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(-) Description

Title :  CRYSTAL STRUCTURE OF NAD+-IA(E380A)-ACTIN COMPLEX
 
Authors :  T. Tsurumura, M. Oda, M. Nagahama, H. Tsuge
Date :  10 Sep 12  (Deposition) - 20 Feb 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Adp-Ribosyltransferase, Toxin-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tsurumura, Y. Tsumori, H. Qiu, M. Oda, J. Sakurai, M. Nagahama, H. Tsuge
Arginine Adp-Ribosylation Mechanism Based On Structural Snapshots Of Iota-Toxin And Actin Complex
Proc. Natl. Acad. Sci. Usa V. 110 4267 2013
PubMed-ID: 23382240  |  Reference-DOI: 10.1073/PNAS.1217227110

(-) Compounds

Molecule 1 - IOTA TOXIN COMPONENT IA
    Chains: A
    EC Number: 2.4.2.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
 
Molecule 2 - ACTIN, ALPHA SKELETAL MUSCLE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ACTA1
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: ALPHA-ACTIN-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 27)

Asymmetric/Biological Unit (6, 27)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA1Ligand/IonCALCIUM ION
3EDO22Ligand/Ion1,2-ETHANEDIOL
4LAR1Ligand/IonLATRUNCULIN A
5NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6PO41Ligand/IonPHOSPHATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:251 , ILE A:259 , ARG A:295 , ARG A:296 , GLY A:298 , GLN A:300 , GLU A:301 , ASN A:335 , SER A:338 , THR A:339 , PHE A:349 , ARG A:352 , EDO A:503BINDING SITE FOR RESIDUE NAD A 501
02AC2SOFTWAREARG A:5 , TRP A:19 , GLU A:23 , ILE A:85 , ASP A:86 , HOH A:680BINDING SITE FOR RESIDUE PO4 A 502
03AC3SOFTWARETYR A:294 , ARG A:296 , SER A:340 , GLY A:342 , SER A:343 , VAL A:344 , PHE A:349 , NAD A:501BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREMET A:346 , SER A:347 , ALA A:348 , MET B:176 , ARG B:177BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWARETYR A:60 , ASP A:61 , MET A:346 , SER A:347 , HOH A:697 , MET B:176 , LYS B:284BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREILE A:80 , THR A:164 , GLY A:165 , GLU A:180 , ASP A:182 , HOH A:608BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWARETYR A:42 , SER A:46 , TYR A:169 , ASN A:171 , LYS A:176BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWARETYR A:60 , GLN A:63 , ASN A:345 , ALA A:350 , LYS A:351 , ASP A:399 , HOH A:626 , HOH A:634 , GLU B:276BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREASN A:90 , HIS A:157 , GLU A:204 , ALA A:205BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWARELYS A:159 , SER A:206 , ILE A:207BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWARELYS A:132 , ASP A:182 , TYR A:183 , SER A:184 , SER A:210 , HOH A:609 , HOH A:673BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREATP B:402 , HOH B:521 , HOH B:522 , HOH B:524 , HOH B:525 , HOH B:526BINDING SITE FOR RESIDUE CA B 401
13BC4SOFTWAREGLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLY B:156 , ASP B:157 , GLY B:158 , VAL B:159 , GLY B:182 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , THR B:303 , MET B:305 , TYR B:306 , LYS B:336 , CA B:401 , EDO B:414 , HOH B:518 , HOH B:521 , HOH B:522 , HOH B:526 , HOH B:527 , HOH B:558 , HOH B:559BINDING SITE FOR RESIDUE ATP B 402
14BC5SOFTWAREGLY B:15 , LEU B:16 , PRO B:32 , ASP B:56 , GLN B:59 , ARG B:62 , LEU B:67 , TYR B:69 , ASP B:157 , ARG B:183 , THR B:186 , ARG B:206 , GLU B:207 , ARG B:210 , HOH B:555BINDING SITE FOR RESIDUE LAR B 403
15BC6SOFTWAREHIS B:73 , GLY B:158 , ASP B:184 , HOH B:581BINDING SITE FOR RESIDUE EDO B 404
16BC7SOFTWAREARG B:183 , ARG B:206BINDING SITE FOR RESIDUE EDO B 405
17BC8SOFTWARESER B:141 , LEU B:142 , SER B:145 , VAL B:298 , MET B:299 , SER B:300 , PRO B:332 , SER B:338BINDING SITE FOR RESIDUE EDO B 406
18BC9SOFTWAREMET B:283 , ARG B:290 , TYR B:294 , PRO B:322BINDING SITE FOR RESIDUE EDO B 407
19CC1SOFTWARETHR B:318 , ALA B:321 , PRO B:322 , SER B:323 , MET B:325 , ILE B:327BINDING SITE FOR RESIDUE EDO B 408
20CC2SOFTWARETHR B:148 , THR B:149 , ASN B:296 , HOH B:585BINDING SITE FOR RESIDUE EDO B 409
21CC3SOFTWAREARG B:62 , TYR B:166 , THR B:203 , ALA B:204 , ASP B:288 , ASP B:292 , HOH B:539BINDING SITE FOR RESIDUE EDO B 410
22CC4SOFTWAREGLU B:83 , HIS B:87 , EDO B:412BINDING SITE FOR RESIDUE EDO B 411
23CC5SOFTWARETYR B:91 , GLU B:99 , THR B:126 , PHE B:127 , SER B:350 , EDO B:411BINDING SITE FOR RESIDUE EDO B 412
24CC6SOFTWARETYR B:198 , SER B:199 , PHE B:200BINDING SITE FOR RESIDUE EDO B 413
25CC7SOFTWARELYS B:213 , GLU B:214 , CYS B:217 , MET B:305 , TYR B:306 , PRO B:307 , ATP B:402 , HOH B:516BINDING SITE FOR RESIDUE EDO B 414
26CC8SOFTWAREGLN B:263 , PRO B:264 , SER B:265 , EDO B:416 , HOH B:590BINDING SITE FOR RESIDUE EDO B 415
27CC9SOFTWARELYS A:351 , PHE B:262 , ALA B:272 , GLY B:273 , HIS B:275 , GLU B:276 , EDO B:415BINDING SITE FOR RESIDUE EDO B 416

