PDBIHM.org

PDB-IHM

System for Archiving Integrative Structures

Ensemble information?

This entry consists of 1 distinct ensemble.

Summary?

This entry consists of 1 model(s). A total of 65 datasets were used to build this entry.

Representation ?

This entry has 1 representation(s).

ID Model(s) Entity ID Molecule name Chain(s) [auth] Total residues Rigid segments Flexible segments Model coverage/
Starting model coverage
(%)		 Scale
1 1 1 Nup84 A 726 - 1-6, 7-20, 21-26, 27-80, 81-95, 96-126, 127-135, 136-364, 365-371, 372-483, 484-505, 506-562, 563-574, 575-726 100.00 /
89.39 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
H
2 Nup85 B 744 - 1-46, 47-126, 127-131, 132-230, 231-234, 235-436, 437-450, 451-492, 493-495, 496-544, 545-552, 553-560, 561-566, 567-585, 586-589, 590-597, 598-602, 603-612, 613-615, 616-634, 635-637, 638-655, 656-660, 661-675, 676-684, 685-699, 700-706, 707-719, 720-724, 725-744 100.00 /
82.93 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
I
3 Nup120 C 1037 - 1, 2-29, 30-52, 53-305, 306-310, 311-711, 712-714, 715-726, 727-732, 733-746, 747-753, 754-766, 767-769, 770-781, 782-806, 807-818, 819-820, 821-833, 834-837, 838-853, 854-861, 862-879, 880-883, 884-895, 896-900, 901-913, 914-916, 917-931, 932-942, 943-955, 956-959, 960-971, 972-975, 976-987, 988-993, 994-1008, 1009-1024, 1025-1036, 1037 100.00 /
86.40 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
J
4 Nup133 D 1157 - 1-55, 56-78, 79-85, 86-125, 126-132, 133-144, 145-161, 162-184, 185-192, 193-200, 201-205, 206-249, 250-257, 258-480, 481-489, 490-763, 764-771, 772-1155, 1156-1157 100.00 /
89.11 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
K
5 Nup145c E 712 - 1-91, 92-99, 100-125, 126-144, 145-148, 149-550, 551-553, 554-560, 561-565, 566-576, 577-586, 587-602, 603-611, 612-624, 625-630, 631-645, 646-653, 654-673, 674-680, 681-689, 690-702, 703-712 100.00 /
74.44 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
L
6 Seh1 F 349 - 1-248, 249-287, 288-346, 347-349 100.00 /
87.97 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
M
7 Sec13 G 297 - 1-9, 10-158, 159-165, 166-296, 297 100.00 /
94.28 		Multiscale: Coarse-grained: 1 - 9 residue(s) per bead
N
8 Dyn2 O 92 - 1-6, 7-92 100.00 /
93.48 		Multiscale: Coarse-grained: 1 - 6 residue(s) per bead
P
9 Nup82 Q 713 - 1-6, 7-16, 17-22, 23-120, 121-122, 123-452, 453-521, 522-612, 613-624, 625-669, 670-677, 678-713 100.00 /
85.55 		Multiscale: Coarse-grained: 1 - 10 residue(s) per bead
R
10 Nup159 S 1460 - 1082-1116, 1117-1126, 1127-1210, 1211-1239, 1240-1265, 1266-1321, 1322-1331, 1332-1372, 1373-1381, 1382-1412, 1413-1428, 1429-1456, 1457-1460 25.96 /
51.45 		Multiscale: Coarse-grained: 1 - 35 residue(s) per bead
T
11 Nsp1 U 823 - 601-636, 637-727, 728-741, 742-778, 779-787, 788-823 27.10 /
73.54 		Multiscale: Coarse-grained: 1 - 36 residue(s) per bead
V
AF
AJ
12 Nic96 W 839 20-56 1-19, 57-204, 205-360, 361-365, 366-374, 375-404, 405-444, 445-454, 455-515, 516-532, 533-747, 748-752, 753-835, 836-839 100.00 /
71.63 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
AA
11 Nsp1 X 823 637-727, 742-778, 788-823 601-636, 728-741, 779-787 27.10 /
73.54 		Multiscale: Coarse-grained: 1 - 36 residue(s) per bead
AB
13 Nup49 Y 472 270-359, 369-407, 433-472 201-269, 360-368, 408-432 57.63 /
62.13 		Multiscale: Coarse-grained: 1 - 69 residue(s) per bead
AC
14 Nup57 Z 541 287-423, 433-476, 505-540 201-286, 424-432, 477-504, 541 63.03 /
63.64 		Multiscale: Coarse-grained: 1 - 86 residue(s) per bead
AD
12 Nic96 AE 839 - 1-19, 20-56, 57-204, 205-360, 361-365, 366-374, 375-404, 405-444, 445-454, 455-515, 516-532, 533-747, 748-752, 753-835, 836-839 100.00 /
