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Title :   STRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION

Authors :   H. Ochi, Y. Hata, N. Tanaka, M. Kakudo, T. Sakurai, S. Aihara, Y. Morita

Date :   14 Mar 83 (Deposition) - 21 Apr 83 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Electron Transport(Cytochrome) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ochi, Y. Hata, N. Tanaka, M. Kakudo, T. Sakurai, S. Aihara, Y. Morita
Structure Of Rice Ferricytochrome C At 2. 0 A Resolution.
J. Mol. Biol. V. 166 407 1983
PubMed-ID: 6304326 | Reference-DOI: 10.1016/S0022-2836(83)80092-8
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	RICE
	Organism Scientific	:	ORYZA SATIVA
	Organism Taxid	:	4530

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:21 , CYS A:22 , CYS A:25 , HIS A:26 , GLN A:36 , GLY A:37 , PRO A:38 , SER A:48 , GLY A:49 , TYR A:54 , TYR A:56 , SER A:57 , ASP A:60 , TRP A:67 , TYR A:75 , THR A:86 , LYS A:87 , MET A:88 , VAL A:89 , PHE A:90 , LEU A:102 , HOH A:123 , HOH A:135	BINDING SITE FOR RESIDUE HEM A 112

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

(no "Cis Peptide Bond" information available for 1CCR)

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_ORYSI	10-111	1	A:9-110
1	CYTC	PS51007	Cytochrome c family profile.	CYC_ORYSJ	10-111	1	A:9-110

(no "Exon" information available for 1CCR)

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:112
 aligned with CYC_ORYSI | A2Y4S9 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
            CYC_ORYSI     1 MASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTANKNMAVIWEENTLYDYLLNPKKYIPGTKMVFPGLKKPQERADLISYLKEATS 112
               SCOP domains d1ccra_ A: Mitochondrial cytochrome c                                                                            SCOP domains
               CATH domains -1ccrA00 A:1-111 Cytochrome c                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------CYTC  PDB: A:9-110 UniProt: 10-111                                                                    - PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1ccr A   0 xASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEENTLYDYLLNPkKYIPGTKMVFPGLkKPQERADLISYLKEATS 111
                            |        9        19        29        39        49        59        69        79|       89    |   99       109  
                            |                                                                              80-M3L        94-M3L             
                            0-ACE

Chain A from PDB  Type:PROTEIN  Length:112
 aligned with CYC_ORYSJ | Q0DI31 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
            CYC_ORYSJ     1 MASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTANKNMAVIWEENTLYDYLLNPKKYIPGTKMVFPGLKKPQERADLISYLKEATS 112
               SCOP domains d1ccra_ A: Mitochondrial cytochrome c                                                                            SCOP domains
               CATH domains -1ccrA00 A:1-111 Cytochrome c                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------CYTC  PDB: A:9-110 UniProt: 10-111                                                                    - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1ccr A   0 xASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEENTLYDYLLNPkKYIPGTKMVFPGLkKPQERADLISYLKEATS 111
                            |        9        19        29        39        49        59        69        79|       89    |   99       109  
                            0-ACE                                                                          80-M3L        94-M3L

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: Mitochondrial cytochrome c (81)

Rice embryos (Oryza sativa) [TaxId: 4530] (1)

d1ccra_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Rice (Oryza sativa) (1)

1ccrA00

A:1-111

(no "Pfam Domain" information available for 1CCR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CYC_ORYSJ | Q0DI31)

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: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.
cellular component
	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.

Chain A (CYC_ORYSI | A2Y4S9)

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: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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (3, 4)

Sites (1, 1)

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