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(-) Description

Title :  DDX3 HELICASE DOMAIN
 
Authors :  B. Rodamilans, G. Montoya
Date :  13 Feb 07  (Deposition) - 13 May 08  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Phosphorylation, Nucleotide-Binding, Helicase, Hydrolase, Rna-Binding, Atp-Binding, Dna-Binding, Nuclear Protein, Host-Virus Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Rodamilans, G. Montoya
Expression, Purification, Crystallization And Preliminary X-Ray Diffraction Analysis Of The Ddx3 Rna Helicase Domain.
Acta Crystallogr. , Sect. F V. 63 283 2007
PubMed-ID: 17401195  |  Reference-DOI: 10.1107/S1744309107006434

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX3X
    ChainsA, B, C
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOLD III
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentHELICASE DOMAIN, RESIDUES 408-579
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDBX, DDX3

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2JGN)

(-) Sites  (0, 0)

(no "Site" information available for 2JGN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JGN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JGN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 25)

Asymmetric Unit (9, 25)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075741Q417PDDX3X_HUMANDisease (MRX102)796052233A/B/CQ416P
2UniProtVAR_075742R475GDDX3X_HUMANDisease (MRX102)  ---B/CR474G
3UniProtVAR_075743R480SDDX3X_HUMANDisease (MRX102)  ---B/CR479S
4UniProtVAR_075744R488HDDX3X_HUMANDisease (MRX102)796052235A/B/CR487H
5UniProtVAR_075745I507TDDX3X_HUMANDisease (MRX102)797045024A/B/CI506T
6UniProtVAR_075746N509IDDX3X_HUMANDisease (MRX102)  ---A/B/CN508I
7UniProtVAR_075747I514TDDX3X_HUMANDisease (MRX102)796052226A/B/CI513T
8UniProtVAR_075748R534HDDX3X_HUMANDisease (MRX102)  ---A/B/CR533H
9UniProtVAR_075750P568LDDX3X_HUMANDisease (MRX102)  ---A/B/CP567L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075741Q417PDDX3X_HUMANDisease (MRX102)796052233AQ416P
4UniProtVAR_075744R488HDDX3X_HUMANDisease (MRX102)796052235AR487H
5UniProtVAR_075745I507TDDX3X_HUMANDisease (MRX102)797045024AI506T
6UniProtVAR_075746N509IDDX3X_HUMANDisease (MRX102)  ---AN508I
7UniProtVAR_075747I514TDDX3X_HUMANDisease (MRX102)796052226AI513T
8UniProtVAR_075748R534HDDX3X_HUMANDisease (MRX102)  ---AR533H
9UniProtVAR_075750P568LDDX3X_HUMANDisease (MRX102)  ---AP567L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075741Q417PDDX3X_HUMANDisease (MRX102)796052233BQ416P
2UniProtVAR_075742R475GDDX3X_HUMANDisease (MRX102)  ---BR474G
3UniProtVAR_075743R480SDDX3X_HUMANDisease (MRX102)  ---BR479S
4UniProtVAR_075744R488HDDX3X_HUMANDisease (MRX102)796052235BR487H
5UniProtVAR_075745I507TDDX3X_HUMANDisease (MRX102)797045024BI506T
6UniProtVAR_075746N509IDDX3X_HUMANDisease (MRX102)  ---BN508I
7UniProtVAR_075747I514TDDX3X_HUMANDisease (MRX102)796052226BI513T
8UniProtVAR_075748R534HDDX3X_HUMANDisease (MRX102)  ---BR533H
9UniProtVAR_075750P568LDDX3X_HUMANDisease (MRX102)  ---BP567L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_075741Q417PDDX3X_HUMANDisease (MRX102)796052233CQ416P
2UniProtVAR_075742R475GDDX3X_HUMANDisease (MRX102)  ---CR474G
3UniProtVAR_075743R480SDDX3X_HUMANDisease (MRX102)  ---CR479S
4UniProtVAR_075744R488HDDX3X_HUMANDisease (MRX102)796052235CR487H
5UniProtVAR_075745I507TDDX3X_HUMANDisease (MRX102)797045024CI506T
6UniProtVAR_075746N509IDDX3X_HUMANDisease (MRX102)  ---CN508I
7UniProtVAR_075747I514TDDX3X_HUMANDisease (MRX102)796052226CI513T
8UniProtVAR_075748R534HDDX3X_HUMANDisease (MRX102)  ---CR533H
9UniProtVAR_075750P568LDDX3X_HUMANDisease (MRX102)  ---CP567L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JGN)

