
62
-69.64
46.33
13
A
SEP
65
-129.20
-146.69
13
A
LEU
67
-79.88
45.63
14
A
ASP
52
-62.17
24.54
14
A
GLN
62
-70.83
45.79
14
A
SEP
65
-128.66
-146.99
15
A
ASP
52
-66.55
16.96
15
A
GLN
62
-74.40
44.29
15
A
SEP
65
-128.70
-147.69
16
A
PRO
37
-48.78
158.28
16
A
ASP
52
-63.23
24.93
16
A
GLN
62
-73.74
44.56
16
A
SEP
65
-128.07
-148.29
16
A
LEU
67
-79.80
41.25
17
A
PRO
37
-46.01
155.69
17
A
ASP
52
-61.81
13.20
17
A
GLN
62
-69.91
47.08
17
A
SEP
65
-128.28
-146.76
17
A
LEU
67
-79.12
41.51
18
A
ASP
52
-68.63
12.82
18
A
GLN
62
-76.36
43.93
18
A
SEP
65
-128.81
-147.10
18
A
LEU
67
-80.71
40.23
19
A
PRO
37
-48.09
158.48
19
A
ASP
52
-61.50
17.31
19
A
GLN
62
-76.67
43.96
19
A
SEP
65
-128.60
-147.43
19
A
LEU
67
-80.01
39.57
20
A
ASP
52
-58.30
11.54
20
A
GLN
62
-70.55
45.90
20
A
SEP
65
-128.14
-147.31
21
A
THR
9
-69.68
4.97
21
A
ASP
52
-60.89
11.08
21
A
GLN
62
-68.44
47.28
21
A
SEP
65
-128.69
-146.73
21
A
LEU
67
-79.42
45.88
22
A
PRO
37
-45.66
159.66
22
A
ASP
52
-61.44
12.44
22
A
GLN
62
-69.39
46.86
22
A
SEP
65
-128.83
-146.68
22
A
LEU
67
-80.14
43.67
23
A
ASP
52
-83.20
39.45
23
A
GLN
62
-72.09
46.28
23
A
SEP
65
-128.04
-147.21
23
A
LEU
67
-80.92
37.78
24
A
ASP
52
-62.94
25.64
24
A
GLN
62
-68.84
47.67
24
A
SEP
65
-127.98
-147.25
24
A
LEU
67
-82.59
37.99
25
A
ASP
52
-62.53
17.33
25
A
GLN
62
-74.83
43.85
25
A
SEP
65
-127.95
-147.94
25
A
LEU
67
-80.94
44.97
26
A
ASP
52
-61.75
16.72
26
A
GLN
62
-71.36
46.22
26
A
SEP
65
-128.34
-147.24
26
A
LEU
67
-80.37
41.76
27
A
PRO
37
-48.94
150.56
27
A
GLN
62
-69.82
47.44
27
A
SEP
65
-129.50
-146.68
27
A
LEU
67
-79.85
44.44
28
A
PRO
38
-43.00
-14.22
28
A
ASP
52
-61.75
13.12
28
A
GLN
62
-69.99
48.26
28
A
SEP
65
-128.79
-146.36
28
A
LEU
67
-79.79
41.49
29
A
ASP
52
-63.27
31.27
29
A
GLN
62
-69.40
48.50
29
A
SEP
65
-127.20
-148.05
30
A
ASP
52
-60.77
15.08
30
A
GLN
62
-70.85
46.85
30
A
SEP
65
-127.97
-147.02
N
Retracted state of S65-phosphorylated ubiquitin
1
N
N
A
THR
22
A
THR
22
HELX_P
A
GLY
35
A
GLY
35
1
AA1
14
A
THR
55
A
THR
55
HELX_P
A
GLN
62
A
GLN
62
1
AA2
8
covale
1.330
both
A
GLU
64
A
C
GLU
64
1_555
A
SEP
65
A
N
SEP
65
1_555
covale
1.335
both
A
SEP
65
A
C
SEP
65
1_555
A
THR
66
A
N
THR
66
1_555
CELL CYCLE
pH-sensitive ubiquitin conformational switch, CELL CYCLE
UBB_HUMAN
UNP
1
1
P0CG47
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
1
76
5XK4
1
76
P0CG47
A
1
1
76
5
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
GLU
16
A
GLU
16
A
GLN
2
A
GLN
2
A
LYS
6
A
LYS
6
A
HIS
68
A
HIS
68
A
LEU
73
A
LEU
73
A
GLN
41
A
GLN
41
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49