71.63 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
AI
13 Nup49 AG 472 - 201-269, 270-359, 360-368, 369-407, 408-432, 433-472 57.63 /
62.13 		Multiscale: Coarse-grained: 1 - 69 residue(s) per bead
AK
14 Nup57 AH 541 - 201-286, 287-423, 424-432, 433-476, 477-504, 505-540, 541 63.03 /
63.64 		Multiscale: Coarse-grained: 1 - 86 residue(s) per bead
AL
15 Nup157 AM 1391 - 1-87, 88-289, 290-300, 301-309, 310-338, 339-457, 458-480, 481-515, 516-534, 535-679, 680-703, 704-730, 731-743, 744-775, 776-785, 786-830, 831-835, 836-892, 893-899, 900-916, 917-920, 921-933, 934-943, 944-1016, 1017-1038, 1039-1141, 1142-1154, 1155-1390, 1391 100.00 /
80.01 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
AQ
16 Nup170 AN 1502 - 1-97, 98-299, 300-310, 311-319, 320-352, 353-471, 472-504, 505-537, 538-573, 574-717, 718-764, 765-791, 792-830, 831-862, 863-883, 884-916, 917-918, 919-930, 931-935, 936-992, 993-999, 1000-1016, 1017-1020, 1021-1033, 1034-1043, 1044-1116, 1117-1140, 1141-1191, 1192-1194, 1195-1243, 1244-1256, 1257-1502 100.00 /
74.37 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
AR
17 Nup188 AO 1655 - 1-11, 12-34, 35-39, 40-91, 92-100, 101-123, 124-130, 131-166, 167-173, 174-224, 225-255, 256-282, 283-287, 288-304, 305-317, 318-434, 435-438, 439-479, 480-492, 493-508, 509-514, 515-530, 531-550, 551-577, 578-583, 584-605, 606-607, 608-619, 620-631, 632-785, 786-792, 793-889, 890-891, 892-1100, 1101-1118, 1119-1133, 1134-1156, 1157-1241, 1242-1246, 1247-1265, 1266-1275, 1276-1292, 1293-1302, 1303-1322, 1323-1331, 1332-1354, 1355-1382, 1383-1567, 1568-1592, 1593-1628, 1629-1632, 1633-1652, 1653-1655 100.00 /
82.18 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
AS
18 Nup192 AP 1683 - 1-362, 363-416, 417-574, 575-601, 602-798, 799-813, 814-849, 850-856, 857-953, 954-960, 961-1126, 1127-1136, 1137-1226, 1227-1233, 1234-1258, 1259-1271, 1272-1366, 1367-1370, 1371-1418, 1419-1420, 1421-1502, 1503-1510, 1511-1559, 1560-1583, 1584-1590, 1591-1596, 1597-1619, 1620-1622, 1623-1644, 1645-1650, 1651-1683 100.00 /
88.53 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
AT
19 Nup53 AU 475 - 1-247, 248-284, 285-303, 304-360, 361-475 100.00 /
19.79 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
AZ
20 Nup59 AV 528 - 1-265, 266-302, 303-345, 346-402, 403-528 100.00 /
17.80 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
BA
21 Ndc1 AW 655 - 1-655 100.00 /
0.00 		Multiscale: Coarse-grained: 55 - 100 residue(s) per bead
BB
22 Pom34 AX 299 - 1-299 100.00 /
0.00 		Multiscale: Coarse-grained: 49 - 50 residue(s) per bead
BC
23 Pom152 AY 1337 - 1-378, 379-472, 473-519, 520-611, 612-615, 616-714, 715-721, 722-818, 819-823, 824-918, 919-930, 931-1026, 1027-1035, 1036-1141, 1142-1149, 1150-1229, 1230-1243, 1244-1337 100.00 /
63.80 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
BD
24 Nup100 BE 959 816-958 551-815, 959 42.65 /
34.96 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
BF
25 Nup116 BG 1113 - 751-965, 966-1111, 1112-1113 32.61 /
40.22 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
BH
27 Gle1 BJ 538 - 1-120 22.30 /
0.00 		Multiscale: Coarse-grained: 20 - 50 residue(s) per bead
28 Nup145 BK 1317 459-605 201-458 30.75 /
36.30 		Multiscale: Coarse-grained: 1 - 25 residue(s) per bead
BL
29 Nup1 BM 1076 - 1-351 32.62 /
0.00 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
30 Nup60 BN 539 - 1-398 73.84 /
0.00 		Multiscale: Coarse-grained: 48 - 50 residue(s) per bead
BO
31 Mlp1 BP 1875 - 238-716 25.55 /
0.00 		Multiscale: Coarse-grained: 29 - 50 residue(s) per bead
32 Mlp2 BQ 1679 - 215-690 28.35 /
0.00 		Multiscale: Coarse-grained: 26 - 50 residue(s) per bead

