3CYT - JenaLib

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Title :   REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

Authors :   T. Takano

Date :   01 Jul 80 (Deposition) - 16 Sep 80 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : I,O
Biol. Unit 1: O  (1x)
Biol. Unit 2: I  (1x)

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

Reference :   T. Takano, R. E. Dickerson
Redox Conformation Changes In Refined Tuna Cytochrome C.
Proc. Natl. Acad. Sci. Usa V. 77 6371 1980
PubMed-ID: 6256733 | Reference-DOI: 10.1073/PNAS.77.11.6371
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C
	Chains	:	O, I
	Engineered	:	YES
	Organism Common	:	ALBACORE
	Organism Scientific	:	THUNNUS ALALUNGA
	Organism Taxid	:	8235

		1	2
Asymmetric Unit	:	I	O
Biological Unit 1 (1x)	:		O
Biological Unit 2 (1x)	:	I

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS O:13 , CYS O:14 , CYS O:17 , HIS O:18 , VAL O:28 , GLY O:29 , PRO O:30 , ARG O:38 , THR O:40 , GLY O:41 , TYR O:46 , TYR O:48 , THR O:49 , ASN O:52 , LYS O:55 , TRP O:59 , TYR O:67 , THR O:78 , LYS O:79 , MET O:80 , PHE O:82 , HOH O:121	BINDING SITE FOR RESIDUE HEM O 104
2	AC2	SOFTWARE	LYS I:13 , CYS I:14 , CYS I:17 , HIS I:18 , VAL I:28 , GLY I:29 , THR I:40 , GLY I:41 , TYR I:46 , TYR I:48 , THR I:49 , ASN I:52 , LYS I:55 , TRP I:59 , TYR I:67 , THR I:78 , LYS I:79 , MET I:80 , PHE I:82 , HOH I:119	BINDING SITE FOR RESIDUE HEM I 104

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_THUAA	1-102	2	I:1-102 O:1-102

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_THUAA	1-102	1	- O:1-102

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC_THUAA	1-102	1	I:1-102 -

(no "Exon" information available for 3CYT)

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
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Chain I from PDB  Type:PROTEIN  Length:104
 aligned with CYC_THUAA | P81459 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:104
                             1                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99    
            CYC_THUAA     - -GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNNDTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 103
               SCOP domains d3cyti_ I: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -3cytI00 I:1-103 Cytochrome c                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: I:1-102 UniProt: 1-102                                                                     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3cyt I   0 xGDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNNDTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 103
                            |        9        19        29        39        49        59        69        79        89        99    
                            |                                                                                                       
                            0-ACE

Chain O from PDB  Type:PROTEIN  Length:104
 aligned with CYC_THUAA | P81459 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:104
                             1                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99    
            CYC_THUAA     - -GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNNDTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 103
               SCOP domains d3cyto_ O: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -3cytO00 O:1-103 Cytochrome c                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: O:1-102 UniProt: 1-102                                                                     - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3cyt O   0 xGDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWNNDTLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS 103
                            |        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 '\|'

Asymmetric 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)

Bluefin tuna (Thunnus thynnus) [TaxId: 8237] (5)

1a	d3cyti_	I:
1b	d3cyto_	O:

Asymmetric 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)

Albacore (Thunnus alalunga) (2)

1a	3cytI00	I:1-103
1b	3cytO00	O:1-103

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

Asymmetric Unit(hide GO term definitions)

Chain I,O (CYC_THUAA | P81459)

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.

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	CYC_THUAA \| P81459	:	1i54 1i55 1lfm 5cyt

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