8.68
-11.383
-0.016
2.382
A
N
VAL
1
ATOM
A
N
VAL
1
1
1.00
1
N
7.18
-10.009
-0.596
2.558
A
CA
VAL
1
ATOM
A
CA
VAL
1
1
1.00
1
C
5.67
-9.359
0.025
3.781
A
C
VAL
1
ATOM
A
C
VAL
1
1
1.00
1
C
5.32
-9.293
1.246
3.889
A
O
VAL
1
ATOM
A
O
VAL
1
1
1.00
1
O
7.59
-9.138
-0.365
1.319
A
CB
VAL
1
ATOM
A
CB
VAL
1
1
1.00
1
C
8.59
-7.711
-0.834
1.560
A
CG1
VAL
1
ATOM
A
CG1
VAL
1
1
1.00
1
C
8.49
-9.718
-1.052
0.096
A
CG2
VAL
1
ATOM
A
CG2
VAL
1
1
1.00
1
C
4.46
-8.910
-0.804
4.727
A
N
GLN
2
ATOM
A
N
GLN
1
2
1.00
1
N
4.31
-8.184
-0.281
5.897
A
CA
GLN
2
ATOM
A
CA
GLN
1
2
1.00
1
C
4.29
-6.776
-0.888
5.960
A
C
GLN
2
ATOM
A
C
GLN
1
2
1.00
1
C
4.08
-6.633
-2.117
5.938
A
O
GLN
2
ATOM
A
O
GLN
1
2
1.00
1
O
4.21
-8.913
-0.648
7.211
A
CB
GLN
2
ATOM
A
CB
GLN
1
2
1.00
1
C
4.44
-8.334
0.018
8.440
A
CG
GLN
2
ATOM
A
CG
GLN
1
2
1.00
1
C
4.91
-8.930
-0.456
9.728
A
CD
GLN
2
ATOM
A
CD
GLN
1
2
1.00
1
C
5.38
-8.890
-1.639
10.034
A
OE1
GLN
2
ATOM
A
OE1
GLN
1
2
1.00
1
O
5.26
-9.426
0.471
10.517
A
NE2
GLN
2
ATOM
A
NE2
GLN
1
2
1.00
1
N
4.16
-5.734
-0.066
6.049
A
N
ILE
3
ATOM
A
N
ILE
1
3
1.00
1
N
4.08
-4.360
-0.573
6.243
A
CA
ILE
3
ATOM
A
A
CA
ILE
1
3
0.50
1
C
4.39
-4.358
-0.573
6.244
A
CA
ILE
3
ATOM
B
A
CA
ILE
1
3
0.50
1
C
4.10
-3.828
0.082
7.509
A
C
ILE
3
ATOM
A
C
ILE
1
3
1.00
1
C
3.80
-3.877
1.296
7.629
A
O
ILE
3
ATOM
A
O
ILE
1
3
1.00
1
O
4.26
-3.460
-0.235
5.052
A
CB
ILE
3
ATOM
A
A
CB
ILE
1
3
0.50
1
C
5.02
-3.405
-0.211
5.099
A
CB
ILE
3
ATOM
B
A
CB
ILE
1
3
0.50
1
C
4.18
-3.997
-0.928
3.796
A
CG1
ILE
3
ATOM
A
A
CG1
ILE
1
3
0.50
1
C
5.40
-4.088
-0.353
3.732
A
CG1
ILE
3
ATOM
B
A
CG1
ILE
1
3
0.50
1
C
4.40
-2.010
-0.632
5.332
A
CG2
ILE
3
ATOM
A
A
CG2
ILE
1
3
0.50
1
C
5.33
-2.146
-1.074
5.192
A
CG2
ILE
3
ATOM
B
A
CG2
ILE
1
3
0.50
1
C
4.27
-3.185
-0.674
2.544
A
CD1
ILE
3
ATOM
A
A
CD1
ILE
1
3
0.50
1
C
5.77
-4.356
-1.769
3.315
A
CD1
ILE
3
ATOM
B
A
CD1
ILE
1
3
0.50
1
C
4.27
-3.360
-0.727
8.459
A
N
VAL
4
ATOM
A
N
VAL
1
4
1.00
1
N
5.01
-2.852
-0.193
9.726
A
CA
VAL
4
ATOM
A
CA
VAL
1
4
1.00
1
C
4.68
-1.439
-0.712
9.946
A
C
VAL
4
ATOM
A
C
VAL
1
4
1.00
1
C
4.66
-1.227
-1.913
9.911
A
O
VAL
4
ATOM
A
O
VAL
1
4
1.00
1
O
6.35
-3.747
-0.638
10.917
A
CB
VAL
4
ATOM
A
CB
VAL
1
4
1.00
1
C
8.30
-3.231
-0.097
12.239
A
CG1
VAL
4
ATOM
A
CG1
VAL
1
4
1.00
1
C
7.62
-5.171
-0.190
10.688
A
CG2
VAL
4
ATOM
A
CG2
VAL
1
4
1.00
1
C
5.23
-0.487
0.208
10.086
A
N
TYR
5
ATOM
A
N
TYR
1
5
1.00
1
N
5.91
0.899
-0.131
10.386
A
CA
TYR
5
ATOM
A
CA
TYR
1
5
1.00
1
C
7.22
1.228
0.149
11.833
