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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL I-BAR DOMAIN (1-259) OF D.DISCOIDEUM IBARA
 
Authors :  G. Witte, J. Faix, P. Runge-Wollmann
Date :  25 Nov 13  (Deposition) - 05 Feb 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  I-Bar Domain, Membrane Remodelling, Signaling Protein, Cytokinesis, Endocytosis, Lipid Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Linkner, G. Witte, H. Zhao, A. Junemann, B. Nordholz, P. Runge-Wollmann, P. Lappalainen, J. Faix
The Inverse Bar Domain Protein Ibara Drives Membrane Remodeling To Control Osmoregulation, Phagocytosis And Cytokinesis.
J. Cell. Sci. V. 127 1279 2014
PubMed-ID: 24463811  |  Reference-DOI: 10.1242/JCS.140756

(-) Compounds

Molecule 1 - SH3 DOMAIN-CONTAINING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DDB_G0274805
    Organism Common: SLIME MOLD
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 44689

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:87 , GLU A:197 , ARG B:87 , GLU B:197 , LEU B:200BINDING SITE FOR RESIDUE PEG B 301
2AC2SOFTWAREASN B:102 , ALA B:105 , ASP B:109 , LYS B:182 , THR B:185 , PHE B:186 , HOH B:408BINDING SITE FOR RESIDUE PEG B 302
3AC3SOFTWAREASN B:213 , LYS C:23 , VAL C:24 , PRO C:27 , PRO C:28 , THR C:31BINDING SITE FOR RESIDUE PEG C 301
4AC4SOFTWAREARG D:60 , HIS D:64 , HOH D:491BINDING SITE FOR RESIDUE ACT D 301
5AC5SOFTWAREHIS C:183 , ASN D:65 , GLY D:66 , ASP D:68 , PHE D:69 , HOH D:423 , HOH D:473BINDING SITE FOR RESIDUE ACT D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NQI)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqi A   9 NPVIEITLKTINNLKVNSPPLFTEVIKAANKYQQQAQALSQAGLVLADTLTRLTIHNGGDFGEGFKKLADAIKDLENRRDDVAKVLLNEFITPNKQAIEDDQKAIATFEKNYKKDRDQmRQDILKLEAKTRKAGKITELNDKIKESEQLNANKLRDVVLmERRKHATFLSQFNQFLEKEIELSADTmSKFSTNLNTHRDLINSQSQLPLEmESmISKQER 238
                                    18        28        38        48        58        68        78        88        98       108       118       128       138    || 158       168       178       188       198      |208       218       228|  |   238
                                                                                                                                                127-MSE         143|                     178-MSE                    205-MSE                 229-MSE     
                                                                                                                                                                 154                                                                           232-MSE  


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqi B   9 NPVIEITLKTINNLKVNSPPLFTEVIKAANKYQQQAQALSQAGLVLADTLTRLTIHNGGDFGEGFKKLADAIKDLENRRDDVAKVLLNEFITPNKQAIEDDQKAIATFEKNYKKDRDQmRQDILKLEAKTTTPEVLKQQITELNDKIKESEQLNANKLRDVVLmERRKHATFLSQFNQFLEKEIELSADTmSKFSTNLNTHRDLINSQSQLPLEmESmISKQE 237
                                    18        28        38        48        58        68        78        88        98       108       118       128       138|      154       164       174   |   184       194       204|      214       224    |  234   
                                                                                                                                                127-MSE    138|                              178-MSE                    205-MSE                 229-MSE    
                                                                                                                                                            145                                                                                    232-MSE 


Chain C from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqi C   7 QQNPVIEITLKTINNLKVNSPPLFTEVIKAANKYQQQAQALSQAGLVLADTLTRLTIHNGGDFGEGFKKLADAIKDLENRRDDVAKVLLNEFITPNKQAIEDDQKAIATFEKNYKKDRDQmRQDILKLEAKTRKTTPEVLKQQITELNDKIKESEQLNANKLRDVVLmERRKHATFLSQFNQFLEKEIELSADTmSKFSTNLNTHRDLINSQSQLPLEmESmISKQE 237
                                    16        26        36        46        56        66        76        86        96       106       116       126|      136  ||   150       160       170       180       190       200    |  210       220       230 |     
                                                                                                                                                  127-MSE     139|                               178-MSE                    205-MSE                 229-MSE    
                                                                                                                                                               144                                                                                     232-MSE 


Chain D from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nqi D   8 QNPVIEITLKTINNLKVNSPPLFTEVIKAANKYQQQAQALSQAGLVLADTLTRLTIHNGGDFGEGFKKLADAIKDLENRRDDVAKVLLNEFITPNKQAIEDDQKAIATFEKNYKKDRDQmRQDILKLEAKTRKAGKKTTPEVLKQQITELNDKIKESEQLNANKLRDVVLmERRKHATFLSQFNQFLEKEIELSADTmSKFSTNLNTHRDLINSQSQLPLEmESmISKQERT 239
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177|      187       197       207       217       227 |  |  237  
                                                                                                                                                 127-MSE                                            178-MSE                    205-MSE                 229-MSE      
                                                                                                                                                                                                                                                          232-MSE
   Legend:   → Mismatch (orange background)
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  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 4NQI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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