General information
PDB ID 6LTJ
Title STRUCTURE OF NUCLEOSOME-BOUND HUMAN BAF COMPLEX
PDB header GENE REGULATION
Date 2020-01-22
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.7
Kind dna
Organism XENOPUS LAEVIS, HOMO SAPIENS
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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:
pdb6ltj.pdb ABCDEFGHIJKLMNOPQR XY 0
Biounits:
6ltj.pdb1.pdb ABCDEFGHIJKLMNOPQR XY 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain Q6PI79_45-132 1.6e-42 1 CL0012 A 41 128 X  H-Bb 
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 B 26 98 Y  H-Bb 
Histone Domain P06897_19-91 9e-16 1 CL0012 C 16 90   
Histone Domain P02281_41-102 1.4e-19 1 CL0012 D 33 98 XY  H-Bb 
Histone Domain Q6PI79_45-132 1.6e-42 1 CL0012 E 44 131 Y  H-Bb H-Mj 
CENP-T_C Domain P62799_26-99 4.1e-08 1 CL0012 F 26 98 X  H-Bb 
Histone Domain P06897_19-91 7.3e-16 1 CL0012 G 15 90   
Histone Domain P02281_33-102 5.1e-20 1 CL0012 H 31 98 Y  H-Bb 
SNF2-rel_dom Domain P51532_757-1052 1.7e-49 1 CL0023 I 757 979   
HSA Domain P51532_461-517 3.3e-16 1 CL0023 I 461 761   
Helicase_C Domain P51532_1080-1194 2e-09 1 CL0023 I 1111 1194   
SWIRM Domain Q8TAQ2_427-512 2.3e-33 1 CL0123 N 427 512   
Myb_DNA-binding Domain Q8TAQ2_598-643 2e-10 1 CL0123 N 602 672   
SWIRM Domain Q8TAQ2_427-512 3.5e-33 1 CL0123 O 427 512   
Myb_DNA-binding Domain Q8TAQ2_598-643 4.5e-13 1 CL0123 O 598 643   
SWIB Domain Q96GM5_293-365 6.1e-25 1 No_clan P 293 365   
Histone_H2A_C Family P06897_92-110 9.8e-12 1 No_clan C 91 110   
Histone_H2A_C Family P06897_92-110 9.4e-11 1 No_clan G 91 109   
Actin Family O96019_12-417 4e-116 1 CL0108 J 12 417   
Actin Family P60709_2-372 4.9e-116 1 CL0108 K 30 372   
SNF5 Family Q12824_161-276 7.1e-29 1 No_clan M 246 373   
SNF5 Family Q12824_94-166 1.6e-24 1 No_clan M 179 258   
SWIRM-assoc_1 Family Q8TAQ2_867-946 9.7e-31 1 No_clan N 863 946   
SWIRM-assoc_3 Family Q8TAQ2_684-703 1.2e-05 0 No_clan N 684 893   
SWIRM-assoc_1 Family Q8TAQ2_867-946 9.9e-29 1 No_clan O 717 946   
SWIRM-assoc_3 Family Q8TAQ2_684-717 3.3e-16 1 No_clan O 684 882   
GCN5L1 Family Q969G3_19-105 0.00027 0 No_clan Q 189 275   
Requiem_N Family Q92785_13-82 6e-38 1 No_clan R 13 82   
BAF250_C Repeat O14497_1976-2231 8e-100 1 CL0020 L 1976 2239   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=1-136 C nucleosome
A/E=1-136 C nucleus
A/E=1-136 F DNA binding
A/E=1-136 F protein heterodimerization activity
B/F=1-103 C host cell nucleus
B/F=1-103 C nucleosome
B/F=1-103 C nucleus
B/F=1-103 F DNA binding
B/F=1-103 F protein heterodimerization activity
B/F=1-103 P DNA-templated transcription, initiation
C/G=1-130 C nucleosome
C/G=1-130 C nucleus
C/G=1-130 F DNA binding
C/G=1-130 F protein heterodimerization activity
I=1-1647 C extracellular space
I=1-1647 C membrane
I=1-1647 C nBAF complex
I=1-1647 C npBAF complex
I=1-1647 C nuclear chromatin
I=1-1647 C nucleolus
I=1-1647 C nucleoplasm
I=1-1647 C nucleus
I=1-1647 C protein-containing complex
I=1-1647 C SWI/SNF complex
I=1-1647 F androgen receptor binding
I=1-1647 F ATP binding
I=1-1647 F DNA binding
I=1-1647 F DNA polymerase binding
I=1-1647 F DNA-dependent ATPase activity
I=1-1647 F helicase activity
I=1-1647 F lysine-acetylated histone binding
I=1-1647 F p53 binding
I=1-1647 F protein N-terminus binding
I=1-1647 F RNA binding
I=1-1647 F RNA polymerase I core promoter sequence-specific DNA binding
I=1-1647 F Tat protein binding
I=1-1647 F transcription coactivator activity
I=1-1647 F transcription corepressor activity
I=1-1647 F transcription factor binding
I=1-1647 P ATP-dependent chromatin remodeling
I=1-1647 P beta-catenin-TCF complex assembly
