Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL RNASE III DOMAIN OF HUMAN DICER
 
Authors :  D. Takeshita, S. Zenno, W. C. Lee, K. Nagata, K. Saigo, M. Tanokura
Date :  05 Feb 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Rna-Binding, Nuclease, Hydrolase, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Takeshita, S. Zenno, W. C. Lee, K. Nagata, K. Saigo, M. Tanokura
Homodimeric Structure And Double-Stranded Rna Cleavage Activity Of The C-Terminal Rnase Iii Domain Of Human Dicer
J. Mol. Biol. V. 374 106 2007
PubMed-ID: 17920623  |  Reference-DOI: 10.1016/J.JMB.2007.08.069

(-) Compounds

Molecule 1 - ENDORIBONUCLEASE DICER
    ChainsA, B, C
    EC Number3.1.26.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL RNASE III DOMAIN, RNASE III 2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRIBONUCLEASE III, HELICASE WITH RNASE MOTIF, HELICASE-MOI

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:47 , ASP C:152 , GLU C:155 , HOH C:508 , HOH C:529 , HOH C:571BINDING SITE FOR RESIDUE MG C 501
2AC2SOFTWAREGLU A:47 , ASP A:152 , GLU A:155 , HOH A:507 , HOH A:514 , HOH A:562BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREGLU B:47 , ASP B:152 , GLU B:155 , HOH B:513 , HOH B:521 , HOH B:571BINDING SITE FOR RESIDUE MG B 503
4AC4SOFTWAREASP A:55 , HOH A:508 , HOH A:559 , ASP C:51 , ASP C:55 , HOH C:535 , HOH C:572BINDING SITE FOR RESIDUE MG C 504
5AC5SOFTWAREASP A:51 , HOH A:526 , HOH A:533 , HOH A:553 , HOH A:563BINDING SITE FOR RESIDUE MG A 505
6AC6SOFTWAREASP B:51 , HOH B:520 , HOH B:543 , HOH B:565 , HOH B:572BINDING SITE FOR RESIDUE MG B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EB1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 30)

Asymmetric Unit (10, 30)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_067091E1705KDICER_HUMANUnclassified  ---A/B/CE47K
02UniProtVAR_067092D1709EDICER_HUMANUnclassified  ---A/B/CD51E
03UniProtVAR_067093D1709GDICER_HUMANUnclassified  ---A/B/CD51G
04UniProtVAR_067094D1709NDICER_HUMANUnclassified  ---A/B/CD51N
05UniProtVAR_067095D1810HDICER_HUMANUnclassified  ---A/B/CD152H
06UniProtVAR_067096D1810NDICER_HUMANUnclassified775912475A/B/CD152N
07UniProtVAR_067097D1810YDICER_HUMANUnclassified  ---A/B/CD152Y
08UniProtVAR_067098E1813GDICER_HUMANUnclassified  ---A/B/CE155G
09UniProtVAR_067099E1813KDICER_HUMANUnclassified  ---A/B/CE155K
10UniProtVAR_067100E1813QDICER_HUMANUnclassified  ---A/B/CE155Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (10, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_067091E1705KDICER_HUMANUnclassified  ---A/CE47K
02UniProtVAR_067092D1709EDICER_HUMANUnclassified  ---A/CD51E
03UniProtVAR_067093D1709GDICER_HUMANUnclassified  ---A/CD51G
04UniProtVAR_067094D1709NDICER_HUMANUnclassified  ---A/CD51N
05UniProtVAR_067095D1810HDICER_HUMANUnclassified  ---A/CD152H
06UniProtVAR_067096D1810NDICER_HUMANUnclassified775912475A/CD152N
07UniProtVAR_067097D1810YDICER_HUMANUnclassified  ---A/CD152Y
08UniProtVAR_067098E1813GDICER_HUMANUnclassified  ---A/CE155G
09UniProtVAR_067099E1813KDICER_HUMANUnclassified  ---A/CE155K
10UniProtVAR_067100E1813QDICER_HUMANUnclassified  ---A/CE155Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (10, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_067091E1705KDICER_HUMANUnclassified  ---BE47K
02UniProtVAR_067092D1709EDICER_HUMANUnclassified  ---BD51E
03UniProtVAR_067093D1709GDICER_HUMANUnclassified  ---BD51G
04UniProtVAR_067094D1709NDICER_HUMANUnclassified  ---BD51N
05UniProtVAR_067095D1810HDICER_HUMANUnclassified  ---BD152H
06UniProtVAR_067096D1810NDICER_HUMANUnclassified775912475BD152N
07UniProtVAR_067097D1810YDICER_HUMANUnclassified  ---BD152Y
08UniProtVAR_067098E1813GDICER_HUMANUnclassified  ---BE155G
09UniProtVAR_067099E1813KDICER_HUMANUnclassified  ---BE155K
10UniProtVAR_067100E1813QDICER_HUMANUnclassified  ---BE155Q

