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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ROQ DOMAIN OF HUMAN ROQUIN IN COMPLEX WITH THE TNF23 RNA DUPLEX
 
Authors :  D. Tan, L. Tong
Date :  31 May 14  (Deposition) - 16 Jul 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Rna Duplex, Winged-Helix Motif, Mrna Secondary Structure, Mrna Decay, Immune Responses, Autoimmunity, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Tan, M. Zhou, M. Kiledjian, L. Tong
The Roq Domain Of Roquin Recognizes Mrna Constitutive-Decay Element And Double-Stranded Rna.
Nat. Struct. Mol. Biol. V. 21 679 2014
PubMed-ID: 25026078  |  Reference-DOI: 10.1038/NSMB.2857

(-) Compounds

Molecule 1 - ROQUIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ROQ DOMAIN (UNP RESIDUES 88-407)
    Gene: RC3H1, KIAA2025, RNF198
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ROQUIN, RING FINGER AND C3H ZINC FINGER PROTEIN 1, RING FINGER AND CCCH-TYPE ZINC FINGER DOMAIN-CONTAINING PROTEIN 1, RING FINGER PROTEIN 198
 
Molecule 2 - 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP* CP*GP*GP*AP*G)-3'
    Chains: C, D
    Engineered: YES
    Other Details: TNF23 DOUBLE-STRANDED RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A CD
Biological Unit 2 (1x):  BCD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric Unit (3, 27)
No.NameCountTypeFull Name
1CL14Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 13)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:184 , ARG A:188 , PHE A:194 , HOH A:773BINDING SITE FOR RESIDUE CL A 501
02AC2SOFTWAREGLY A:196 , PRO A:197 , ALA A:198 , MSE A:199 , HOH A:742BINDING SITE FOR RESIDUE CL A 502
03AC3SOFTWAREGLN A:144 , GLY A:150 , ARG A:153 , HOH A:911BINDING SITE FOR RESIDUE CL A 503
04AC4SOFTWARETYR A:96 , LYS A:100 , LEU A:145 , THR B:93BINDING SITE FOR RESIDUE CL A 504
05AC5SOFTWARESER A:305 , ASP A:310 , GLN A:311BINDING SITE FOR RESIDUE CL A 505
06AC6SOFTWAREASN A:175 , HOH A:659 , HOH A:918BINDING SITE FOR RESIDUE CL A 506
07AC7SOFTWARESER A:312 , LYS A:314 , SER A:315BINDING SITE FOR RESIDUE CL A 507
08AC8SOFTWAREALA A:186 , ARG A:190 , HOH A:676 , HOH A:770 , HOH B:681BINDING SITE FOR RESIDUE CL A 508
09AC9SOFTWAREARG B:188 , PHE B:194BINDING SITE FOR RESIDUE CL B 501
10BC1SOFTWAREGLU A:148 , ARG A:151 , HOH A:855 , GLU B:147 , GLU B:148 , ARG B:151BINDING SITE FOR RESIDUE CL B 502
11BC2SOFTWAREGLN B:144 , GLY B:150 , ARG B:153 , HOH B:911BINDING SITE FOR RESIDUE CL B 503
12BC3SOFTWARELYS B:256 , LYS B:270 , GLU B:271BINDING SITE FOR RESIDUE CL B 504
13BC4SOFTWAREHOH A:697 , ALA B:186 , ARG B:190 , HOH B:682BINDING SITE FOR RESIDUE CL B 505
14BC5SOFTWAREARG B:233 , PHE B:234 , HOH B:963BINDING SITE FOR RESIDUE CL B 506
15BC6SOFTWAREMSE B:155 , ARG B:156 , ILE B:363 , ASP B:364 , GLN B:376 , HOH B:725 , HOH B:881BINDING SITE FOR RESIDUE GOL B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QIK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QIK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QIK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QIK)

(-) Exons   (0, 0)

(no "Exon" information available for 4QIK)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...........hhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qik A  89 GVEDTKHYEEAKKCVEELALYLKPLSSARGVGLNSTTQSVLSRPmQRKLVTLVHCQLVEEEGRIRAmRAARSLGERTVTELILQHQNPQQLSSNLWAAVRARGCQFLGPAmQEEALKLVLLALEDGSALSRKVLVLFVVQRLEPRFPQASKTSIGHVVQLLYRASCFKSLmQLKEEFRTYEALRREHDSQIVQIAmEAGLRIAPDQWSSLLYGDQSHKSHmQSIIDKLQTPASFAQSVQELTIALQRTGDPANLNRLRPHLELLANIDPSPDAPPPTWEQLENGLVAVRTVVHGLVDYIQNH 398
                                    98       108       118       128    |  138       148      |158       168       178       188       198|      208       218       228       238       248       266|      276       286     | 296       306       316|      326       336       346       356       366       376       386       396  
                                                                      133-MSE               155-MSE                                     199-MSE                                                  256| |                      292-MSE                  317-MSE                                                                             
                                                                                                                                                                                                  265 |                                                                                                                                   
                                                                                                                                                                                                    267-MSE                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qik B  88 SGVEDTKHYEEAKKCVEELALYLKPLVLSRPmQRKLVTLVHCQLVEEEGRIRAmRAARSLGERTVTELILQHQNPQQLSSNLWAAVRARGCQFLGPAmQEEALKLVLLALEDGSALSRKVLVLFVVQRLEPRFPQASKTSIGHVVQLLYRASCFKVTKRDEDSSLmQLKEEFRTYEALRREHDSQIVQIAmEAGLRIAPDQWSSLLYGDQSHKSHmQSIIDKLQTPASFAQSVQELTIALQRTGDPANLNRLRPHLELLANIDPSPDAPPPTWEQLENGLVAVRTVVHGLVDYIQNH 398
                                    97       107     ||131 |     141       151   |   161       171       181       191       201       211       221       231       241       251       261     | 271       281       291|      301       311     | 321       331       341       351       361       371       381       391       
                                                   113|    |                   155-MSE                                     199-MSE                                                             267-MSE                  292-MSE                  317-MSE                                                                             
                                                    128    |                                                                                                                                                                                                                                                                         
                                                         133-MSE                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:RNA  Length:18
                                                  
                 4qik C   3 AUGUUUUCUGGAAAACGG  21
                                    12|       
                                    12|       
                                     14       


Chain D from PDB  Type:RNA  Length:18
                                                  
                 4qik D   5 GUUUUCUGUGAAAACGGA  22
                                    14
   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 4QIK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QIK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QIK)

(-) Gene Ontology  (35, 35)

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        RC3H1_HUMAN | Q5TC82: 3x1o 4qil 4ulw 4ywq

(-) Related Entries Specified in the PDB File

4qil CRYSTAL STRUCTURE OF THE ROQ DOMAIN OF HUMAN ROQUIN IN COMPLEX WITH THE HMG19 STEM-LOOP RNA