I=1-1647 P chromatin organization
I=1-1647 P chromatin remodeling
I=1-1647 P interleukin-7-mediated signaling pathway
I=1-1647 P negative regulation of androgen receptor signaling pathway
I=1-1647 P negative regulation of cell growth
I=1-1647 P negative regulation of transcription by RNA polymerase II
I=1-1647 P negative regulation of transcription, DNA-templated
I=1-1647 P nervous system development
I=1-1647 P neural retina development
I=1-1647 P nucleosome disassembly
I=1-1647 P positive regulation by host of viral transcription
I=1-1647 P positive regulation of DNA-binding transcription factor activity
I=1-1647 P positive regulation of glucose mediated signaling pathway
I=1-1647 P positive regulation of pri-miRNA transcription by RNA polymerase II
I=1-1647 P positive regulation of transcription by RNA polymerase II
I=1-1647 P positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
I=1-1647 P positive regulation of transcription, DNA-templated
I=1-1647 P positive regulation of Wnt signaling pathway
I=1-1647 P regulation of transcription by RNA polymerase II
J=12-417 C Ino80 complex
J=12-417 C npBAF complex
J=12-417 C NuA4 histone acetyltransferase complex
J=12-417 C nuclear chromatin
J=12-417 C nucleoplasm
J=12-417 C nucleus
J=12-417 C plasma membrane
J=12-417 C protein-containing complex
J=12-417 C SWI/SNF complex
J=12-417 F chromatin binding
J=12-417 F transcription coactivator activity
J=12-417 P ATP-dependent chromatin remodeling
J=12-417 P blastocyst formation
J=12-417 P chromatin remodeling
J=12-417 P DNA recombination
J=12-417 P DNA repair
J=12-417 P histone H2A acetylation
J=12-417 P histone H4 acetylation
J=12-417 P nervous system development
J=12-417 P neural retina development
J=12-417 P protein deubiquitination
J=12-417 P regulation of growth
J=12-417 P regulation of transcription by RNA polymerase II
J=12-417 P signal transduction
J=12-417 P spinal cord development
K=1-375 C actin cytoskeleton
K=1-375 C actin filament
K=1-375 C adherens junction
K=1-375 C apical junction complex
K=1-375 C axon
K=1-375 C blood microparticle
K=1-375 C cell-cell junction
K=1-375 C cytoplasm
K=1-375 C cytoplasmic ribonucleoprotein granule
K=1-375 C cytoskeleton
K=1-375 C cytosol
K=1-375 C dense body
K=1-375 C extracellular exosome
K=1-375 C extracellular space
K=1-375 C focal adhesion
K=1-375 C glutamatergic synapse
K=1-375 C lamellipodium
K=1-375 C membrane
K=1-375 C NuA4 histone acetyltransferase complex
K=1-375 C nuclear chromatin
K=1-375 C nucleoplasm
K=1-375 C nucleus
K=1-375 C plasma membrane
K=1-375 C presynapse
K=1-375 C protein-containing complex
K=1-375 C ribonucleoprotein complex
K=1-375 C synapse
K=1-375 C tight junction
K=1-375 C vesicle
K=1-375 F ATP binding
K=1-375 F identical protein binding
K=1-375 F kinesin binding
K=1-375 F nitric-oxide synthase binding
K=1-375 F protein kinase binding
K=1-375 F structural constituent of cytoskeleton
K=1-375 F structural constituent of postsynaptic actin cytoskeleton
K=1-375 F Tat protein binding
K=1-375 F tau protein binding
K=1-375 P adherens junction assembly
K=1-375 P apical protein localization
K=1-375 P ATP-dependent chromatin remodeling
K=1-375 P axonogenesis
K=1-375 P cell junction assembly
K=1-375 P cell motility
K=1-375 P cellular response to cytochalasin B
K=1-375 P ephrin receptor signaling pathway
K=1-375 P establishment or maintenance of cell polarity
K=1-375 P Fc-gamma receptor signaling pathway involved in phagocytosis
K=1-375 P maintenance of blood-brain barrier
K=1-375 P membrane organization
K=1-375 P morphogenesis of a polarized epithelium
K=1-375 P negative regulation of protein binding