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

(-) PROSITE Motifs  (3, 8)

Asymmetric Unit (3, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_3_2PS50142 Ribonuclease III family domain profile.DICER_HUMAN1666-1824
 
 
1283-1372
  3A:8-166
B:8-166
C:8-166
-
2RNASE_3_1PS00517 Ribonuclease III family signature.DICER_HUMAN1702-1710
 
 
  3A:44-52
B:44-52
C:44-52
3DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.DICER_HUMAN1849-1914
 
  2A:191-192
B:191-191
Biological Unit 1 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_3_2PS50142 Ribonuclease III family domain profile.DICER_HUMAN1666-1824
 
 
1283-1372
  2A:8-166
-
C:8-166
-
2RNASE_3_1PS00517 Ribonuclease III family signature.DICER_HUMAN1702-1710
 
 
  2A:44-52
-
C:44-52
3DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.DICER_HUMAN1849-1914
 
  1A:191-192
-
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_3_2PS50142 Ribonuclease III family domain profile.DICER_HUMAN1666-1824
 
 
1283-1372
  2-
B:8-166
-
-
2RNASE_3_1PS00517 Ribonuclease III family signature.DICER_HUMAN1702-1710
 
 
  2-
B:44-52
-
3DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.DICER_HUMAN1849-1914
 
  2-
B:191-191

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3bENST000003930633bENSE00001514082chr14:95608055-9560802036DICER_HUMAN-00--
1.5ENST000003930635ENSE00001514081chr14:95607096-95606996101DICER_HUMAN-00--
1.8bENST000003930638bENSE00002152580chr14:95599840-95599652189DICER_HUMAN1-48480--
1.9bENST000003930639bENSE00000660064chr14:95599014-95598852163DICER_HUMAN49-103550--
1.10ENST0000039306310ENSE00000660065chr14:95597976-95597846131DICER_HUMAN103-146440--
1.11ENST0000039306311ENSE00000660066chr14:95596529-95596395135DICER_HUMAN147-191450--
1.12aENST0000039306312aENSE00000660067chr14:95595969-95595809161DICER_HUMAN192-245540--
1.13ENST0000039306313ENSE00000660068chr14:95593085-95592917169DICER_HUMAN245-301570--
1.14aENST0000039306314aENSE00000660069chr14:95591005-95590533473DICER_HUMAN302-4591580--
1.15ENST0000039306315ENSE00000660070chr14:95584091-95583959133DICER_HUMAN459-503450--
1.16aENST0000039306316aENSE00000660071chr14:95583032-95582790243DICER_HUMAN504-584810--
1.17ENST0000039306317ENSE00000660072chr14:95582158-95582004155DICER_HUMAN585-636520--
1.18bENST0000039306318bENSE00000660073chr14:95579561-95579429133DICER_HUMAN636-680450--
1.19ENST0000039306319ENSE00000660074chr14:95578584-9557850976DICER_HUMAN681-706260--
1.20bENST0000039306320bENSE00001364566chr14:95577793-95577654140DICER_HUMAN706-752470--
1.21aENST0000039306321aENSE00000858391chr14:95574840-95574661180DICER_HUMAN753-812600--
1.22bENST0000039306322bENSE00000660077chr14:95574430-95574217214DICER_HUMAN813-884720--
1.23ENST0000039306323ENSE00000660078chr14:95574098-95573945154DICER_HUMAN884-935520--
1.24ENST0000039306324ENSE00000660079chr14:95572560-95572378183DICER_HUMAN935-996620--
1.25ENST0000039306325ENSE00000660080chr14:95572120-95572015106DICER_HUMAN996-1031360--
1.26ENST0000039306326ENSE00000660081chr14:95571583-95571408176DICER_HUMAN1032-1090590--
1.27aENST0000039306327aENSE00000660082chr14:95570463-95569683781DICER_HUMAN1090-13502610--
1.28ENST0000039306328ENSE00000660083chr14:95566272-95566117156DICER_HUMAN1351-1402520--
1.29aENST0000039306329aENSE00000660084chr14:95563050-95562162889DICER_HUMAN1403-16992973A:2-41
B:2-41
C:2-41
40
40
40
1.30ENST0000039306330ENSE00000660085chr14:95560493-95560225269DICER_HUMAN1699-1788903A:41-121
B:41-121
C:41-121
81
81
81
1.31aENST0000039306331aENSE00000660087chr14:95557702-95557540163DICER_HUMAN1789-1843553A:142-185
B:142-185
C:142-185
44
44
44
1.32aENST0000039306332aENSE00000660089chr14:95557446-9555737176DICER_HUMAN1843-1868263A:185-192
B:185-191
C:185-190
8
7
6
1.32eENST0000039306332eENSE00001305539chr14:95557000-955525664435DICER_HUMAN1868-1922550--

