1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Swanson, K.A.
Kang, R.S.
Stamenova, S.D.
Hicke, L.
Radhakrishnan, I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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 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
UK
Embo J.
EMJODG
0897
0261-4189
22
4597
4606
10.1093/emboj/cdg471
12970172
Solution Structure of Vps27 UIM-Ubiquitin Complex Important for Endosomal Sorting and Receptor Downregulation
2003
10.2210/pdb1q0w/pdb
pdb_00001q0w
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
2824.103
Vacuolar protein sorting-associated protein VPS27
Amino-terminal UIM, residues 256 to 278
1
syn
polymer
8568.769
Ubiquitin
1
man
polymer
no
no
YPEDEEELIRKAIELSLKESRNSA
YPEDEEELIRKAIELSLKESRNSA
A
polypeptide(L)
no
no
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
B
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
Escherichia coli
sample
(UBI1 OR RPL40A OR YIL148W) AND (UBI2 OR RPL40B OR YKR094C) AND (UBI3 OR RPS31 OR YLR167W OR L9470.14) AND (UBI4 OR SCD2 OR YLL039C)
4932
Saccharomyces cerevisiae
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
pET3-a
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-10-07
1
1
2008-04-29
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
Solution structure of tandem UIMs of Vps27
Crystal structure of the Vps27 carboxy-terminal UIM
HELIX
Author determined secondary structure
SHEET
Author determined secondary structure
RCSB
Y
RCSB
2003-07-17
REL
REL
The sequence was synthesized using a peptide synthesizer. The sequence contains a non-native tyrosine residue at the amino-terminus (residue number 255). The sequence occurs naturally in S. Cerevisiae.
sample
The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
80
20
3D_15N-separated_NOESY
2D double half-filtered NOESY
3D_13C-separated_NOESY
2D double half-filtered NOESY
3D 13C-filtered,13C-edited NOESY
20 mM sodium phosphate, pH 6.0, 0.2% NaN3
6.0
1
atm
298
K
THE STRUCTURES ARE BASED ON A TOTAL OF 2138 DISTANCE RESTRAINTS, INCLUDING 2062 NOE-DERIVED DISTANCE RESTRAINTS [1625 UNAMBIGUOUS AND 437 AMBIGUOUS RESTRAINTS], 76 HYDROGEN BONDING DISTANCE RESTRAINTS, AND 112 TORSION ANGLE RESTRAINTS.
TORSION ANGLE DYNAMICS AND SIMULATED ANNEALING
1
closest to the average
1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM
90% H2O/10% D2O
1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM
100% D2O
Varian Instruments
collection
VNMR
6.1B
Accelrys
data analysis
Felix
98.0
Brunger et al.
refinement
CNS
1.1
Linge and Nilges
refinement
ARIA
1.2
600
Varian
INOVA
TYR
255
n
1
TYR
255
A
PRO
256
n
2
PRO
256
A
GLU
257
n
3
GLU
257
A
ASP
258
n
4
ASP
258
A
GLU
259
n
5
GLU
259
A
GLU
260
n
6
GLU
260
A
GLU
261
n
7
GLU
261
A
LEU
262
n
8
LEU
262
A
ILE
263
n
9
ILE
263
A
ARG
264
n
10
ARG
264
A
LYS
265
n
11
LYS
265
A
ALA
266
n
12
ALA
266
A
ILE
267
n
13
ILE
267
A
GLU
268
n
14
GLU
268
A
LEU
269
n
15
LEU
269
A
SER
270
n
16
SER
270