K=1-375 P platelet aggregation
K=1-375 P positive regulation of gene expression, epigenetic
K=1-375 P positive regulation of norepinephrine uptake
K=1-375 P postsynaptic actin cytoskeleton organization
K=1-375 P protein deubiquitination
K=1-375 P protein localization to adherens junction
K=1-375 P regulation of cyclin-dependent protein serine/threonine kinase activity
K=1-375 P regulation of norepinephrine uptake
K=1-375 P regulation of protein localization to plasma membrane
K=1-375 P regulation of transepithelial transport
K=1-375 P regulation of transmembrane transporter activity
K=1-375 P retina homeostasis
K=1-375 P substantia nigra development
L=991-2285 C brahma complex
L=991-2285 C nBAF complex
L=991-2285 C npBAF complex
L=991-2285 C nuclear chromatin
L=991-2285 C nucleoplasm
L=991-2285 C nucleus
L=991-2285 C SWI/SNF complex
L=991-2285 F DNA binding
L=991-2285 F nuclear receptor binding
L=991-2285 F nucleosome binding
L=991-2285 F transcription coactivator activity
L=991-2285 P androgen receptor signaling pathway
L=991-2285 P ATP-dependent chromatin remodeling
L=991-2285 P cardiac chamber development
L=991-2285 P cardiac muscle cell differentiation
L=991-2285 P chromatin remodeling
L=991-2285 P chromatin-mediated maintenance of transcription
L=991-2285 P embryo implantation
L=991-2285 P forebrain development
L=991-2285 P formation of primary germ layer
L=991-2285 P glucocorticoid receptor signaling pathway
L=991-2285 P heterochromatin maintenance
L=991-2285 P intracellular estrogen receptor signaling pathway
L=991-2285 P negative regulation of transcription by RNA polymerase II
L=991-2285 P neural tube closure
L=991-2285 P nucleosome disassembly
L=991-2285 P nucleosome mobilization
L=991-2285 P optic cup formation involved in camera-type eye development
L=991-2285 P placenta blood vessel development
L=991-2285 P positive regulation of transcription, DNA-templated
L=991-2285 P regulation of transcription by RNA polymerase II
L=991-2285 P stem cell population maintenance
L=991-2285 P toxin transport
M=1-113, M=172-385 C brahma complex
M=1-113, M=172-385 C fibrillar center
M=1-113, M=172-385 C intracellular membrane-bounded organelle
M=1-113, M=172-385 C nBAF complex
M=1-113, M=172-385 C npBAF complex
M=1-113, M=172-385 C nuclear chromatin
M=1-113, M=172-385 C nucleolus
M=1-113, M=172-385 C nucleoplasm
M=1-113, M=172-385 C nucleus
M=1-113, M=172-385 C protein-containing complex
M=1-113, M=172-385 C SWI/SNF complex
M=1-113, M=172-385 F DNA binding
M=1-113, M=172-385 F p53 binding
M=1-113, M=172-385 F RNA polymerase I core promoter sequence-specific DNA binding
M=1-113, M=172-385 F Tat protein binding
M=1-113, M=172-385 F transcription coactivator activity
M=1-113, M=172-385 P ATP-dependent chromatin remodeling
M=1-113, M=172-385 P cell cycle
M=1-113, M=172-385 P chromatin remodeling
M=1-113, M=172-385 P DNA integration
M=1-113, M=172-385 P DNA repair
M=1-113, M=172-385 P negative regulation of histone H3-K9 dimethylation
M=1-113, M=172-385 P negative regulation of histone H3-K9 trimethylation
M=1-113, M=172-385 P nervous system development
M=1-113, M=172-385 P nucleosome disassembly
M=1-113, M=172-385 P positive regulation by host of viral transcription
M=1-113, M=172-385 P positive regulation of DNA-binding transcription factor activity
M=1-113, M=172-385 P positive regulation of glucose mediated signaling pathway
M=1-113, M=172-385 P positive regulation of histone H3-K9 acetylation
M=1-113, M=172-385 P positive regulation of histone H4 acetylation
M=1-113, M=172-385 P positive regulation of transcription by RNA polymerase II
M=1-113, M=172-385 P positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
