General information
PDB ID 6TDA
Title STRUCTURE OF SWI/SNF CHROMATIN REMODELER RSC BOUND TO A NUCLEOSOME
PDB header DNA BINDING PROTEIN
Date 2019-11-08
Experimental method ELECTRON MICROSCOPY
Resolution (A) 15
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC CONSTRUCT, SACCHAROMYCES CEREVISIAE S288C
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6tda.pdb ABCDEFGHKLMNOPQRSTUVX IJ 0
Biounits:
6tda.pdb1.pdb ABCDEFGHKLMNOPQRSTUVX IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P84233_37-132 2.4e-45 1 CL0012 A 39 131 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62799_18-99 5.1e-08 1 CL0012 B 19 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain P06897_19-91 9.2e-16 1 CL0012 C 15 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 2.9e-21 1 CL0012 D 30 98 JI  H-Bb S-Bb L-Bb 
Histone Domain P84233_37-132 8.2e-45 1 CL0012 E 40 131 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P62799_26-99 4.7e-08 1 CL0012 F 25 98 IJ  H-Bb H-Mj S-Bb L-Bb 
Histone Domain P06897_19-91 9.2e-16 1 CL0012 G 15 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 2.9e-21 1 CL0012 H 30 98 IJ  H-Bb S-Bb L-Bb 
SWIRM Domain P43609_83-168 9.7e-29 1 CL0123 L 83 168   
SWIRM Domain P43609_83-168 9.7e-29 1 CL0123 L 1083 1168   
ZZ Domain P43609_254-298 1.8e-16 1 CL0006 L 195 298   
Myb_DNA-binding Domain P43609_312-358 3.3e-09 1 CL0123 L 1312 1358   
Myb_DNA-binding Domain P43609_312-358 5.6e-09 1 CL0123 L 305 358   
SWIB Domain P25632_60-130 6.9e-06 1 No_clan O 230 343   
Bromodomain Domain Q07979_29-122 8.9e-06 1 No_clan P 35 122   
SNF2-rel_dom Domain P32597_473-769 8.7e-75 1 CL0023 S 473 769 I  H-Bb 
Helicase_C Domain P32597_791-905 1.6e-20 1 CL0023 S 791 905 J  L-Bb L-Mj 
HSA Domain P32597_322-369 0.00011 1 CL0023 S 296 405   
Histone_H2A_C Family P06897_92-120 2.5e-15 1 No_clan C 91 116   
Histone_H2A_C Family P06897_92-120 2.5e-15 1 No_clan G 91 116   
SNF5 Family Q06168_271-400 1.9e-24 1 No_clan K 271 400   
SNF5 Family Q06168_198-278 7.1e-19 1 No_clan K 198 276   
SWIRM-assoc_1 Family P43609_406-486 7.9e-08 1 No_clan L 406 487   
SWIRM-assoc_1 Family P43609_530-596 9.5e-07 1 No_clan L 1370 1487   
Actin Family Q12406_2-466 2.8e-45 1 CL0108 T 2 464   
Actin Family Q05123_18-375 6.9e-13 1 CL0108 U 18 288   
Rtt102p Family P53330_5-90 3.6e-06 1 No_clan V 33 90   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=2-136 C nucleoplasm
A/E=2-136 C nucleosome
A/E=2-136 F DNA binding
A/E=2-136 F protein heterodimerization activity
B/F=2-103 C host cell nucleus
B/F=2-103 C nucleosome
B/F=2-103 C nucleus
B/F=2-103 F DNA binding
B/F=2-103 F protein heterodimerization activity
B/F=2-103 P DNA-templated transcription, initiation
D/H=5-126 C nucleosome
D/H=5-126 C nucleus
D/H=5-126 F DNA binding
D/H=5-126 F protein heterodimerization activity
K=1-426 C nucleus
K=1-426 C RSC-type complex
K=1-426 C SWI/SNF complex
K=1-426 P ATP-dependent chromatin remodeling
K=1-426 P chromatin remodeling at centromere
K=1-426 P chromosome segregation
K=1-426 P DNA repair
K=1-426 P double-strand break repair
K=1-426 P G2/M transition of mitotic cell cycle
K=1-426 P nucleosome disassembly
K=1-426 P regulation of nuclear cell cycle DNA replication
K=1-426 P regulation of transcription by RNA polymerase II
K=1-426 P transcription elongation from RNA polymerase II promoter
L=1-557 C nucleus
L=1-557 C RSC-type complex
L=1-557 C SWI/SNF complex
L=1-557 F DNA binding
L=1-557 F histone binding
L=1-557 F zinc ion binding
L=1-557 P ATP-dependent chromatin remodeling
L=1-557 P double-strand break repair via nonhomologous end joining
L=1-557 P nucleosome disassembly
L=1-557 P positive regulation of transcription, DNA-templated
L=1-557 P regulation of transcription, DNA-templated
L=1-557 P transcription elongation from RNA polymerase II promoter
M=1-435 C nucleus
M=1-435 C RSC-type complex
M=1-435 P ATP-dependent chromatin remodeling
M=1-435 P nucleosome disassembly
M=1-435 P transcription elongation from RNA polymerase II promoter
N=1-581 C nucleus
N=1-581 C RSC-type complex
N=1-581 C SWI/SNF complex
N=1-581 F transcription regulatory region sequence-specific DNA binding
N=1-581 P ATP-dependent chromatin remodeling
N=1-581 P cellular response to hydrogen peroxide
N=1-581 P nucleosome disassembly
N=1-581 P regulation of transcription by RNA polymerase II
N=1-581 P regulation of transcription, DNA-templated
