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(-) Description

Title :  CRYSTAL STRUCTURE OF A NUCLEAR ACTIN TERNARY COMPLEX
 
Authors :  Z. C. Chen, T. T. Cao
Date :  20 Feb 16  (Deposition) - 27 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,H
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,H  (1x)
Keywords :  Nuclear Actin, Arp4, Chromatin Remodeling, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. T. Cao, L. F. Sun, Y. X. Jiang, S. J. Huang, J. W. Wang, Z. C. Chen
Crystal Structure Of A Nuclear Actin Ternary Complex
Proc. Natl. Acad. Sci. Usa 2016
PubMed: search  |  Reference-DOI: 10.1073/PNAS.1602818113

(-) Compounds

Molecule 1 - ACTIN-RELATED PROTEIN 4
    ChainsA, C
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    GeneARP4, ACT3, YJL081C, J1012
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymACTIN-LIKE PROTEIN ARP4,ACTIN-LIKE PROTEIN 4
 
Molecule 2 - ACTIN
    ChainsB, D
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    GeneACT1
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES BAYANUS
    Organism Taxid4931
 
Molecule 3 - HELICASE SWR1
    ChainsH, E
    EC Number3.6.4.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 340-410
    GeneSWR1, YDR334W, D9651.6
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymSWI2/SNF2-RELATED 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEH
Biological Unit 1 (1x)AB  E 
Biological Unit 2 (1x)  CD H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:159 , ATP A:1002binding site for residue MG A 1001
2AC2SOFTWAREGLY A:22 , SER A:23 , TYR A:24 , THR A:25 , GLY A:161 , HIS A:162 , ASP A:163 , THR A:164 , GLN A:240 , LYS A:243 , GLY A:412 , GLY A:413 , THR A:414 , ILE A:417 , GLN A:449 , MG A:1001binding site for residue ATP A 1002
3AC3SOFTWAREASP B:11 , LYS B:18binding site for residue MG B 401
4AC4SOFTWAREGLY C:22 , SER C:23 , TYR C:24 , THR C:25 , GLY C:161 , HIS C:162 , ASP C:163 , GLN C:240 , LYS C:243 , GLU C:244 , GLY C:413 , THR C:414 , GLN C:449 , MG C:502binding site for residue ATP C 501
5AC5SOFTWAREATP C:501binding site for residue MG C 502
6AC6SOFTWAREASP D:154 , VAL D:339binding site for residue MG D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I9E)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Lys A:67 -Asp A:68
2Lys A:213 -Pro A:214
3Leu A:440 -Thr A:441
4Ser B:155 -Gly B:156
5Lys C:67 -Asp C:68
6Lys C:213 -Pro C:214
7Gly C:443 -His C:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I9E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I9E)

(-) Exons   (0, 0)

(no "Exon" information available for 5I9E)

(-) 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:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee...eeeeee.......eeee.eeeee.......ee.hhhhhh.....eeeee.ee..ee.hhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh.....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.....eee..hhhhhhhhhhhhh..........eee.....ee.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.......ee.....ee..hhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhheeeehhhhhh.hhhhhhhhhhhhhh......ee....hhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9e A   0 PMSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDIPANWPRSNSGVELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGVERLLNDRFR 489
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 ||    388       398       408       418       428       438       448       458       468       478       488 
                                                                                                                                                                                                                                                                                                                                                 311|                                                                                                            
                                                                                                                                                                                                                                                                                                                                                  381                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..ee..eehhhhhhh.....ee..ee..ee.hhhhhhhhhhhhhh.....hhhhh.eeeee....hhhhhhhhhhhhhhh.....eeeeehhhhhhhhh....eeeeee....eeeeeee..ee.....eee..hhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhh.....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9e B   5 VAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRSYVGDEAQSKRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGRDLTDYLMKILSERTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSYELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYDESGPSIVHHKCF 375
                                    14        24        34  ||    58        68        78        88        98       108       118       128       138       148       158       168       178       188       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374 
                                                           37|                                                                                                                                             196|                                                                                                                                                                            
                                                            52                                                                                                                                              203                                                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...eeeeee.......eeee.eeeee.......ee.hhhhhh.....eeeee.ee..ee.hhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh.....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhh..........eee.....ee.......hhhhhhhhhhhhhhhhhhhhh..........hhhhhh.......ee.....ee..hhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhheeeehhhhhh.hhhhhhhhhhhhhh......ee...hhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9e C   1 MSNAALQVYGVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQSIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTENRKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKSTRRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDIPANWPRSIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGVER 482
                                    10|       23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   ||  388       398       408       418       428       438       448       458       468       478    
                                    10|                                                                                                                                                                                                                                                                                                  307|                                                                                                   
                                     14                                                                                                                                                                                                                                                                                                   383                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..eee.eehhhhhhh....eee..ee..ee.hhhhhhhhhhhhhh.....hhhhh.eeeee....hhhhhhhhhhhhhhh.....eeeeehhhhhhhhh....eeeeee....eeeeeee..ee.....eee..hhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9e D   5 VAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRSYVGDEAQSKRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMTQIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDLAGRDLTDYLMKILSERAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMSGGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQEYDESGPSIVHHKCF 375
                                    14        24        34  ||    58        68        78        88        98       108       118       128       138       148       158       168       178       188       205       215       225       235  ||   257       267       277       287       297       307       317       327       337       347       357       367        
                                                           37|                                                                                                                                             196|                               238|                                                                                                                            
                                                            52                                                                                                                                              204                                251                                                                                                                            

Chain E from PDB  Type:PROTEIN  Length:41
                                                                         
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 5i9e E 350 IHTDHLINQGIHMSKLFRSSTKARIARAKKVSQMIEQHFKH 390
                                   359       369       379       389 

Chain H from PDB  Type:PROTEIN  Length:44
                                                                            
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 5i9e H 350 IHTDHLINQGIHMSKLFRSSTKARIARAKKVSQMIEQHFKHVAG 393
                                   359       369       379       389    

   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 5I9E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I9E)

(-) Gene Ontology  (31, 39)

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 Related Entries

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        ARP4_YEAST | P804283qb0
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(-) Related Entries Specified in the PDB File

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