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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF THE OXIDIZED FORM OF NINE HEME CYTOCHROME C AT PH 7.5
 
Authors :  I. Bento, V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, M. A. Carrondo
Date :  22 Apr 03  (Deposition) - 18 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Electron Transport, Multiheme Cytochrome C, Electron Transfer, Electron Transpor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Bento, V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, M. A. Carrondo
Redox-Bohr And Other Cooperativity Effects In The Nine-Heme Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774: Crystallographic And Modeling Studies
J. Biol. Chem. V. 278 36455 2003
PubMed-ID: 12750363  |  Reference-DOI: 10.1074/JBC.M301745200

(-) Compounds

Molecule 1 - NINE-HEME CYTOCHROME C
    Atcc27774
    ChainsA, B
    Organism ScientificDESULFOVIBRIO DESULFURICANS
    Organism Taxid876
    Synonym9HCC

 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  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3HEC18Ligand/IonHEME C
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3HEC9Ligand/IonHEME C
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3HEC9Ligand/IonHEME C

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA B:69 , HOH B:2087BINDING SITE FOR RESIDUE ACT B1303
02AC2SOFTWARESER A:8 , ALA A:10 , ILE A:14 , PHE A:35 , HIS A:37 , HIS A:40 , ILE A:44 , CYS A:47 , CYS A:50 , HIS A:51 , PRO A:56 , VAL A:57 , SER A:58 , HEC A:1296 , HOH A:2292 , HOH A:2293 , HOH A:2294 , HOH A:2295 , HOH A:2296 , HOH A:2297 , HOH A:2298BINDING SITE FOR RESIDUE HEC A1294
03AC3SOFTWARECYS A:50 , HIS A:52 , THR A:53 , ASP A:55 , VAL A:57 , CYS A:59 , THR A:61 , CYS A:62 , HIS A:63 , GLU A:70 , ILE A:74 , ARG A:78 , ALA A:79 , ARG A:88 , PRO A:94 , VAL A:95 , HOH A:2299 , HOH A:2300 , HOH A:2301BINDING SITE FOR RESIDUE HEC A1295
04AC4SOFTWAREVAL A:33 , PHE A:35 , ASN A:36 , HIS A:40 , LYS A:43 , VAL A:95 , SER A:96 , CYS A:97 , CYS A:100 , HIS A:101 , GLN A:104 , LYS A:212 , LEU A:213 , ALA A:216 , HEC A:1294 , HEC A:1298 , HOH A:2302 , HOH A:2303 , HOH A:2304 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308BINDING SITE FOR RESIDUE HEC A1296
05AC5SOFTWARETHR A:105 , ARG A:108 , GLU A:110 , CYS A:111 , CYS A:114 , HIS A:115 , VAL A:118 , PRO A:120 , LYS A:121 , ARG A:122 , TRP A:126 , ILE A:208 , ASP A:211 , LEU A:213 , PHE A:217 , HIS A:218 , ILE A:223 , LEU A:224 , THR A:227 , HOH A:2309 , HOH A:2310 , HOH A:2311BINDING SITE FOR RESIDUE HEC A1297
06AC6SOFTWAREMET A:16 , PHE A:17 , PRO A:18 , ALA A:29 , MET A:30 , LYS A:31 , PRO A:32 , VAL A:33 , LEU A:76 , MET A:80 , HIS A:81 , CYS A:97 , TRP A:126 , CYS A:127 , CYS A:130 , HIS A:131 , HEC A:1296 , HOH A:2031 , HOH A:2312 , ARG B:231 , PRO B:239 , SER B:243BINDING SITE FOR RESIDUE HEC A1298
07AC7SOFTWAREVAL A:172 , ALA A:177 , PRO A:178 , PHE A:195 , HIS A:197 , LEU A:201 , LEU A:224 , CYS A:225 , CYS A:228 , HIS A:229 , LEU A:236 , PRO A:238 , LYS A:240 , CYS A:241 , TYR A:263 , HEC A:1301 , HOH A:2242 , HOH A:2313 , HOH A:2314 , HOH A:2316 , LYS B:26BINDING SITE FOR RESIDUE HEC A1299
08AC8SOFTWARECYS A:228 , HIS A:230 , ARG A:231 , LYS A:240 , CYS A:241 , CYS A:244 , HIS A:245 , GLY A:255 , ARG A:256 , PRO A:257 , ALA A:262 , LEU A:265 , GLN A:266 , HOH A:2317 , HOH A:2318 , HOH A:2319BINDING SITE FOR RESIDUE HEC A1300