N=1-581 P rRNA processing
N=1-581 P rRNA transcription
N=1-581 P transcription elongation from RNA polymerase II promoter
N=1-581 P transfer RNA gene-mediated silencing
O=1-483 C RSC-type complex
O=1-483 P ATP-dependent chromatin remodeling
O=1-483 P nucleosome disassembly
O=1-483 P nucleosome positioning
O=1-483 P positive regulation of transcription elongation from RNA polymerase II promoter
P=1-502 C nucleus
P=1-502 C RSC-type complex
P=1-502 F sequence-specific DNA binding
P=1-502 P ATP-dependent chromatin remodeling
P=1-502 P chromatin remodeling
P=1-502 P nucleosome disassembly
P=1-502 P regulation of transcription by RNA polymerase II
P=1-502 P transcription elongation from RNA polymerase II promoter
Q=1-78 C nucleus
Q=1-78 C RSC-type complex
Q=1-78 P chromatin remodeling
Q=1-78 P G2/M transition of mitotic cell cycle
Q=1-78 P nucleosome disassembly
Q=1-78 P transcription elongation from RNA polymerase II promoter
R=1-625 C RSC-type complex
R=1-625 F chromatin binding
R=1-625 F lysine-acetylated histone binding
R=1-625 P ATP-dependent chromatin remodeling
R=1-625 P nucleosome disassembly
R=1-625 P transcription elongation from RNA polymerase II promoter
S=1-1359 C chromosome, centromeric region
S=1-1359 C nucleus
S=1-1359 C RSC-type complex
S=1-1359 F ATP binding
S=1-1359 F ATPase activity
S=1-1359 F DNA binding
S=1-1359 F DNA helicase activity
S=1-1359 F DNA translocase activity
S=1-1359 F DNA-dependent ATPase activity
S=1-1359 F helicase activity
S=1-1359 F lysine-acetylated histone binding
S=1-1359 P ATP-dependent chromatin remodeling
S=1-1359 P base-excision repair
S=1-1359 P chromatin remodeling at centromere
S=1-1359 P chromosome segregation
S=1-1359 P cytoskeleton organization
S=1-1359 P double-strand break repair
S=1-1359 P meiotic cell cycle
S=1-1359 P nucleosome disassembly
S=1-1359 P nucleosome positioning
S=1-1359 P positive regulation of transcription by RNA polymerase II
S=1-1359 P regulation of transcription, DNA-templated
S=1-1359 P transcription elongation from RNA polymerase II promoter
S=1-1359 P transfer RNA gene-mediated silencing
T=1-477 C NuA4 histone acetyltransferase complex
T=1-477 C nucleus
T=1-477 C RSC-type complex
T=1-477 C SWI/SNF complex
T=1-477 F chromatin binding
T=1-477 F structural molecule activity
T=1-477 P ATP-dependent chromatin remodeling
T=1-477 P chromatin organization
T=1-477 P histone H4 acetylation
T=1-477 P nucleosome disassembly
T=1-477 P nucleosome mobilization
T=1-477 P positive regulation of transcription by RNA polymerase II
T=1-477 P regulation of transcription by RNA polymerase II
T=1-477 P regulation of transcription, DNA-templated
T=1-477 P transcription elongation from RNA polymerase II promoter
U=1-467 C nucleus
U=1-467 C RSC-type complex
U=1-467 C SWI/SNF complex
U=1-467 F structural molecule activity
U=1-467 P ATP-dependent chromatin remodeling
U=1-467 P chromatin organization
U=1-467 P nucleosome disassembly
U=1-467 P nucleosome mobilization
U=1-467 P nucleosome positioning
U=1-467 P positive regulation of transcription by RNA polymerase II
U=1-467 P regulation of transcription by RNA polymerase II
U=1-467 P regulation of transcription, DNA-templated
U=1-467 P transcription elongation from RNA polymerase II promoter
V=1-157 C nucleus
V=1-157 C RSC-type complex
V=1-157 C SWI/SNF complex
V=1-157 P chromatin remodeling
V=1-157 P chromosome segregation
V=1-157 P nucleosome disassembly
V=1-157 P transcription elongation from RNA polymerase II promoter
Sequences
Download file with secondary structure created by Stride  
6tda.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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N (protein): 
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O (protein): 
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P (protein): 
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Q (protein): 
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R (protein): 
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S (protein): 
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T (protein): 
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U (protein): 
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V (protein): 
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X (protein): 
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