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(-) Description

Title :  CRYSTAL STRUCTURE OF AN OXIDIZED FORM OF YEAST ISO-1-CYTOCHROME C AT PH 8.8
 
Authors :  L. J. Mcclelland, T. -C. Mou, M. E. Jeakins-Cooley, S. R. Sprang, B. E. Bo
Date :  20 Sep 13  (Deposition) - 04 Jun 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidized Form At Ph 8. 8, All Alpha Proteins, Cytochrome C, Electron Carrier, Peroxidase Activity, Heme Binding, Mitochondria, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Mcclelland, T. C. Mou, M. E. Jeakins-Cooley, S. R. Sprang, B. E. Bowler
Structure Of A Mitochondrial Cytochrome C Conformer Competent For Peroxidase Activity.
Proc. Natl. Acad. Sci. Usa V. 111 6648 2014
PubMed-ID: 24760830  |  Reference-DOI: 10.1073/PNAS.1323828111

(-) Compounds

Molecule 1 - CYTOCHROME C ISO-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRBS_BTR1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CYC1, YJR048W, J1653
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO48Ligand/IonSULFATE ION
4TBU3Ligand/IonTERTIARY-BUTYL ALCOHOL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO44Ligand/IonSULFATE ION
4TBU1Ligand/IonTERTIARY-BUTYL ALCOHOL
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO44Ligand/IonSULFATE ION
4TBU2Ligand/IonTERTIARY-BUTYL ALCOHOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:13 , CYS A:14 , CYS A:17 , HIS A:18 , GLY A:29 , PRO A:30 , ILE A:35 , SER A:40 , GLY A:41 , TYR A:46 , TYR A:48 , THR A:49 , ASN A:52 , TRP A:59 , MET A:64 , TYR A:67 , LEU A:68 , THR A:78 , LYS A:79 , MET A:80 , PHE A:82 , LEU A:85 , HOH A:303 , HOH A:304BINDING SITE FOR RESIDUE HEM A 201
02AC2SOFTWARETHR A:49 , ASP A:50 , HOH A:310 , HOH A:343 , HOH A:386 , HOH A:433BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWARELYS A:79 , MET A:80 , HOH A:308 , HOH A:376BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARESER A:2 , ALA A:3 , LYS A:4 , HOH A:353BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWARELYS A:86 , LYS A:87 , GLU A:88 , HOH A:349 , HOH A:438BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWAREGLN A:16 , CYS A:17BINDING SITE FOR RESIDUE TBU A 206
07AC7SOFTWAREARG A:38 , HOH A:490 , SER B:2 , ALA B:3 , LYS B:4 , HOH B:302 , HOH B:316BINDING SITE FOR RESIDUE SO4 B 201
08AC8SOFTWAREARG B:13 , CYS B:14 , CYS B:17 , HIS B:18 , GLY B:29 , PRO B:30 , ILE B:35 , SER B:40 , GLY B:41 , TYR B:46 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , MET B:64 , TYR B:67 , LEU B:68 , THR B:78 , LYS B:79 , MET B:80 , PHE B:82 , HOH B:305 , HOH B:306 , HOH B:318BINDING SITE FOR RESIDUE HEM B 202
09AC9SOFTWARELYS B:79 , MET B:80 , HOH B:307 , HOH B:372BINDING SITE FOR RESIDUE SO4 B 203
10BC1SOFTWARETHR B:49 , ASP B:50 , HOH B:312 , HOH B:355 , HOH B:359 , HOH B:402BINDING SITE FOR RESIDUE SO4 B 204
11BC2SOFTWAREGLU B:88 , HOH B:356 , HOH B:432BINDING SITE FOR RESIDUE SO4 B 205
12BC3SOFTWAREHOH A:316 , GLU B:61 , ASN B:62 , GLU B:66 , TYR B:74 , HOH B:317 , HOH B:324BINDING SITE FOR RESIDUE GOL B 206
13BC4SOFTWAREGLN B:16 , CYS B:17BINDING SITE FOR RESIDUE TBU B 207
14BC5SOFTWAREALA A:51 , LYS A:54 , LYS A:55 , PRO A:76 , ALA B:51 , LYS B:54 , LYS B:55 , ILE B:75 , PRO B:76BINDING SITE FOR RESIDUE TBU B 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MU8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MU8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MU8)

(-) Exons   (0, 0)

(no "Exon" information available for 4MU8)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4mu8 A  -4 EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPAKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103
                               ||    6        16        26        36        46        56        66        76        86        96       
                              -1|                                                                                                      
                                1                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4mu8 B  -4 EFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPAKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103
                               ||    6        16        26        36        46        56        66        76        86        96       
                              -1|                                                                                                      
                                1
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4MU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MU8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MU8)

(-) Gene Ontology  (10, 10)

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        CYC1_YEAST | P00044: 1chh 1chi 1chj 1cie 1cif 1cig 1cih 1crg 1crh 1cri 1crj 1csu 1csv 1csw 1csx 1cty 1ctz 1fhb 1irv 1irw 1kyo 1lms 1nmi 1rap 1raq 1s6v 1u74 1ycc 1yfc 1yic 2b0z 2b10 2b11 2b12 2bcn 2gb8 2hv4 2jqr 2jti 2lir 2lit 2mhm 2n18 2orl 2pcc 2ycc 3cx5 3tyi 4n0k 4p4q 4q5p 4qao 4ye1 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5kke 5klu 5kpf 5lft 5lyc 5t7h

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