M=1-113, M=172-385 P regulation of transcription by RNA polymerase II
M=1-113, M=172-385 P single stranded viral RNA replication via double stranded DNA intermediate
N/O=1-1214 C nBAF complex
N/O=1-1214 C npBAF complex
N/O=1-1214 C nuclear chromatin
N/O=1-1214 C nucleoplasm
N/O=1-1214 C protein-containing complex
N/O=1-1214 C SWI/SNF complex
N/O=1-1214 F histone binding
N/O=1-1214 F transcription coactivator activity
N/O=1-1214 P ATP-dependent chromatin remodeling
N/O=1-1214 P chromatin remodeling
N/O=1-1214 P negative regulation of transcription, DNA-templated
N/O=1-1214 P nervous system development
N/O=1-1214 P nucleosome disassembly
N/O=1-1214 P positive regulation of transcription, DNA-templated
N/O=1-1214 P regulation of transcription by RNA polymerase II
P=1-515 C intracellular membrane-bounded organelle
P=1-515 C nBAF complex
P=1-515 C npBAF complex
P=1-515 C nucleoplasm
P=1-515 C SWI/SNF complex
P=1-515 F chromatin binding
P=1-515 F molecular adaptor activity
P=1-515 F signaling receptor binding
P=1-515 F transcription coactivator activity
P=1-515 P cellular response to fatty acid
P=1-515 P chromatin remodeling
P=1-515 P chromatin-mediated maintenance of transcription
P=1-515 P nervous system development
P=1-515 P nucleosome disassembly
P=1-515 P regulation of transcription by RNA polymerase II
Q=1-411 C nBAF complex
Q=1-411 C npBAF complex
Q=1-411 C nuclear chromatin
Q=1-411 C nuclear chromosome
Q=1-411 C nucleoplasm
Q=1-411 C nucleus
Q=1-411 C protein-containing complex
Q=1-411 C SWI/SNF complex
Q=1-411 F chromatin binding
Q=1-411 F DNA binding
Q=1-411 F N-acetyltransferase activity
Q=1-411 F nuclear receptor binding
Q=1-411 F protein N-terminus binding
Q=1-411 F RNA binding
Q=1-411 F transcription coactivator activity
Q=1-411 P ATP-dependent chromatin remodeling
Q=1-411 P chromatin remodeling
Q=1-411 P negative regulation of transcription, DNA-templated
Q=1-411 P neurogenesis
Q=1-411 P nucleosome disassembly
Q=1-411 P regulation of transcription by RNA polymerase II
R=1-100, R=209-391 C centrosome
R=1-100, R=209-391 C cytosol
R=1-100, R=209-391 C histone acetyltransferase complex
R=1-100, R=209-391 C intracellular membrane-bounded organelle
R=1-100, R=209-391 C nBAF complex
R=1-100, R=209-391 C nuclear chromatin
R=1-100, R=209-391 C nucleoplasm
R=1-100, R=209-391 C nucleus
R=1-100, R=209-391 F H3K9me3 modified histone binding
R=1-100, R=209-391 F histone acetyltransferase activity
R=1-100, R=209-391 F histone binding
R=1-100, R=209-391 F lysine-acetylated histone binding
R=1-100, R=209-391 F metal ion binding
R=1-100, R=209-391 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
R=1-100, R=209-391 F transcription corepressor activity
R=1-100, R=209-391 P apoptotic process
R=1-100, R=209-391 P apoptotic signaling pathway
R=1-100, R=209-391 P negative regulation of myeloid progenitor cell differentiation
R=1-100, R=209-391 P negative regulation of transcription by RNA polymerase II
R=1-100, R=209-391 P negative regulation of transcription, DNA-templated
R=1-100, R=209-391 P nervous system development
R=1-100, R=209-391 P positive regulation of transcription by RNA polymerase II
Sequences
Download file with secondary structure created by Stride  
6ltj.pdb1.pdb:   [ download sequences in FASTA format ]
X (dna): 
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Y (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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I (protein): 
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J (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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