09AC9SOFTWARECYS A:114 , ILE A:117 , SER A:193 , PHE A:195 , THR A:196 , ARG A:199 , HIS A:200 , SER A:203 , LEU A:204 , ARG A:207 , CYS A:267 , CYS A:270 , HIS A:271 , MET A:274 , VAL A:276 , ARG A:278 , PRO A:279 , HEC A:1299 , HEC A:1302 , HOH A:2321BINDING SITE FOR RESIDUE HEC A1301
10BC1SOFTWAREILE A:183 , ASP A:184 , ALA A:185 , LEU A:186 , ALA A:187 , ASP A:188 , LYS A:189 , TYR A:190 , MET A:260 , TYR A:263 , HIS A:264 , MET A:268 , HIS A:271 , ASP A:281 , ASP A:283 , CYS A:284 , CYS A:287 , HIS A:288 , HEC A:1301 , HOH A:2322 , HOH A:2323BINDING SITE FOR RESIDUE HEC A1302
11BC2SOFTWARESER B:8 , ALA B:10 , ILE B:14 , MET B:16 , PHE B:35 , HIS B:37 , ILE B:44 , CYS B:47 , CYS B:50 , HIS B:51 , PRO B:56 , SER B:58 , CYS B:59 , HOH B:2282 , HOH B:2284 , HOH B:2285 , HOH B:2286 , HOH B:2287BINDING SITE FOR RESIDUE HEC B1294
12BC3SOFTWARECYS B:50 , HIS B:52 , VAL B:57 , CYS B:59 , THR B:61 , CYS B:62 , HIS B:63 , GLU B:70 , GLY B:71 , ARG B:78 , ALA B:79 , ARG B:88 , PRO B:94 , VAL B:95 , HOH B:2288 , HOH B:2289 , HOH B:2290BINDING SITE FOR RESIDUE HEC B1295
13BC4SOFTWAREVAL B:33 , PHE B:35 , ASN B:36 , HIS B:40 , VAL B:95 , SER B:96 , CYS B:97 , CYS B:100 , HIS B:101 , LYS B:212 , ALA B:216 , HOH B:2165 , HOH B:2291 , HOH B:2292 , HOH B:2293 , HOH B:2294 , HOH B:2295BINDING SITE FOR RESIDUE HEC B1296
14BC5SOFTWARETHR B:105 , ARG B:108 , GLU B:110 , CYS B:111 , CYS B:114 , HIS B:115 , PRO B:120 , LYS B:121 , ARG B:122 , TRP B:126 , ILE B:208 , ASP B:211 , PHE B:217 , HIS B:218 , ILE B:223 , THR B:227 , HOH B:2296BINDING SITE FOR RESIDUE HEC B1297
15BC6SOFTWAREARG A:231 , PRO A:239 , SER A:243 , MET B:16 , PHE B:17 , PRO B:18 , ALA B:29 , MET B:30 , LYS B:31 , PRO B:32 , VAL B:33 , LEU B:76 , MET B:80 , HIS B:81 , CYS B:97 , TRP B:126 , CYS B:127 , CYS B:130 , HIS B:131 , GOL B:1305 , HOH B:2297 , HOH B:2298BINDING SITE FOR RESIDUE HEC B1298
16BC7SOFTWAREHOH A:2024 , VAL B:172 , ALA B:177 , PRO B:178 , PHE B:195 , HIS B:197 , LEU B:201 , LEU B:224 , CYS B:225 , CYS B:228 , HIS B:229 , LEU B:236 , LYS B:240 , CYS B:241 , TYR B:263 , HEC B:1301 , HOH B:2177 , HOH B:2299 , HOH B:2300BINDING SITE FOR RESIDUE HEC B1299
17BC8SOFTWARECYS B:228 , HIS B:230 , ARG B:231 , LYS B:240 , CYS B:241 , CYS B:244 , HIS B:245 , ARG B:256 , PRO B:257 , ALA B:262 , LEU B:265 , GLN B:266 , HOH B:2301 , HOH B:2302 , HOH B:2303BINDING SITE FOR RESIDUE HEC B1300
18BC9SOFTWARECYS B:114 , ILE B:183 , SER B:193 , PHE B:195 , THR B:196 , ARG B:199 , HIS B:200 , SER B:203 , ARG B:207 , CYS B:267 , CYS B:270 , HIS B:271 , MET B:274 , VAL B:276 , PRO B:279 , HEC B:1299 , HEC B:1302 , HOH B:2304 , HOH B:2305 , HOH B:2307 , HOH B:2308BINDING SITE FOR RESIDUE HEC B1301
19CC1SOFTWAREILE B:183 , ASP B:184 , ALA B:185 , LEU B:186 , ALA B:187 , ASP B:188 , LYS B:189 , TYR B:190 , MET B:260 , TYR B:263 , HIS B:264 , MET B:268 , HIS B:271 , ARG B:280 , ASP B:281 , CYS B:284 , CYS B:287 , HIS B:288 , HEC B:1301 , HOH B:2309 , HOH B:2310BINDING SITE FOR RESIDUE HEC B1302
20CC2SOFTWAREGLY A:27 , ALA A:29 , PRO A:32 , MET A:137 , MET A:142 , HOH A:2324 , THR B:237BINDING SITE FOR RESIDUE GOL A1303
21CC3SOFTWARETHR A:237 , GLY B:27 , ALA B:29 , LYS B:31 , PRO B:32 , MET B:137 , HOH B:2311 , HOH B:2312BINDING SITE FOR RESIDUE GOL B1304
22CC4SOFTWAREARG A:256 , ASP B:77 , HIS B:81 , TRP B:126 , HEC B:1298 , HOH B:2313 , HOH B:2314 , HOH B:2315 , HOH B:2316BINDING SITE FOR RESIDUE GOL B1305
23CC5SOFTWAREGLU A:124 , HOH A:2130 , LYS B:121 , ARG B:231 , SER B:232 , PRO B:233 , HOH B:2317BINDING SITE FOR RESIDUE GOL B1306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OFW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:278 -Pro A:279
2Arg B:278 -Pro B:279

