General information
PDB ID 4ZUX
Title SAGA DUB MODULE UBP8/SGF11/SUS1/SGF73 BOUND TO UBIQITINATED NUCLEOSOME
PDB header HYDROLASE/DNA
Date 2015-05-17
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.82
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC CONSTRUCT, SACCHAROMYCES CEREVISIAE (STRAIN YJM789), 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:
pdb4zux.pdb ABCDEFGHKLMNOPQRUVWXYZabcdefghijklmn IJST 0
Biounits:
4zux.pdb1.pdb ABCDEFGHUVWXYZabcd IJ 1
4zux.pdb2.pdb KLMNOPQRefghijklmn ST 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 7.9e-46 1 CL0012 A 38 131 IJ   
Sgf11_N Domain Q03067_6-44 1.2e-23 1 No_clan b 7 44 IJ   
CENP-T_C Domain P62799_18-99 4.9e-08 1 CL0012 B 25 98 IJ   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 c 3 74 IJ   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 C 16 90 IJ   
zf_C2H2_13 Domain P53165_59-98 4.4e-22 1 CL0361 d 59 98 I   
Histone Domain P02281_33-102 7.2e-22 1 CL0012 D 28 98 IJ   
Histone Domain P84233_37-132 2.5e-45 1 CL0012 E 39 131 IJ   
zf-UBP Domain P50102_46-108 5.9e-11 1 CL0229 e 46 108   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 F 26 98 IJ   
Sgf11_N Domain Q03067_6-44 8.7e-24 1 No_clan g 6 44   
Histone Domain P06897_19-91 8.9e-16 1 CL0012 G 14 90 IJ   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 h 3 74   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 H 29 98 IJ   
zf_C2H2_13 Domain P53165_59-98 4.4e-22 1 CL0361 i 59 98   
zf-UBP Domain P50102_46-108 3.5e-10 1 CL0229 j 43 108   
Histone Domain P84233_37-132 7.9e-46 1 CL0012 K 38 131 ST   
Sgf11_N Domain Q03067_6-44 9.4e-24 1 No_clan l 6 44 S   
CENP-T_C Domain P62799_18-99 4.9e-08 1 CL0012 L 25 98 ST   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 m 3 74 ST   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 M 16 90 ST   
zf_C2H2_13 Domain P53165_59-98 4.1e-22 1 CL0361 n 59 98 S   
Histone Domain P02281_33-102 7.2e-22 1 CL0012 N 28 98 ST   
Histone Domain P84233_37-132 2.5e-45 1 CL0012 O 39 131 ST   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 P 26 98 ST   
Histone Domain P06897_19-91 8.9e-16 1 CL0012 Q 14 90 ST   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 R 29 98 ST   
zf-UBP Domain P50102_46-108 5.8e-11 1 CL0229 U 46 108   
Sgf11_N Domain Q03067_6-44 8.7e-24 1 No_clan W 6 44   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 X 3 74   
zf_C2H2_13 Domain P53165_59-98 3.6e-22 1 CL0361 Y 59 98   
zf-UBP Domain P50102_46-108 5.9e-11 1 CL0229 Z 46 108   
EnY2 Family Q6WNK7_9-89 3.2e-21 1 No_clan a 9 89 IJ   
Sgf11 Family Q03067_67-95 3.5e-14 1 CL0361 b 67 95 J   
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan C 91 118   
UCH Family P50102_137-465 1e-60 1 CL0125 e 137 465 S   
EnY2 Family Q6WNK7_9-89 1.3e-21 1 No_clan f 10 89   
Histone_H2A_C Family P06897_92-120 3e-17 1 No_clan G 91 118   
Sgf11 Family Q03067_67-95 3.6e-14 1 CL0361 g 67 95   
UCH Family P50102_137-465 2.4e-60 1 CL0125 j 137 465 T   
EnY2 Family Q6WNK7_9-89 2.2e-25 1 No_clan k 9 89 ST   
Sgf11 Family 3.8e-14 1 CL0361 l 67 95 T
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan M 91 118   
Histone_H2A_C Family P06897_92-120 3e-17 1 No_clan Q 91 118   
UCH Family P50102_137-465 1.1e-59 1 CL0125 U 137 465 I   
EnY2 Family Q6WNK7_9-89 2.6e-25 1 No_clan V 9 89   
Sgf11 Family Q03067_67-95 3.6e-14 1 CL0361 W 67 95   
UCH Family P50102_137-465 4.2e-61 1 CL0125 Z 137 465   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E/K/O=1-136 C nucleoplasm
A/E/K/O=1-136 C nucleosome
A/E/K/O=1-136 F DNA binding
A/E/K/O=1-136 F protein heterodimerization activity
B/F/L/P=1-103 C host cell nucleus
B/F/L/P=1-103 C nucleosome
B/F/L/P=1-103 C nucleus
B/F/L/P=1-103 F DNA binding
B/F/L/P=1-103 F protein heterodimerization activity
B/F/L/P=1-103 P DNA-templated transcription, initiation
C/G/M/Q=1-130 C nucleosome
C/G/M/Q=1-130 C nucleus