Datasets used for modeling ?

There are 65 unique datasets used to build the models in this entry.
ID Dataset type Database name Data access code
1
Integrative model
Not available
2
Integrative model
Zenodo
3
Experimental model
PDB
4
Comparative model
Zenodo
5
Experimental model
PDB
6
Experimental model
Zenodo
7
Experimental model
Zenodo
8
Comparative model
Zenodo
9
Comparative model
Zenodo
10
Comparative model
Zenodo
11
Comparative model
Zenodo
12
Comparative model
Zenodo
13
Comparative model
Zenodo
14
Integrative model
Not available
15
Integrative model
Zenodo
16
Experimental model
PDB
17
Comparative model
Zenodo
18
Comparative model
Zenodo
19
Experimental model
PDB
20
Experimental model
Zenodo
21
Mass Spectrometry data
Zenodo
22
Crosslinking-MS data
Zenodo
23
Crosslinking-MS data
Zenodo
24
EM raw micrographs
EMPIAR
25
3DEM volume
EMDB
26
3DEM volume
Zenodo
27
SAS data
Zenodo
28
SAS data
Zenodo
29
SAS data
Zenodo
30
SAS data
Zenodo
31
SAS data
Zenodo
32
SAS data
Zenodo
33
SAS data
Zenodo
34
SAS data
Zenodo
35
SAS data
Zenodo
36
SAS data
Zenodo
37
SAS data
Zenodo
38
SAS data
Zenodo
39
SAS data
Zenodo
40
SAS data
Zenodo
41
SAS data
Zenodo
42
SAS data
Zenodo
43
SAS data
Zenodo
44
SAS data
Zenodo
45
SAS data
Zenodo
46
SAS data
Zenodo
47
SAS data
Zenodo
48
SAS data
SASBDB
49
SAS data
SASBDB
50
SAS data
SASBDB
51
SAS data
SASBDB
52
SAS data
SASBDB
53
SAS data
Zenodo
54
SAS data
Zenodo
55
SAS data
Zenodo
56
SAS data
Zenodo
57
SAS data
Zenodo
58
SAS data
Zenodo
59
SAS data
Zenodo
60
SAS data
Zenodo
61
SAS data
Zenodo
62
SAS data
Zenodo
63
EM raw micrographs
EMPIAR
64
2DEM class average
Zenodo
65
2DEM class average
Zenodo

Methodology and software?

This entry is a result of 1 distinct protocol.
Step number Protocol ID Method name Method type Method description Number of computed models Multi state modeling Multi scale modeling
1
1
Sampling
Replica exchange monte carlo
None
500
False
True
2
1
Sampling
Replica exchange monte carlo
None
3000
False
True
3
1
Sampling
Replica exchange monte carlo
None
1000
False
True
There are 13 software packages reported in this entry.
ID Software name Software version Software classification Software location
1
develop-0a5706e202
integrative model building
2
67456c0
integrative model building
3
2.0.16
protein homology detection
4
4.00
secondary structure prediction
5
3
disorder prediction
6
Not available
domain boundary prediction
7
Not available
coiled-coil prediction
8
2.20
image processing
9
1.40
image processing
10
SGD
Not available
database
11
Not available
helix prediction
12
9.15
comparative modeling
13
9.13
comparative modeling