General information
PDB ID 2HYI
Title STRUCTURE OF THE HUMAN EXON JUNCTION COMPLEX WITH A TRAPPED DEAD-BOX HELICASE BOUND TO RNA
PDB header HYDROLASE/RNA BINDING PROTEIN/RNA
Date 2006-08-06
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.3
Kind rna
Organism HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
PRIDB
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb2hyi.pdb ABCDGHIJ FL 0
Biounits:
2hyi.pdb1.pdb ABCD F 1
2hyi.pdb2.pdb GHIJ L 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RRM_1 Domain Q9Y5S9_75-145 5.3e-19 1 CL0221 B 75 145   
DEAD Domain P38919_62-228 2.2e-42 1 CL0023 C 62 228 F   
Btz Domain 0.0000000081 1 No_clan D 170 217 F
Btz Domain 0.00000012 1 No_clan D 194 246
RRM_1 Domain Q9Y5S9_75-145 5.3e-19 1 CL0221 H 75 145   
DEAD Domain P38919_62-228 2.2e-42 1 CL0023 I 62 228 L   
Btz Domain O15234_176-246 0.000000053 1 No_clan J 194 246   
Btz Domain 0.0000014 1 No_clan J 176 217 L
Mago_nashi Family P61326_5-146 2.6e-80 1 No_clan A 5 146   
Helicase_C Family P38919_263-372 2.3e-31 1 CL0023 C 263 372 F   
Mago_nashi Family P61326_5-146 2.6e-80 1 No_clan G 5 146   
Helicase_C Family P38919_263-372 2.3e-31 1 CL0023 I 263 372 L   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Alpha and beta proteins (a+b)
  Fold: Mago nashi protein
    Superfamily: Mago nashi protein
      Family: Mago nashi protein
Mago nashi protein A 3 145 -
Class: Alpha and beta proteins (a+b)
  Fold: Ferredoxin-like
    Superfamily: RNA-binding domain, RBD
      Family: Canonical RBD
RNA-binding protein 8 B 64 154 -
Class: Alpha and beta proteins (a/b)
  Fold: P-loop containing nucleoside triphosphate hydrolases
    Superfamily: P-loop containing nucleoside triphosphate hydrolases
      Family: Tandem AAA-ATPase domain
Probable ATP-dependent RNA helicase DDX48 C 22 243 F -
Class: Alpha and beta proteins (a/b)
  Fold: P-loop containing nucleoside triphosphate hydrolases
    Superfamily: P-loop containing nucleoside triphosphate hydrolases
      Family: Tandem AAA-ATPase domain
Probable ATP-dependent RNA helicase DDX48 C 244 411 F -
Class: Alpha and beta proteins (a+b)
  Fold: Mago nashi protein
    Superfamily: Mago nashi protein
      Family: Mago nashi protein
Mago nashi protein G 3 145 -
Class: Alpha and beta proteins (a+b)
  Fold: Ferredoxin-like
    Superfamily: RNA-binding domain, RBD
      Family: Canonical RBD
RNA-binding protein 8 H 64 154 -
Class: Alpha and beta proteins (a/b)
  Fold: P-loop containing nucleoside triphosphate hydrolases
    Superfamily: P-loop containing nucleoside triphosphate hydrolases
      Family: Tandem AAA-ATPase domain
Probable ATP-dependent RNA helicase DDX48 I 22 243 L -
Class: Alpha and beta proteins (a/b)
  Fold: P-loop containing nucleoside triphosphate hydrolases
    Superfamily: P-loop containing nucleoside triphosphate hydrolases
      Family: Tandem AAA-ATPase domain
Probable ATP-dependent RNA helicase DDX48 I 244 411 L -
GO terms
Protein chains: GO type: GO description:
A/G=1-146 C cytosol
A/G=1-146 C exon-exon junction complex
A/G=1-146 C catalytic step 2 spliceosome
A/G=1-146 C nuclear speck
A/G=1-146 C nucleoplasm
A/G=1-146 F RNA binding
A/G=1-146 P termination of RNA polymerase II transcription
A/G=1-146 P nuclear mRNA splicing, via spliceosome
A/G=1-146 P regulation of translation
A/G=1-146 P mRNA export from nucleus
A/G=1-146 P mRNA 3'-end processing
A/G=1-146 P nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
B/H=64-154 F mRNA binding
B/H=64-154 F nucleotide binding
C/I=1-411 F poly(A) RNA binding
C/I=1-411 F ATP-dependent RNA helicase activity
C/I=1-411 F ATP binding
C/I=1-411 P positive regulation of nuclear mRNA splicing, via spliceosome
C/I=1-411 P nuclear-transcribed mRNA poly(A) tail shortening
C/I=1-411 P mRNA transport
C/I=1-411 P positive regulation of transcription from RNA polymerase II promoter
C/I=1-411 P positive regulation of translation
C/I=1-411 P rRNA processing
C/I=1-411 P cytokine-mediated signaling pathway
C/I=1-411 P negative regulation of translation
D/J=170-246 C perinuclear region of cytoplasm
D/J=170-246 C ribonucleoprotein complex
D/J=170-246 P RNA splicing
D/J=170-246 P gene expression
D/J=170-246 P response to stress
D/J=170-246 P intracellular mRNA localization
D/J=170-246 P mRNA processing
Sequences
Download file with secondary structure created by Stride  
2hyi.pdb1.pdb:   [ download sequences in FASTA format ]
A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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F (rna): 
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2hyi.pdb2.pdb:   [ download sequences in FASTA format ]
G (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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L (rna): 
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