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003999591aENSE00002159009X:41192651-41193550900DDX3X_HUMAN1-15150--
1.3ENST000003999593ENSE00001541023X:41196661-4119671858DDX3X_HUMAN16-35200--
1.5ENST000003999595ENSE00001729448X:41198289-4119833648DDX3X_HUMAN35-51170--
1.6ENST000003999596ENSE00001541017X:41200737-41200869133DDX3X_HUMAN51-95450--
1.7bENST000003999597bENSE00001541014X:41201748-41201906159DDX3X_HUMAN95-148540--
1.8ENST000003999598ENSE00001541011X:41201990-41202089100DDX3X_HUMAN148-181340--
1.9ENST000003999599ENSE00001779651X:41202469-41202604136DDX3X_HUMAN182-227460--
1.10ENST0000039995910ENSE00001759311X:41202990-4120307586DDX3X_HUMAN227-255290--
1.11ENST0000039995911ENSE00001730138X:41203283-4120338199DDX3X_HUMAN256-288330--
1.12ENST0000039995912ENSE00001618043X:41203492-41203652161DDX3X_HUMAN289-342540--
1.13ENST0000039995913ENSE00001595336X:41204433-41204577145DDX3X_HUMAN342-390490--
1.14bENST0000039995914bENSE00001795791X:41204657-41204801145DDX3X_HUMAN391-439493A:410-437
B:408-438
C:411-438 (gaps)
28
31
28
1.15ENST0000039995915ENSE00001768220X:41205482-41205663182DDX3X_HUMAN439-499613A:439-498 (gaps)
B:438-498 (gaps)
C:438-498 (gaps)
60
61
61
1.16ENST0000039995916ENSE00001645000X:41205758-41205875118DDX3X_HUMAN500-539403A:505-538
B:499-538 (gaps)
C:499-538
34
40
40
1.17bENST0000039995917bENSE00001605521X:41206112-41206265154DDX3X_HUMAN539-590523A:538-575
B:538-575
C:538-574
38
38
37
1.18ENST0000039995918ENSE00001799515X:41206565-41206704140DDX3X_HUMAN590-637480--
1.19cENST0000039995919cENSE00001875435X:41206893-412094622570DDX3X_HUMAN637-662260--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:151
 aligned with DDX3X_HUMAN | O00571 from UniProtKB/Swiss-Prot  Length:662

    Alignment length:166
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570      
          DDX3X_HUMAN   411 TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY 576
               SCOP domains d2jgna_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains 2jgnA00 A:410-575 P-loop con taining nucleotide triphosphate h        ydrolases                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhhhhhhh-....eeeee.hhhhhhhhhhhhhhh...eeee.--------hhhhhhhhh....eeeee.------......eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------P----------------------------------------------------------------------H------------------T-I----T-------------------H---------------------------------L-------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.14b  PDB: A:410-437   ------------------------------------------------------------Exon 1.16  PDB: A:505-538 [INCOMPLETE]  ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.15  PDB: A:439-498 (gaps) UniProt: 439-499            ---------------------------------------Exon 1.17b  PDB: A:538-575             Transcript 1 (2)
                 2jgn A 410 TSENITQKVVWVEESDKRSFLLDLLNAT-KDSLTLVFVETKKGADSLEDFLYHEGYACTSIH--------EEALHQFRSGKSPILVATA------DISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY 575
                                   419       429       439       449       459       469 |       -|      489        |-     | 509       519       529       539       549       559       569      
                                                     437 |                             471      480               498    505                                                                      
                                                       439                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with DDX3X_HUMAN | O00571 from UniProtKB/Swiss-Prot  Length:662