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OFW)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC9_DESDA72-323
 
  2A:42-293
B:42-293
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC9_DESDA72-323
 
  1A:42-293
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC9_DESDA72-323
 
  1-
B:42-293

(-) Exons   (0, 0)

(no "Exon" information available for 1OFW)

(-) 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:293
 aligned with CYC9_DESDA | Q9RN68 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:293
                                    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   
           CYC9_DESDA    31 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 323
               SCOP domains d1ofwa_ A: Nine-heme cytochrome c                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ofwA02 A:1-99,A:130-167 Cytochrome C3                                                             1ofwA01 A:100-129,A:168-292   1ofwA02 A:1-99,A:130-167 Cytochrome C31ofwA01 A:100-129,A:168-292 Cytochrome C3                                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee................eeeehhhhhhhh.hhhhhh......hhhhh.....hhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhh...eee.........eeehhhhhhhhhhhh...hhhhhhhh...hhhhhhh...........hhhhh.............hhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------MULTIHEME_CYTC  PDB: A:42-293 UniProt: 72-323                                                                                                                                                                                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ofw A   1 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 293
                                    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   

Chain B from PDB  Type:PROTEIN  Length:293
 aligned with CYC9_DESDA | Q9RN68 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:293
                                    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   
           CYC9_DESDA    31 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 323
               SCOP domains d1ofwb_ B: Nine-heme cytochrome c                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ofwB02 B:1-99,B:130-167 Cytochrome C3                                                             1ofwB01 B:100-129,B:168-292   1ofwB02 B:1-99,B:130-167 Cytochrome C31ofwB01 B:100-129,B:168-292 Cytochrome C3                                                                                    - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofwB01 B:180-290                                                                               --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofwB02 B:180-290                                                                               --- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofwB03 B:180-290                                                                               --- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofwB04 B:180-290                                                                               --- Pfam domains (4)
         Sec.struct. author ............eeee................eeeehhhhhhhh.hhhhh.......hhhhh.....hhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh...eee.........eeehhhhhhhhhhhh...hhhhhhhh...hhhhhhh...........hhhhhh............hhhhhhhhhhhhhhhhh........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------MULTIHEME_CYTC  PDB: B:42-293 UniProt: 72-323                                                                                                                                                                                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ofw B   1 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 293
                                    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   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a1ofwA02A:1-99,A:130-167
1b1ofwA01A:100-129,A:168-292
1c1ofwB01B:100-129,B:168-292
1d1ofwB02B:1-99,B:130-167

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYC9_DESDA | Q9RN68)
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: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: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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  CYC9_DESDA | Q9RN68
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC9_DESDA | Q9RN6819hc 1ofy

(-) Related Entries Specified in the PDB File

19hc NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
1ofy THREE DIMENSIONAL STRUCTURE OF THE REDUCED FORM OF NINE-HEME CYTOCHROME C AT PH 7.5