A
C
TYR
5
ATOM
A
C
TYR
1
5
1.00
1
C
8.70
1.148
1.299
12.278
A
O
TYR
5
ATOM
A
O
TYR
1
5
1.00
1
O
6.10
1.832
0.704
9.527
A
CB
TYR
5
ATOM
A
CB
TYR
1
5
1.00
1
C
6.41
1.720
0.503
8.044
A
CG
TYR
5
ATOM
A
CG
TYR
1
5
1.00
1
C
6.78
0.917
1.307
7.273
A
CD1
TYR
5
ATOM
A
CD1
TYR
1
5
1.00
1
C
6.27
2.463
-0.461
7.413
A
CD2
TYR
5
ATOM
A
CD2
TYR
1
5
1.00
1
C
7.73
0.859
1.146
5.893
A
CE1
TYR
5
ATOM
A
CE1
TYR
1
5
1.00
1
C
6.62
2.399
-0.635
6.049
A
CE2
TYR
5
ATOM
A
CE2
TYR
1
5
1.00
1
C
7.02
1.621
0.168
5.285
A
CZ
TYR
5
ATOM
A
CZ
TYR
1
5
1.00
1
C
9.55
1.582
-0.055
3.909
A
OH
TYR
5
ATOM
A
OH
TYR
1
5
1.00
1
O
8.70
1.662
-0.866
12.561
A
N
LYS
6
ATOM
A
N
LYS
1
6
1.00
1
N
10.61
2.121
-0.697
13.949
A
CA
LYS
6
ATOM
A
CA
LYS
1
6
1.00
1
C
15.54
3.464
-1.423
14.200
A
C
LYS
6
ATOM
A
C
LYS
1
6
1.00
1
C
12.86
3.999
-2.220
13.387
A
O
LYS
6
ATOM
A
O
LYS
1
6
1.00
1
O
11.79
1.121
-1.286
14.900
A
CB
LYS
6
ATOM
A
CB
LYS
1
6
1.00
1
C
13.41
-0.312
-0.847
14.694
A
CG
LYS
6
ATOM
A
CG
LYS
1
6
1.00
1
C
15.25
-1.147
-1.342
15.840
A
CD
LYS
6
ATOM
A
CD
LYS
1
6
1.00
1
C
17.66
-2.614
-0.974
15.677
A
CE
LYS
6
ATOM
A
CE
LYS
1
6
1.00
1
C
18.79
-3.345
-1.046
16.989
A
NZ
LYS
6
ATOM
A
NZ
LYS
1
6
1.00
1
N
19.24
4.021
-1.261
15.304
A
OXT
LYS
6
ATOM
A
OXT
LYS
1
6
1.00
1
O
26.57
6.024
-4.169
13.136
A
O
HOH
101
HETATM
B
O
HOH
2
1.00
1
O
0.034922
0.000000
0.013036
-0.000000
0.204918
0.000000
0.000000
-0.000000
0.029810
0.000000
0.000000
0.000000
Landau, M.
Eisenberg, D.
Sawaya, M.R.
Dannenberg, J.
Kobko, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
110.470
90.000
28.635
4.880
35.807
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
N
O
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
N
N
25
S
C
N
26
N
C
N
27
N
O
N
28
S
C
N
29
N
C
N
30
N
C
N
31
N
C
N
32
N
O
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
N
N
47
S
C
N
48
N
C
N
49
N
O
N
50
N
C
N
51
N
C
N
52
N
C
N
53
N
C
N
54
N
N
N
55
N
O
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
N
N
72
S
C
N
73
N
C
N
74
N
O
N
75
N
C
Y
76
N
C
Y
77
N
C
Y
78
N
C
Y
79
N
C
Y
80
N
C
Y
81
N
C
N
82
N
O
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
O
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
doub
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
doub
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
Y
78
N
doub
Y
79
N
sing
Y
80
N
sing
N
81
N
sing
Y
82
N
doub
N
83
N
sing
Y
84
N
doub
N
85
N
sing
Y
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
US
Nat.Struct.Mol.Biol.