(-) 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:171
 aligned with DICER_HUMAN | Q9UPY3 from UniProtKB/Swiss-Prot  Length:1922

    Alignment length:191
                                  1669      1679      1689      1699      1709      1719      1729      1739      1749      1759      1769      1779      1789      1799      1809      1819      1829      1839      1849 
         DICER_HUMAN   1660 NHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANVP 1850
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh--------------------.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------K---E----------------------------------------------------------------------------------------------------H--G------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------G----------------------------------------------------------------------------------------------------N--K------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------N----------------------------------------------------------------------------------------------------Y--Q------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) ------RNASE_3_2  PDB: A:8-166 UniProt: 1666-1824                                                                                                                     ------------------------DS PROSITE (1)
                PROSITE (2) ------------------------------------------RNASE_3_1-------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.29a  PDB: A:2-41 [INCOMPLETE]    -----------------------------------------------------------------------------------------Exon 1.31a  PDB: A:142-185 UniProt: 1789-1843          ------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.30  PDB: A:41-121 UniProt: 1699-1788 [INCOMPLETE]                                  ------------------------------------------------------1.32a    Transcript 1 (2)
                2eb1 A    2 NHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEK--------------------EDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANVP  192
                                    11        21        31        41        51        61        71        81        91       101       111       121         -         -|      151       161       171       181       191 
                                                                                                                                                 121                  142                                                  

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with DICER_HUMAN | Q9UPY3 from UniProtKB/Swiss-Prot  Length:1922

    Alignment length:190
                                  1669      1679      1689      1699      1709      1719      1729      1739      1749      1759      1769      1779      1789      1799      1809      1819      1829      1839      1849
         DICER_HUMAN   1660 NHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANV 1849
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh--------------------.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------K---E----------------------------------------------------------------------------------------------------H--G------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------G----------------------------------------------------------------------------------------------------N--K------------------------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------N----------------------------------------------------------------------------------------------------Y--Q------------------------------------ SAPs(SNPs) (3)
                PROSITE (1) ------RNASE_3_2  PDB: B:8-166 UniProt: 1666-1824                                                                                                                     ------------------------D PROSITE (1)
                PROSITE (2) ------------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.29a  PDB: B:2-41 [INCOMPLETE]    -----------------------------------------------------------------------------------------Exon 1.31a  PDB: B:142-185 UniProt: 1789-1843          ------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.30  PDB: B:41-121 UniProt: 1699-1788 [INCOMPLETE]                                  ------------------------------------------------------1.32a   Transcript 1 (2)
                2eb1 B    2 NHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEK--------------------EDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSANV  191
                                    11        21        31        41        51        61        71        81        91       101       111       121         -         -|      151       161       171       181       191
                                                                                                                                                 121                  142                                                 