C/G/M/Q=1-130 F DNA binding
C/G/M/Q=1-130 F protein heterodimerization activity
D/H/N/R=5-126 C nucleosome
D/H/N/R=5-126 C nucleus
D/H/N/R=5-126 F DNA binding
D/H/N/R=5-126 F protein heterodimerization activity
U/Z/e/j=1-471 C DUBm complex
U/Z/e/j=1-471 C SAGA complex
U/Z/e/j=1-471 C SLIK (SAGA-like) complex
U/Z/e/j=1-471 F molecular adaptor activity
U/Z/e/j=1-471 F thiol-dependent ubiquitin-specific protease activity
U/Z/e/j=1-471 F zinc ion binding
U/Z/e/j=1-471 P histone deubiquitination
U/Z/e/j=1-471 P histone H3-K4 methylation
U/Z/e/j=1-471 P histone H3-K79 methylation
U/Z/e/j=1-471 P RNA splicing
U/Z/e/j=1-471 P ubiquitin-dependent protein catabolic process
V/a/f/k=1-96 C DUBm complex
V/a/f/k=1-96 C nuclear pore
V/a/f/k=1-96 C nucleoplasm
V/a/f/k=1-96 C P-body
V/a/f/k=1-96 C SAGA complex
V/a/f/k=1-96 C transcription export complex 2
V/a/f/k=1-96 F chromatin binding
V/a/f/k=1-96 F enzyme activator activity
V/a/f/k=1-96 F transcription coactivator activity
V/a/f/k=1-96 P histone deubiquitination
V/a/f/k=1-96 P histone H3-K4 methylation
V/a/f/k=1-96 P histone H3-K79 methylation
V/a/f/k=1-96 P nuclear retention of pre-mRNA at the site of transcription
V/a/f/k=1-96 P poly(A)+ mRNA export from nucleus
V/a/f/k=1-96 P positive regulation of transcription by RNA polymerase II
V/a/f/k=1-96 P posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
V/a/f/k=1-96 P regulation of protein localization
V/a/f/k=1-96 P regulation of transcription by RNA polymerase II
V/a/f/k=1-96 P transcription elongation from RNA polymerase II promoter
W/b/g/l=1-99 C DUBm complex
W/b/g/l=1-99 C nucleus
W/b/g/l=1-99 C SAGA complex
W/b/g/l=1-99 F enzyme activator activity
W/b/g/l=1-99 F transcription coactivator activity
W/b/g/l=1-99 F zinc ion binding
W/b/g/l=1-99 P histone deubiquitination
W/b/g/l=1-99 P positive regulation of transcription, DNA-templated
W/b/g/l=1-99 P regulation of transcription by RNA polymerase II
X/c/h/m=153-228 C cytoplasm
X/c/h/m=153-228 C cytosol
X/c/h/m=153-228 C endocytic vesicle membrane
X/c/h/m=153-228 C endoplasmic reticulum membrane
X/c/h/m=153-228 C endosome membrane
X/c/h/m=153-228 C extracellular exosome
X/c/h/m=153-228 C extracellular space
X/c/h/m=153-228 C host cell
X/c/h/m=153-228 C mitochondrial outer membrane
X/c/h/m=153-228 C mitochondrion
X/c/h/m=153-228 C neuron projection
X/c/h/m=153-228 C neuronal cell body
X/c/h/m=153-228 C nucleoplasm
X/c/h/m=153-228 C nucleus
X/c/h/m=153-228 C plasma membrane
X/c/h/m=153-228 C vesicle
X/c/h/m=153-228 F protein tag
X/c/h/m=153-228 F ubiquitin protein ligase binding
X/c/h/m=153-228 P activation of MAPK activity
X/c/h/m=153-228 P anaphase-promoting complex-dependent catabolic process
X/c/h/m=153-228 P cellular protein metabolic process
X/c/h/m=153-228 P cytokine-mediated signaling pathway
X/c/h/m=153-228 P DNA damage response, detection of DNA damage
X/c/h/m=153-228 P endosomal transport
X/c/h/m=153-228 P energy homeostasis
X/c/h/m=153-228 P error-free translesion synthesis
X/c/h/m=153-228 P error-prone translesion synthesis
X/c/h/m=153-228 P fat pad development
X/c/h/m=153-228 P female gonad development
X/c/h/m=153-228 P female meiosis I
X/c/h/m=153-228 P global genome nucleotide-excision repair
X/c/h/m=153-228 P hypothalamus gonadotrophin-releasing hormone neuron development
X/c/h/m=153-228 P I-kappaB kinase/NF-kappaB signaling
X/c/h/m=153-228 P interleukin-1-mediated signaling pathway
X/c/h/m=153-228 P interstrand cross-link repair
X/c/h/m=153-228 P intracellular transport of virus
X/c/h/m=153-228 P JNK cascade
X/c/h/m=153-228 P male meiosis I
X/c/h/m=153-228 P membrane organization
X/c/h/m=153-228 P mitochondrion transport along microtubule
X/c/h/m=153-228 P modification-dependent protein catabolic process
X/c/h/m=153-228 P MyD88-dependent toll-like receptor signaling pathway
X/c/h/m=153-228 P MyD88-independent toll-like receptor signaling pathway