A
LEU
271
n
17
LEU
271
A
LYS
272
n
18
LYS
272
A
GLU
273
n
19
GLU
273
A
SER
274
n
20
SER
274
A
ARG
275
n
21
ARG
275
A
ASN
276
n
22
ASN
276
A
SER
277
n
23
SER
277
A
ALA
278
n
24
ALA
278
A
MET
1
n
1
MET
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
PHE
4
n
4
PHE
4
B
VAL
5
n
5
VAL
5
B
LYS
6
n
6
LYS
6
B
THR
7
n
7
THR
7
B
LEU
8
n
8
LEU
8
B
THR
9
n
9
THR
9
B
GLY
10
n
10
GLY
10
B
LYS
11
n
11
LYS
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
THR
14
n
14
THR
14
B
LEU
15
n
15
LEU
15
B
GLU
16
n
16
GLU
16
B
VAL
17
n
17
VAL
17
B
GLU
18
n
18
GLU
18
B
SER
19
n
19
SER
19
B
SER
20
n
20
SER
20
B
ASP
21
n
21
ASP
21
B
THR
22
n
22
THR
22
B
ILE
23
n
23
ILE
23
B
ASP
24
n
24
ASP
24
B
ASN
25
n
25
ASN
25
B
VAL
26
n
26
VAL
26
B
LYS
27
n
27
LYS
27
B
SER
28
n
28
SER
28
B
LYS
29
n
29
LYS
29
B
ILE
30
n
30
ILE
30
B
GLN
31
n
31
GLN
31
B
ASP
32
n
32
ASP
32
B
LYS
33
n
33
LYS
33
B
GLU
34
n
34
GLU
34
B
GLY
35
n
35
GLY
35
B
ILE
36
n
36
ILE
36
B
PRO
37
n
37
PRO
37
B
PRO
38
n
38
PRO
38
B
ASP
39
n
39
ASP
39
B
GLN
40
n
40
GLN
40
B
GLN
41
n
41
GLN
41
B
ARG
42
n
42
ARG
42
B
LEU
43
n
43
LEU
43
B
ILE
44
n
44
ILE
44
B
PHE
45
n
45
PHE
45
B
ALA
46
n
46
ALA
46
B
GLY
47
n
47
GLY
47
B
LYS
48
n
48
LYS
48
B
GLN
49
n
49
GLN
49
B
LEU
50
n
50
LEU
50
B
GLU
51
n
51
GLU
51
B
ASP
52
n
52
ASP
52
B
GLY
53
n
53
GLY
53
B
ARG
54
n
54
ARG
54
B
THR
55
n
55
THR
55
B
LEU
56
n
56
LEU
56
B
SER
57
n
57
SER
57
B
ASP
58
n
58
ASP
58
B
TYR
59
n
59
TYR
59
B
ASN
60
n
60
ASN
60
B
ILE
61
n
61
ILE
61
B
GLN
62
n
62
GLN
62
B
LYS
63
n
63
LYS
63
B
GLU
64
n
64
GLU
64
B
SER
65
n
65
SER
65
B
THR
66
n
66
THR
66
B
LEU
67
n
67
LEU
67
B
HIS
68
n
68
HIS
68
B
LEU
69
n
69
LEU
69
B
VAL
70
n
70
VAL
70
B
LEU
71
n
71
LEU
71
B
ARG
72
n
72
ARG
72
B
LEU
73
n
73
LEU
73
B
ARG
74
n
74
ARG
74
B
GLY
75
n
75
GLY
75
B
GLY
76
n
76
GLY
76
B
author_defined_assembly
2
dimeric
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
B
O
ILE
13
B
O
ILE
13
B
N
VAL
5
B
N
VAL
5
B
N
LYS
6
B
N
LYS
6
B
O
LEU
67
B
O
LEU
67
B
O
HIS
68
B
O
HIS
68
B
N
ILE
44
B
N
ILE
44
B
N
PHE
45
B
N
PHE
45
B
O
LYS
48
B
O
LYS
48
2
B
B
H
HD21
THR
ASN
22
25
1.32
14
A
B
HA
HG22
ILE
VAL
263
70
1.34
16
A
B
HA
HG22
ILE
VAL
263
70
1.33
1
A
PRO
256
-78.17
47.98
1
A
GLU
257
-145.11
52.12
1
A
SER
274
-80.25
41.96
1
A
ASN
276
-79.97
42.22
1
B
ASP
52
-76.76
49.44
2
A
PRO
256
-76.94
38.96
2
A
GLU
257
63.61
135.14
2
A
SER
274
-81.92
47.48
2
A
ASN
276
56.90
-127.05
2
A
SER
277
-69.76
-140.52
2
B
THR
7
-74.05
-151.50
2
B
THR
9
-153.42
54.85
2
B
ARG
74
-173.28
130.83
3
A
ARG
275
-75.06
34.04
3
A
ASN
276
-82.55
45.55
3
B
LEU
8
-75.04
43.62
3
B
THR
9
-149.57
33.02
3
B
VAL
17
-148.80
-156.74
3
B
ARG
72
-76.78
47.34
3
B
LEU
73
64.40
131.91
4
B
THR
22
-71.67
-152.98
4
B
GLU
51
-67.35
-156.19
4
B
ASP
52
-142.28
43.25
4
B
LEU
73
49.52
-135.37
5
A
PRO
256
-66.27
-134.70
5
A
SER
274
-86.55
39.34
5
A
SER
277
-80.58
41.99
5
B
SER
20
-86.04
39.31
5
B
ARG
74
-176.72
-44.93
6
A
GLU
257
66.47
135.15
6
A
SER
277
57.67
-143.98
