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PDB-IHM

System for Archiving Integrative Structures

Ensemble information?

This entry consists of 1 distinct ensemble.

Summary?

This entry consists of 22 model(s). A total of 11 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 1-22 1 Unknown MLP Protein A 1875 71-183, 197-221, 239-281, 285-324, 340-371, 435-463, 535-570, 575-617, 622-668, 689-717, 745-773, 791-840, 844-893, 930-986, 990-1088, 1092-1127, 1143-1199, 1212-1251, 1254-1286, 1290-1339, 1343-1385, 1408-1457 1-70, 184-196, 222-238, 282-284, 325-339, 372-434, 464-534, 571-574, 618-621, 669-688, 718-744, 774-790, 841-843, 894-929, 987-989, 1089-1091, 1128-1142, 1200-1211, 1252-1253, 1287-1289, 1340-1342, 1386-1407, 1458-1875 100.00 /
54.99 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
B
2 Nucleoporin NUP1 C 1076 1-32, 85-104, 106-123 33-84, 105, 124-335 31.13 /
20.90 		Multiscale: Coarse-grained: 1 - 30 residue(s) per bead
3 Nucleoporin NUP2 D 720 83-136, 602-720 51-82 28.47 /
84.39 		Multiscale: Coarse-grained: 1 - 30 residue(s) per bead
E
4 Nucleoporin NUP60 F 539 27-47, 91-104, 106-119, 121-140, 142-162 1-26, 48-90, 105, 120, 141, 163-398, 505-539 80.33 /
20.79 		Multiscale: Coarse-grained: 1 - 30 residue(s) per bead
G
5 Nucleoporin NUP120 H 1037 1-29, 53-305, 311-711, 714-1036 30-52, 306-310, 712-713, 1037 100.00 /
97.01 		Multiscale: Coarse-grained: 1 - 23 residue(s) per bead
I
6 Nucleoporin NUP85 J 744 47-126, 132-230, 235-436, 451-744 1-46, 127-131, 231-234, 437-450 100.00 /
90.73 		Multiscale: Coarse-grained: 1 - 46 residue(s) per bead
6 Nucleoporin NUP85 K 744 47-126, 132-230, 235-436, 451-739 1-46, 127-131, 231-234, 437-450, 740-744 100.00 /
90.05 		Multiscale: Coarse-grained: 1 - 46 residue(s) per bead
L
7 Nucleoporin NUP145C M 712 119-712 1-118 100.00 /
83.43 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
N
8 Protein transport protein SEC13 O 297 8-157, 170-293 1-7, 158-169, 294-297 100.00 /
92.26 		Multiscale: Coarse-grained: 1 - 12 residue(s) per bead
P
9 Nucleoporin SEH1 Q 349 1-248, 288-346 249-287, 347-349 100.00 /
87.97 		Multiscale: Coarse-grained: 1 - 39 residue(s) per bead
R
10 Nucleoporin NUP84 S 726 7-20, 27-80, 96-126, 136-364, 372-483, 506-562, 575-726 1-6, 21-26, 81-95, 127-135, 365-371, 484-505, 563-574 100.00 /
89.39 		Multiscale: Coarse-grained: 1 - 22 residue(s) per bead
T
11 Nucleoporin NUP133 U 1157 63-183, 198-480, 490-763, 772-1155 1-62, 184-197, 481-489, 764-771, 1156-1157 100.00 /
91.79 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead
11 Nucleoporin NUP133 V 1157 56-77, 86-125, 133-144, 162-184, 193-200, 206-249, 258-480, 490-763, 772-1155 1-55, 78-85, 126-132, 145-161, 185-192, 201-205, 250-257, 481-489, 764-771, 1156-1157 100.00 /
89.02 		Multiscale: Coarse-grained: 1 - 50 residue(s) per bead

Datasets used for modeling ?

There are 11 unique datasets used to build the models in this entry.
ID Dataset type Database name Data access code
11
3DEM volume
Zenodo
7
Crosslinking-MS data
Zenodo
8
Crosslinking-MS data
Zenodo
1
De Novo model
Zenodo
2
De Novo model
Zenodo
3
De Novo model
Zenodo
4
De Novo model
Zenodo
6
Experimental model
Zenodo
10
3DEM volume
Zenodo
5
Experimental model
PDB
9
3DEM volume
EMDB

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
1000
False
True
2
1
Sampling
Replica exchange monte carlo
None
15467933
False
True
There are 3 software packages reported in this entry.
ID Software name Software version Software classification Software location
1
2.19.0
integrative model building
3
1.0.0
Coiled-coil model building
2
2.19.0
integrative model building