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(-) Description

Title :  ELECTRON TRANSFER COMPLEXES:EXPERIMENTAL MAPPING OF THE REDOX-DEPENDENT CYTOCHROME C ELECTROSTATIC SURFACE
 
Authors :  M. De March, R. De Zorzi, A. Casini, L. Messori, S. Geremia, N. Demitri C. Gabbiani, A. Guerri
Date :  22 Jul 10  (Deposition) - 25 Jan 12  (Release) - 25 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Globular Protein, Electron Carrier, Mitochondrial Respiration, Electron Trasport Chain, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. De March, R. De Zorzi, A. Casini, L. Messori, S. Geremia
Electron Transfer Complexes:Experimental Mapping Of The Redox-Dependent Cytochrome C Electrostatic Surface
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C
    ChainsA, B, C
    Organism CommonDOMESTIC HORSE,EQUINE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2HEC3Ligand/IonHEME C
3NO318Ligand/IonNITRATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEC1Ligand/IonHEME C
3NO37Ligand/IonNITRATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEC1Ligand/IonHEME C
3NO38Ligand/IonNITRATE ION
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEC1Ligand/IonHEME C
3NO33Ligand/IonNITRATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:13 , CYS A:14 , CYS A:17 , HIS A:18 , THR A:28 , GLY A:29 , PRO A:30 , THR A:40 , GLY A:41 , TYR A:48 , THR A:49 , ASN A:52 , TRP A:59 , LEU A:64 , TYR A:67 , LEU A:68 , THR A:78 , LYS A:79 , MET A:80 , ILE A:81 , PHE A:82 , LEU A:94 , HOH A:131 , HOH A:211BINDING SITE FOR RESIDUE HEC A 105
02AC2SOFTWAREVAL A:11 , HOH A:141 , HOH A:168 , PHE C:82 , ALA C:83 , GLY C:84BINDING SITE FOR RESIDUE NO3 A 106
03AC3SOFTWAREPHE A:82 , ALA A:83 , GLY A:84 , HOH A:179 , LYS B:8 , VAL B:11 , GLN B:12BINDING SITE FOR RESIDUE NO3 A 107
04AC4SOFTWARELYS A:13 , GLY A:84 , LYS A:86 , LYS A:87 , GLU A:90BINDING SITE FOR RESIDUE NO3 A 108
05AC5SOFTWARETHR A:19 , VAL A:20 , GLU A:21 , HOH A:236 , THR C:28 , ILE C:81 , HOH C:124BINDING SITE FOR RESIDUE NO3 A 109
06AC6SOFTWARETHR A:28 , ILE A:81 , HOH A:178 , PHE B:10 , THR B:19 , VAL B:20 , GLU B:21BINDING SITE FOR RESIDUE NO3 A 110
07AC7SOFTWAREGLY A:77 , HOH A:132 , HOH A:261 , LYS C:39 , ILE C:57 , THR C:58 , LYS C:60 , THR C:63BINDING SITE FOR RESIDUE NO3 A 111
08AC8SOFTWAREGLY A:45 , PHE A:46 , THR A:47 , HOH A:118 , HOH A:180 , LYS B:53BINDING SITE FOR RESIDUE NO3 A 112
09AC9SOFTWARELYS B:13 , CYS B:14 , GLN B:16 , CYS B:17 , HIS B:18 , THR B:28 , GLY B:29 , PRO B:30 , THR B:40 , GLY B:41 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , LEU B:64 , TYR B:67 , LEU B:68 , THR B:78 , LYS B:79 , MET B:80 , ILE B:81 , PHE B:82 , LEU B:94 , HOH B:119 , HOH B:135BINDING SITE FOR RESIDUE HEC B 105
10BC1SOFTWARELYS A:53 , HIS B:26 , GLY B:45 , PHE B:46 , THR B:47 , HOH B:276 , LYS C:25BINDING SITE FOR RESIDUE NO3 B 106
11BC2SOFTWARELYS B:27 , THR B:28 , NO3 B:111 , LYS C:25 , LYS C:27BINDING SITE FOR RESIDUE NO3 B 107
12BC3SOFTWAREPHE B:82 , ALA B:83 , GLY B:84 , HOH B:147 , HOH B:332 , VAL C:11BINDING SITE FOR RESIDUE NO3 B 108
13BC4SOFTWARELYS B:13 , GLY B:84 , ILE B:85 , LYS B:86 , HOH B:163 , LYS C:8BINDING SITE FOR RESIDUE NO3 B 109
14BC5SOFTWARELYS B:39 , GLY B:56 , ILE B:57 , THR B:58 , LYS B:60 , THR B:63 , HOH B:194 , HOH B:355 , GLY C:77 , HOH C:196BINDING SITE FOR RESIDUE NO3 B 110
15BC6SOFTWARELYS A:25 , HIS A:26 , LYS A:27 , THR A:28 , HOH A:347 , LYS B:25 , LYS B:27 , NO3 B:107 , HOH B:133BINDING SITE FOR RESIDUE NO3 B 111
16BC7SOFTWARELYS A:100 , PHE B:36 , LYS B:60 , GLU B:61 , LYS B:99 , HOH B:136BINDING SITE FOR RESIDUE NO3 B 112
17BC8SOFTWARELYS A:39 , GLY A:56 , ILE A:57 , THR A:58 , LYS A:60 , HOH A:142 , GLY B:77 , HOH B:263 , HOH B:354BINDING SITE FOR RESIDUE NO3 B 113
18BC9SOFTWAREALA A:15 , LYS C:13 , CYS C:14 , CYS C:17 , HIS C:18 , THR C:28 , GLY C:29 , PRO C:30 , THR C:40 , GLY C:41 , PHE C:46 , TYR C:48 , THR C:49 , ASN C:52 , TRP C:59 , TYR C:67 , LEU C:68 , THR C:78 , LYS C:79 , MET C:80 , ILE C:81 , PHE C:82 , LEU C:98 , HOH C:121 , HOH C:124 , HOH C:136BINDING SITE FOR RESIDUE HEC C 105
19CC1SOFTWAREGLU A:4 , LYS A:7 , LYS C:72 , ALA C:83BINDING SITE FOR RESIDUE NO3 C 106
20CC2SOFTWARETHR B:28 , ILE B:81 , THR C:19 , VAL C:20 , GLU C:21 , HOH C:117 , HOH C:318BINDING SITE FOR RESIDUE NO3 C 107
21CC3SOFTWARELYS A:8 , HOH A:351 , LYS C:13 , GLY C:84 , ILE C:85 , LYS C:86 , HOH C:345BINDING SITE FOR RESIDUE NO3 C 108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O20)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103
 