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with DICER_HUMAN | Q9UPY3 from UniProtKB/Swiss-Prot  Length:1922

    Alignment length:189
                                  1669      1679      1689      1699      1709      1719      1729      1739      1749      1759      1769      1779      1789      1799      1809      1819      1829      1839         
         DICER_HUMAN   1660 NHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGMDSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSAN 1848
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.--------------------.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------K---E----------------------------------------------------------------------------------------------------H--G----------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------G----------------------------------------------------------------------------------------------------N--K----------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------N----------------------------------------------------------------------------------------------------Y--Q----------------------------------- SAPs(SNPs) (3)
                PROSITE (1) ------RNASE_3_2  PDB: C:8-166 UniProt: 1666-1824                                                                                                                     ------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.29a  PDB: C:2-41 [INCOMPLETE]    -----------------------------------------------------------------------------------------Exon 1.31a  PDB: C:142-185 UniProt: 1789-1843          ----- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.30  PDB: C:41-121 UniProt: 1699-1788 [INCOMPLETE]                                  ------------------------------------------------------1.32a  Transcript 1 (2)
                2eb1 C    2 NHLISGFENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEK--------------------EDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLIEKFSAN  190
                                    11        21        31        41        51        61        71        81        91       101       111       121         -         -|      151       161       171       181         
                                                                                                                                                 121                  142                                                

   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  (0, 0)

(no "SCOP Domain" information available for 2EB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EB1)

(-) Gene Ontology  (47, 47)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DICER_HUMAN | Q9UPY3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004530    deoxyribonuclease I activity    Catalysis of the endonucleolytic cleavage of DNA to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end products.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016891    endoribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0070883    pre-miRNA binding    Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0004525    ribonuclease III activity    Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
    GO:0035197    siRNA binding    Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006309    apoptotic DNA fragmentation    The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
    GO:0036404    conversion of ds siRNA to ss siRNA    The process in which double-stranded small interfering RNA (ds siRNA) molecules are converted to single-stranded small interfering RNA (ss siRNA).
    GO:0033168    conversion of ds siRNA to ss siRNA involved in RNA interference    The process in which double-stranded siRNA molecules are converted to single-stranded siRNAs; required for the formation of a mature RITS complex during RNA interference.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0035280    miRNA loading onto RISC involved in gene silencing by miRNA    The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC).
    GO:0010626    negative regulation of Schwann cell proliferation    Any process that decreases the frequency or extent of the multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0021675    nerve development    The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0032290    peripheral nervous system myelin formation    The process in which the wraps of cell membrane that constitute myelin are laid down around an axon by an oligodendrocyte in the peripheral nervous system.
    GO:0014040    positive regulation of Schwann cell differentiation    Any process that activates or increases the frequency, rate or extent of Schwann cell differentiation.
    GO:0031643    positive regulation of myelination    Any process that activates or increases the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0031054    pre-miRNA processing    Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
    GO:0035196    production of miRNAs involved in gene silencing by miRNA    Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
    GO:0030422    production of siRNA involved in RNA interference    Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
    GO:0035087    siRNA loading onto RISC involved in RNA interference    The transfer of small interfering RNA molecules (siRNAs) from the Dicer family of enzymes that cleave the double-stranded RNA, onto the nuclease-containing RNA-initiated silencing complex (RISC), in the context of RNA interference.
    GO:0030423    targeting of mRNA for destruction involved in RNA interference    The process in which small interfering RNAs target cognate mRNA molecules for degradation.
cellular component
    GO:0033167    ARC complex    A ribonucleoprotein complex that contains members of the Argonaute family of proteins, additional protein subunits, and duplex siRNA; required for heterochromatin assembly and siRNA generation. Possibly involved in the conversion of ds siRNA to ss siRNA.
    GO:0016442    RISC complex    A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
    GO:0070578    RISC-loading complex    A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2eb1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2eb1
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DICER_HUMAN | Q9UPY3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.26.3
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DICER_HUMAN | Q9UPY3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DICER_HUMAN | Q9UPY34ngb 4ngc 4ngd 4ngf 4ngg 4nh3 4nh5 4nh6 4nha 4wyq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EB1)