6
B
LEU
8
51.87
-103.76
6
B
THR
9
-153.46
58.46
6
B
LYS
33
-67.12
-70.53
6
B
LEU
73
61.28
133.14
7
A
SER
277
74.00
-43.43
7
B
THR
9
-152.30
-46.05
7
B
THR
22
-69.11
-173.47
7
B
ASP
52
-76.45
49.31
8
A
ARG
275
58.12
-133.15
8
A
SER
277
-179.30
44.57
8
B
THR
22
-78.70
-158.16
8
B
GLU
51
-68.71
-148.47
8
B
ASP
52
-151.30
45.34
8
B
ARG
74
66.06
135.57
9
A
GLU
257
-144.61
-64.78
9
A
SER
274
-84.12
48.03
9
A
ASN
276
-175.63
53.87
9
A
SER
277
-172.61
-49.58
9
B
SER
20
-92.31
39.06
9
B
ASP
21
-78.27
-148.81
9
B
GLU
51
-68.35
-145.82
9
B
ASP
52
-163.36
49.94
9
B
ARG
74
61.18
-127.39
10
A
GLU
257
-146.40
45.52
10
A
ARG
275
65.74
-78.85
11
A
SER
274
-85.99
39.09
11
B
THR
22
-71.75
-152.01
11
B
GLU
51
-65.97
-146.64
11
B
ASP
52
-156.49
45.03
12
A
ARG
275
74.50
-41.90
12
A
ASN
276
-70.06
-137.72
12
A
SER
277
-171.03
48.92
12
B
SER
20
-82.39
41.44
12
B
LEU
73
60.39
128.61
12
B
ARG
74
-173.76
131.17
13
A
ASN
276
-156.56
39.30
13
B
SER
20
-99.57
34.41
13
B
LYS
33
-72.79
-71.71
13
B
GLU
51
-65.27
-149.45
13
B
ASP
52
-150.99
40.14
14
A
PRO
256
-69.47
-141.77
14
A
SER
277
-79.97
42.56
14
B
GLN
2
-119.36
76.40
14
B
THR
22
-71.92
-155.96
14
B
GLN
62
-71.37
-144.20
14
B
ARG
74
-75.58
-142.49
15
A
SER
277
-179.39
136.94
15
B
THR
9
-147.60
-48.99
15
B
LEU
73
66.82
132.47
16
A
ASN
276
-168.75
-43.30
16
A
SER
277
-160.23
49.63
16
B
THR
7
-92.96
-158.33
16
B
THR
9
-76.38
34.91
16
B
THR
22
-72.40
-153.15
16
B
GLU
51
-67.12
-160.59
16
B
ARG
72
-59.32
107.23
16
B
LEU
73
47.44
-135.00
16
B
ARG
74
-175.41
-42.57
17
A
ASN
276
-172.92
135.42
17
A
SER
277
-161.29
-44.48
17
B
THR
7
-89.33
-152.80
17
B
ARG
74
65.43
133.78
18
A
ASN
276
66.04
135.74
18
A
SER
277
63.85
129.62
18
B
THR
7
-79.90
-151.44
18
B
THR
9
-152.71
-43.11
18
B
ALA
46
63.40
-72.84
18
B
LEU
50
-77.31
38.45
18
B
GLU
51
39.13
-144.58
18
B
ASP
52
-168.46
36.91
18
B
ARG
74
-173.05
-44.34
19
A
ASN
276
-172.61
-43.52
19
A
SER
277
-162.12
45.52
19
B
THR
22
-70.13
-153.50
19
B
LEU
50
-76.96
31.40
19
B
GLU
51
43.16
-147.82
19
B
ASP
52
-160.33
45.28
20
B
THR
7
-88.28
-152.53
20
B
THR
22
-74.64
-157.32
20
B
GLU
51
-68.17
-155.38
20
B
ASP
52
-123.21
-55.47
20
B
LEU
73
53.72
-136.61
Solution structure of Vps27 amino-terminal UIM-ubiquitin complex
1
N
N
2
N
N
A
ASP
258
A
ASP
4
HELX_P
A
GLU
273
A
GLU
19
1
1
16
B
THR
22
B
THR
22
HELX_P
B
GLU
34
B
GLU
34
5
2
13
B
LEU
56
B
LEU
56
HELX_P
B
TYR
59
B
TYR
59
1
3
4
TRANSPORT PROTEIN
PROTEIN-PROTEIN COMPLEX, TRANSPORT PROTEIN
VPS27_YEAST
UNP
1
256
P40343
TPEDEEELIRKAIELSLKESRNSA
UBIQ_YEAST
UNP
2
1
P61864
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
256
279
1Q0W
255
278
P40343
A
1
1
24
1
76
1Q0W
1
76
P61864
B
2
1
76
1
THR
engineered mutation
TYR
255
1Q0W
A
P40343
UNP
256
1
5
anti-parallel
parallel
anti-parallel
anti-parallel
B
THR
12
B
THR
12
B
GLU
16
B
GLU
16
B
GLN
2
B
GLN
2
B
THR
7
B
THR
7
B
THR
66
B
THR
66
B
LEU
71
B
LEU
71
B
GLN
41
B
GLN
41
B
PHE
45
B
PHE
45
B
LYS
48
B
LYS
48
B
GLN
49
B
GLN
49
1
P 1