    Alignment length:168
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568        
          DDX3X_HUMAN   409 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY 576
               SCOP domains d2jgnb_ B: automated matches                                                                                                                                             SCOP domains
               CATH domains 2jgnB00 B:408-575 P-loop contai  ning nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.hhhhhhhhhhhhhhhhh--..eeeee.hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeee...-----.....eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------P---------------------------------------------------------G----S-------H------------------T-I----T-------------------H---------------------------------L-------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.14b  PDB: B:408-438     ------------------------------------------------------------Exon 1.16  PDB: B:499-538 (gaps)        ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.15  PDB: B:438-498 (gaps) UniProt: 439-499            ---------------------------------------Exon 1.17b  PDB: B:538-575             Transcript 1 (2)
                 2jgn B 408 GSTSENITQKVVWVEESDKRSFLLDLLNATG--SLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVA-----ISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY 575
                                   417       427       437|  |   447       457       467       477       487       497  |    507       517       527       537       547       557       567        
                                                        438  |                                                        500   506                                                                     
                                                           441                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with DDX3X_HUMAN | O00571 from UniProtKB/Swiss-Prot  Length:662

    Alignment length:164
                                   421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571    
          DDX3X_HUMAN   412 SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMA 575
               SCOP domains d2jgnc_ C: automated matc he  s                                                                                                                                      SCOP domains
               CATH domains 2jgnC00 C:411-574 P-loop  co  ntaining nucleotide triphosphate hy   drolases                                                                                         CATH domains
           Pfam domains (1) ------------------------- --  -----------------Helicase_C-2jgnC01    C:458-535                                               --------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------- --  -----------------Helicase_C-2jgnC02    C:458-535                                               --------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------- --  -----------------Helicase_C-2jgnC03    C:458-535                                               --------------------------------------- Pfam domains (3)
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhh-..--..eeeee.hhhhhhhhhhhhhhh...eeee.....---hhhhhhhhhh....eeeee.............eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----P---------------------------------------------------------G----S-------H------------------T-I----T-------------------H---------------------------------L------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.14b UniProt: 391-439 ------------------------------------------------------------Exon 1.16  PDB: C:499-538               ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.15  PDB: C:438-498 (gaps) UniProt: 439-499            ---------------------------------------Exon 1.17b  PDB: C:538-574            Transcript 1 (2)
                 2jgn C 411 SENITQKVVWVEESDKRSFLLDLLN-TG--SLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRS---REEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMA 574
                                   420       430    | || -|      450       460       470    |  480       490       500       510       520       530       540       550       560       570    
                                                  435 ||  |                               475 479                                                                                               
                                                    437|  |                                                                                                                                     
                                                     438  |                                                                                                                                     
                                                        441                                                                                                                                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (69, 69)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DDX3X_HUMAN | O00571)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0043273    CTPase activity    Catalysis of the reaction: CTP + H2O = CDP + phosphate. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0035613    RNA stem-loop binding    Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
    GO:0008190    eukaryotic initiation factor 4E binding    Interacting selectively and non-covalently with eukaryotic initiation factor 4E, a polypeptide factor involved in the initiation of ribosome-mediated translation.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0048027    mRNA 5'-UTR binding    Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008143    poly(A) binding    Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0031369    translation initiation factor binding    Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0071243    cellular response to arsenic-containing substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0071470    cellular response to osmotic stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0008625    extrinsic apoptotic signaling pathway via death domain receptors    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:0042256    mature ribosome assembly    The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional ribosome.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:2001243    negative regulation of intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0031333    negative regulation of protein complex assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:1900087    positive regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0071651    positive regulation of chemokine (C-C motif) ligand 5 production    Any process that activates or increases the frequency, rate, or extent of production of chemokine (C-C motif) ligand 5.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045727    positive regulation of translation    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0045948    positive regulation of translational initiation    Any process that activates or increases the frequency, rate or extent of translational initiation.
    GO:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:1903608    protein localization to cytoplasmic stress granule    A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    GO:0034063    stress granule assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0022627    cytosolic small ribosomal subunit    The small subunit of a ribosome located in the cytosol.
    GO:0005852    eukaryotic translation initiation factor 3 complex    A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        DDX3X_HUMAN | O005712i4i 3jrv 4o2c 4o2e 4o2f 4px9 4pxa 5e7i 5e7j 5e7m

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