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H0X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:249 -Gly A:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H0X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H0X)

(-) Exons   (0, 0)

(no "Exon" information available for 4H0X)

(-) Sequences/Alignments

Asymmetric/Biological 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4h0xa1 A:1-209 automated matches                                                                                                                                                                                d4h0xa2 A:210-413 automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeeeee.hhhhhh.............hhhhhhhhhhhhh..eeeeeeeeee..............eeeeeee......eeeee..eeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......eeeeeeehhhhhh....hhhhh..hhhhhhhhhhhhh..eee....eeee.....hhhhh...eeeeeee.......hhhhh.......eeee....eeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0x A   1 AFIERPEDFLKDKENAIQWEKKEAERVEKNLDTLEKEALELYKKDSEQISNYSQTRQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEKFAFNKEIRTENQNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYINSNDVKTLIEQDYSIKIDKIVRIVIEGKQYIKAEASIVNSLDFKDDVSKGDLWGKENYSDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVYRRSGPQEFGLTLTSPEYDFNKIENIDAFKEKWEGKVITYPNFISTSIGSVNMSAFAKRKIILRINIPKDSPGAYLSAIPGYAGEYAVLLNHGSKFKINKVDSYKDGTVTKLILDATLIN 413
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410   


Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4h0xb1 B:5-146 Actin                                                                                                             d4h0xb2 B:147-374 Actin                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee.........hhhhhhh..........ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhh......eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhh...eehhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0x B   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKC 374
                                    14        24        34 |||    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366        
                                                          36||                                                                                                                                                                                                                                                                                                                                    
                                                           39|                                                                                                                                                                                                                                                                                                                                    
                                                            50
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H0X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H0X)

(-) Gene Ontology  (19, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly A:249 - Gly A:250   [ RasMol ]  
 

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  4h0x
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  ACTS_RABIT | P68135
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  Q46220_CLOPF | Q46220
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  2.4.2.31
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACTS_RABIT | P68135: 1alm 1atn 1eqy 1esv 1h1v 1ijj 1j6z 1kxp 1lcu 1lot 1m8q 1ma9 1mvw 1nwk 1o18 1o19 1o1a 1o1b 1o1c 1o1d 1o1e 1o1f 1o1g 1p8z 1qz5 1qz6 1rdw 1rfq 1rgi 1s22 1sqk 1t44 1uy5 1wua 1y64 1yxq 2a3z 2a40 2a41 2a42 2a5x 2asm 2aso 2asp 2d1k 2ff3 2ff6 2fxu 2gwj 2gwk 2hmp 2pav 2pbd 2q0r 2q0u 2q1n 2q31 2q36 2q97 2v51 2v52 2vcp 2vyp 2w49 2w4u 2y83 2yje 2yjf 2zwh 3b5u 3buz 3cjb 3cjc 3daw 3ffk 3g37 3hbt 3j4k 3j8a 3j8i 3j8j 3j8k 3jbi 3jbj 3jbk 3m1f 3m3n 3m6g 3mfp 3mn5 3sjh 3tpq 3tu5 3u8x 3u9z 3ue5 4a7f 4a7h 4a7l 4a7n 4b1v 4b1w 4b1x 4b1y 4b1z 4eah 4gy2 4h03 4h0t 4h0v 4h0y 4k41 4k42 4k43 4pkg 4pkh 4pki 4pl8 4v0u 4wyb 4z94 5h53 5jlf 5kg8
UniProtKB/TrEMBL
        Q46220_CLOPF | Q46220: 1giq 1gir 3buz 4gy2 4h03 4h0t 4h0v 4h0y

(-) Related Entries Specified in the PDB File

1giq CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADH
1gir CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADPH
3buz CRYSTAL STRUCTURE OF IA-BTAD-ACTIN COMPLEX
4gy2 STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, APO-IA-ACTIN
4h03 STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA-ACTIN
4h0t STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, IA-ADPR-ACTIN
4h0v STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA(E378S)-ACTIN
4h0y STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA(E380S)-ACTIN