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6M6B:
Cryo-EM structure of Thermus thermophilus Mfd in complex with RNA polymerase and ATP-gamma-S
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PDB ID:
6M6B
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MMDB ID:
194096
PDB Deposition Date:
2020/3/14
Updated in MMDB:
2020/10
Experimental Method:
electron microscopy
Resolution:
4.1 Å
Source Organism:
Thermus thermophilus HB8
▼
Taxonomy
Molecule
Thermus thermophilus HB8
A, B, C, D, E
Thermus thermophilus HB27
M
Thermus thermophilus
T, N
Similar Structures:
VAST+
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Biological Unit
Asymmetric Unit
Biological Unit for 6M6B: octameric; determined by author
Molecular Graphic
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3D view
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Interactions
?
A
A: DNA-directed RNA polymerase subunit alpha
B
B: DNA-directed RNA polymerase subunit alpha
C
C: DNA-directed RNA polymerase subunit beta
D
D: DNA-directed RNA polymerase subunit beta'
E
E: DNA-directed RNA polymerase subunit omega
M
M: Transcription-repair-coupling factor
T
T: template strand DNA
N
N: nontemplate strand DNA
1
ZN: ZINC ION
1
ZN: ZINC ION
2
MG: MAGNESIUM ION
3
AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
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Protein
Nucleotide
Chemical
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Format:
ASN.1 (Cn3D)
PDB
XML
JSON
PNG (image)
Data Set:
alpha-Carbons
Single 3D structure
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Molecular Components in 6M6B
Label
Count
Molecule
Proteins (6 molecules)
A
B
2
DNA-directed RNA Polymerase Subunit Alpha
2 Proteins
SS Diagram
3D Domains
1
250
315
315 residues, click to see VAST similar structures.
helix 33-45
helix 76-84
helix 207-223
strand 10-17
strand 19-26
strand 27-30
strand 49-59
strand 86-90
strand 95-103
strand 104-111
strand 119-123
strand 127-134
strand 136-144
strand 145-148
strand 149-153
strand 164-172
strand 173-181
strand 182-185
strand 191-202
Domain 1 (1-47): click to see VAST similar structures
1
Domain 2 (48-172): click to see VAST similar structures
2
Domain 1 (173-315): click to see VAST similar structures
1
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C
1
DNA-directed RNA Polymerase Subunit Beta
1 Protein
SS Diagram
3D Domains
1
250
500
750
1000
1119
1119 residues, click to see VAST similar structures.
helix 21-30
helix 44-51
helix 79-87
helix 193-201
helix 203-211
helix 215-222
helix 231-242
helix 250-260
helix 271-281
helix 304-315
helix 336-359
helix 377-387
helix 400-408
helix 555-564
helix 583-590
helix 769-778
helix 884-897
helix 912-930
helix 938-950
helix 959-969
helix 1034-1043
helix 1046-1053
helix 1060-1072
helix 1083-1095
strand 2-6
strand 66-70
strand 71-76
strand 90-104
strand 105-120
strand 126-130
strand 131-142
strand 144-150
strand 158-164
strand 171-178
strand 180-187
strand 188-192
strand 290-295
strand 296-301
strand 331-335
strand 391-394
strand 409-412
strand 451-455
strand 459-463
strand 465-476
strand 477-480
strand 483-487
strand 495-498
strand 502-505
strand 507-510
strand 512-517
strand 520-525
strand 530-533
strand 578-581
strand 594-597
strand 598-602
strand 603-608
strand 609-616
strand 618-625
strand 627-632
strand 633-642
strand 647-651
strand 653-659
strand 660-663
strand 664-667
strand 669-677
strand 686-692
strand 700-716
strand 717-723
strand 747-750
strand 751-756
strand 757-762
strand 784-793
strand 796-800
strand 801-808
strand 820-833
strand 837-842
strand 844-854
strand 857-862
strand 864-867
strand 868-872
strand 899-903
strand 974-978
strand 988-997
Domain 1 (1-13): click to see VAST similar structures
1
Domain 2 (14-143): click to see VAST similar structures
2
Domain 3 (144-323): click to see VAST similar structures
3
Domain 2 (324-457): click to see VAST similar structures
2
Domain 4 (458-544): click to see VAST similar structures
4
Domain 1 (545-592): click to see VAST similar structures
1
Domain 5 (593-659): click to see VAST similar structures
5
Domain 1 (660-696): click to see VAST similar structures
1
Domain 6 (697-835): click to see VAST similar structures
6
Domain 1 (836-1015): click to see VAST similar structures
1
Domain 7 (1016-1077): click to see VAST similar structures
7
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D
1
DNA-directed RNA Polymerase Subunit Beta'
1 Protein
SS Diagram
3D Domains
1
250
500
750
1000
1250
1524
1524 residues, click to see VAST similar structures.