 
  3A:1-102
B:1-102
C:1-102
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103
 
 
  1A:1-102
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103
 
 
  1-
B:1-102
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103
 
 
  1-
-
C:1-102

(-) Exons   (0, 0)

(no "Exon" information available for 3O20)

(-) 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:105
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
            CYC_HORSE     1 MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3o20a_ A: Mitochondrial cytochrome c                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..................................hhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: A:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3o20 A   0 xGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                            |        9        19        29        39        49        59        69        79        89        99     
                            |                                                                                                        
                            0-ACE                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
            CYC_HORSE     1 MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3o20b_ B: Mitochondrial cytochrome c                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..................................hhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: B:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3o20 B   0 xGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                            |        9        19        29        39        49        59        69        79        89        99     
                            0-ACE                                                                                                    

Chain C from PDB  Type:PROTEIN  Length:105
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
            CYC_HORSE     1 MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3o20c_ C: Mitochondrial cytochrome c                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..................................hhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: C:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3o20 C   0 xGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                            |        9        19        29        39        49        59        69        79        89        99     
                            0-ACE                                                                                                    

   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  (1, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O20)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CYC_HORSE | P00004)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0045155    electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity    Enables the directed movement of electrons from the CoQH2-cytochrome c reductase complex and the cytochrome c oxidase complex.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006123    mitochondrial electron transport, cytochrome c to oxygen    The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
    GO:0006122    mitochondrial electron transport, ubiquinol to cytochrome c    The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC_HORSE | P000041akk 1crc 1fi7 1fi9 1giw 1hrc 1i5t 1lc1 1lc2 1m60 1ocd 1u75 1wej 2frc 2giw 2n3b 2pcb 3jbt 3nbs 3nbt 3o1y 3wc8 3wui 4nfg 4rsz 5iy5 5wve

(-) Related Entries Specified in the PDB File

1kyo YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C
1l9j X-RAY STRUCTURE OF THE CYTOCHROME-C(2)-PHOTOSYNTHETIC REACTION CENTER ELECTRON TRANSFER COMPLEX FROM RHODOBACTER SPHAEROIDES IN TYPE I CO-CRYSTALS
2pcb CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C.
2pcc CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C.