X/c/h/m=153-228 P negative regulation of apoptotic process
X/c/h/m=153-228 P negative regulation of transcription by RNA polymerase II
X/c/h/m=153-228 P negative regulation of transforming growth factor beta receptor signaling pathway
X/c/h/m=153-228 P neuron projection morphogenesis
X/c/h/m=153-228 P nucleotide-binding oligomerization domain containing signaling pathway
X/c/h/m=153-228 P nucleotide-excision repair, DNA damage recognition
X/c/h/m=153-228 P nucleotide-excision repair, DNA duplex unwinding
X/c/h/m=153-228 P nucleotide-excision repair, DNA gap filling
X/c/h/m=153-228 P nucleotide-excision repair, DNA incision
X/c/h/m=153-228 P nucleotide-excision repair, DNA incision, 5'-to lesion
X/c/h/m=153-228 P nucleotide-excision repair, preincision complex assembly
X/c/h/m=153-228 P positive regulation of apoptotic process
X/c/h/m=153-228 P positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
X/c/h/m=153-228 P positive regulation of NF-kappaB transcription factor activity
X/c/h/m=153-228 P positive regulation of protein monoubiquitination
X/c/h/m=153-228 P positive regulation of protein ubiquitination
X/c/h/m=153-228 P positive regulation of transcription by RNA polymerase II
X/c/h/m=153-228 P protein deubiquitination
X/c/h/m=153-228 P protein polyubiquitination
X/c/h/m=153-228 P protein targeting to peroxisome
X/c/h/m=153-228 P protein ubiquitination
X/c/h/m=153-228 P regulation of mitochondrial membrane potential
X/c/h/m=153-228 P regulation of mRNA stability
X/c/h/m=153-228 P regulation of neuron death
X/c/h/m=153-228 P regulation of proteasomal protein catabolic process
X/c/h/m=153-228 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
X/c/h/m=153-228 P seminiferous tubule development
X/c/h/m=153-228 P stress-activated MAPK cascade
X/c/h/m=153-228 P transcription-coupled nucleotide-excision repair
X/c/h/m=153-228 P transforming growth factor beta receptor signaling pathway
X/c/h/m=153-228 P translesion synthesis
X/c/h/m=153-228 P transmembrane transport
X/c/h/m=153-228 P TRIF-dependent toll-like receptor signaling pathway
X/c/h/m=153-228 P viral life cycle
X/c/h/m=153-228 P virion assembly
X/c/h/m=153-228 P Wnt signaling pathway
Y/d/i/n=1-104 C cytosol
Y/d/i/n=1-104 C DUBm complex
Y/d/i/n=1-104 C nucleus
Y/d/i/n=1-104 C SAGA complex
Y/d/i/n=1-104 C SLIK (SAGA-like) complex
Y/d/i/n=1-104 F enzyme activator activity
Y/d/i/n=1-104 F structural molecule activity
Y/d/i/n=1-104 P cellular protein-containing complex assembly
Y/d/i/n=1-104 P chromatin organization
Y/d/i/n=1-104 P histone acetylation
Y/d/i/n=1-104 P histone deubiquitination
Y/d/i/n=1-104 P mRNA export from nucleus
Y/d/i/n=1-104 P positive regulation of RNA polymerase II transcription preinitiation complex assembly
Y/d/i/n=1-104 P regulation of nucleocytoplasmic transport
Y/d/i/n=1-104 P regulation of protein localization to chromatin
Y/d/i/n=1-104 P regulation of transcription by RNA polymerase II
Y/d/i/n=1-104 P RITS complex assembly
Sequences
Download file with secondary structure created by Stride  
4zux.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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U (protein): 
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V (protein): 
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W (protein): 
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X (protein): 
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Y (protein): 
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Z (protein): 
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4zux.pdb2.pdb:   [ download sequences in FASTA format ]
S (dna): 
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T (dna): 
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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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