1545-9993
16
973
978
10.1038/nsmb.1643
19684598
Molecular mechanisms for protein-encoded inheritance.
2009
10.2210/pdb4np8/pdb
pdb_00004np8
100
1
CCD
2008-02-25
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.9792
1.0
24-ID-E
APS
0.9792
SYNCHROTRON
APS BEAMLINE 24-ID-E
749.917
Microtubule-associated protein tau
UNP residues 623-628
1
syn
polymer
18.015
water
1
nat
water
Neurofibrillary tangle protein, Paired helical filament-tau, PHF-tau
no
no
VQIVYK
VQIVYK
A
polypeptide(L)
n
n
n
n
n
n
1
1.56
21.29
VAPOR DIFFUSION, HANGING DROP
7.5
reservoir contained 14% iso-Propanol, 0.07M HEPES-Na pH 7.5, 0.14M Sodium Citrate, and 30% Glycerol, vapor diffusion, hanging drop, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Data collection
Database references
Refinement description
1
0
2013-12-18
1
1
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
2013-12-18
SPRSDE
SAME SEQUENCE, BUT DIFFERENT PACKING.
SAME SEQUENCE, BUT WITH ORANGE G LIGAND BOUND.
RCSB
Y
RCSB
2013-11-20
REL
REL
HOH
water
9606
human
Homo sapiens
sample
2ON9
PDB
experimental model
HOH
7
2
HOH
HOH
101
A
VAL
1
n
1
VAL
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
VAL
4
n
4
VAL
4
A
TYR
5
n
5
TYR
5
A
LYS
6
n
6
LYS
6
A
author_defined_assembly
8
octameric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_565
x,y+1,z
crystal symmetry operation
0.0000000000
4.8800000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_575
x,y+2,z
crystal symmetry operation
0.0000000000
9.7600000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_585
x,y+3,z
crystal symmetry operation
0.0000000000
14.6400000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_455
-x-1/2,y+1/2,-z
crystal symmetry operation
-14.3175000000
2.4400000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_465
-x-1/2,y+3/2,-z
crystal symmetry operation
-14.3175000000
7.3200000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_475
-x-1/2,y+5/2,-z
crystal symmetry operation
-14.3175000000
12.2000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_485
-x-1/2,y+7/2,-z
crystal symmetry operation
-14.3175000000
17.0800000000
0.0000000000
26.570
7.5741
3.800
0.0900
0.0000
-0.1100
-0.2100
-0.0000
0.1300
0.9610
0.9550
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
0.1959
0.1770
0.1791
1.5100
16.7800
91
823
11.1000
92.5800
0.2070
0.1940
1.000
0.500
0.8187
1.8950
0.0650
0.0982
0.0894
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.0980
0.0890
0.8000
0.8000
1.2000
2ON9
MAXIMUM LIKELIHOOD
MASK
1.5100
16.7800
1
54
0
0
53
0.012
0.020
59
0.001
0.020
70
1.399
2.014
81
0.442
3.000
160
4.383
5.000
7
38.771
25.000
2
9.004
15.000
13
0.097
0.200
11
0.008
0.020
60
0.000
0.020
12
0.2760
0.2230
1.5470
4
45
49
20
73.1300
15.1
1.50
90
4NP8
825
825
-3.0
0.1600
1
8.1
4.1
94.4
0.3760
1.50
1.62
4.7
156
1
4.0
82.1
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
program
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
program
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
Structure of an amyloid forming peptide VQIVYK from the second repeat region of tau (alternate polymorph)
1
N
N
2
N
N
The biological unit is a pair of beta sheets. One sheet is constructed from chain A and unit cell translations along the b direction (i.e. X,Y+1,Z; X,Y+2,Z; X,Y+3,Z, etc.). The second sheet is constructed from -1/2-X,1/2+Y,-Z; -1/2-X,3/2+Y,-Z; -1/2-X,5/2+Y,-Z; etc.).
PROTEIN FIBRIL
amyloid-like protofibril, PROTEIN FIBRIL
TAU_HUMAN
UNP
1
623
P10636
VQIVYK
623
628
4NP8
1
6
P10636
A
1
1
6
5
C 1 2 1