helix 14-22
helix 110-117
helix 120-128
helix 155-162
helix 458-466
helix 471-482
helix 486-505
helix 540-560
helix 565-582
helix 646-654
helix 655-663
helix 670-677
helix 686-695
helix 753-761
helix 783-793
helix 810-818
helix 846-855
helix 877-890
helix 893-900
helix 908-921
helix 925-944
helix 960-980
helix 985-1014
helix 1019-1026
helix 1031-1039
helix 1067-1089
helix 1090-1102
helix 1137-1144
helix 1168-1180
helix 1222-1230
helix 1256-1264
helix 1332-1339
helix 1342-1359
helix 1366-1376
helix 1398-1410
helix 1423-1430
helix 1433-1440
helix 1444-1452
helix 1462-1469
helix 1490-1500
strand 7-11
strand 23-26
strand 32-35
strand 36-39
strand 55-58
strand 71-75
strand 76-82
strand 89-95
strand 98-101
strand 131-136
strand 140-143
strand 144-147
strand 149-154
strand 166-171
strand 182-186
strand 187-192
strand 194-198
strand 199-202
strand 391-396
strand 397-403
strand 413-417
strand 418-422
strand 426-431
strand 432-440
strand 441-449
strand 452-456
strand 512-515
strand 516-521
strand 525-531
strand 533-538
strand 625-633
strand 640-645
strand 699-704
strand 712-717
strand 718-721
strand 725-728
strand 744-749
strand 769-772
strand 774-777
strand 802-807
strand 826-830
strand 831-835
strand 841-845
strand 862-869
strand 870-876
strand 1106-1109
strand 1117-1122
strand 1123-1127
strand 1130-1134
strand 1147-1150
strand 1151-1156
strand 1157-1162
strand 1163-1166
strand 1184-1189
strand 1199-1202
strand 1272-1275
strand 1277-1287
strand 1288-1297
strand 1298-1306
strand 1316-1321
strand 1323-1326
strand 1377-1383
strand 1392-1397
strand 1415-1420
strand 1454-1458
Domain 1 (1-12): click to see VAST similar structures
1
Domain 2 (13-29): click to see VAST similar structures
2
Domain 3 (48-85): click to see VAST similar structures
3
Domain 2 (86-105): click to see VAST similar structures
2
Domain 4 (106-164): click to see VAST similar structures
4
Domain 5 (165-396): click to see VAST similar structures
5
Domain 6 (397-450): click to see VAST similar structures
6
Domain 4 (451-468): click to see VAST similar structures
4
Domain 1 (469-508): click to see VAST similar structures
1
Domain 2 (509-523): click to see VAST similar structures
2
Domain 7 (524-603): click to see VAST similar structures
7
Domain 8 (604-765): click to see VAST similar structures
8
Domain 9 (766-797): click to see VAST similar structures
9
Domain 10 (798-838): click to see VAST similar structures
10
Domain 9 (839-952): click to see VAST similar structures
9
Domain 11 (953-1053): click to see VAST similar structures
11
Domain 12 (1090-1104): click to see VAST similar structures
12
Domain 13 (1114-1194): click to see VAST similar structures
13
Domain 12 (1213-1268): click to see VAST similar structures
12
Domain 14 (1269-1329): click to see VAST similar structures
14
Domain 12 (1330-1376): click to see VAST similar structures
12
Domain 15 (1377-1421): click to see VAST similar structures
15
Domain 12 (1422-1431): click to see VAST similar structures
12
Domain 1 (1432-1479): click to see VAST similar structures
1
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E
1
DNA-directed RNA Polymerase Subunit Omega
1 Protein
SS Diagram
3D Domains
1
99
99 residues, click to see VAST similar structures.
helix 5-13
helix 16-33
helix 61-70
helix 83-92
strand 46-51
strand 52-57
Domain 1 (1-76): click to see VAST similar structures
1
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M
1
Transcription-repair-coupling Factor
1 Protein
SS Diagram
3D Domains
1
250
500
750
978
978 residues, click to see VAST similar structures.
helix 408-419
helix 445-459
helix 478-490
helix 501-515
helix 531-542
helix 578-588
helix 637-650
helix 665-674
helix 689-701
helix 735-743
helix 764-774
helix 782-795
helix 814-824
strand 322-328
strand 330-335
strand 336-340
strand 349-356
strand 357-363
strand 371-374
strand 463-470
strand 493-499
strand 521-526
strand 547-552
strand 566-572
strand 591-596
strand 613-618
strand 628-634
strand 653-658
strand 679-683
strand 705-710
strand 723-728
strand 752-758
Domain 1 (1-391): click to see VAST similar structures
1
Domain 2 (433-623): click to see VAST similar structures
2
Domain 3 (624-804): click to see VAST similar structures
3
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Nucleotides(2 molecules)
T
1
Template Strand DNA
1 Nucleotide
1
10
20
30
40
50
60
63
N
1
Nontemplate Strand DNA
1 Nucleotide
1
10
20
30
40
50
60
63
Chemicals and Non-standard biopolymers (4 molecules)
1
2
ZINC ION
2
1
MAGNESIUM ION
3
1
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
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Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.
"
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
Nucleic Acids Res. 2014 Jan; 42(Database issue)
:D297-303
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