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Description

Title :   HIGH-RESOLUTION REFINEMENT OF YEAST ISO-1-CYTOCHROME C AND COMPARISONS WITH OTHER EUKARYOTIC CYTOCHROMES C

Authors :   G. V. Louie, G. D. Brayer

Date :   09 May 90 (Deposition) - 15 Jul 91 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.23

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

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

Reference :   G. V. Louie, G. D. Brayer
High-Resolution Refinement Of Yeast Iso-1-Cytochrome C And Comparisons With Other Eukaryotic Cytochromes C.
J. Mol. Biol. V. 214 527 1990
PubMed-ID: 2166169 | Reference-DOI: 10.1016/0022-2836(90)90197-T
(for further references see the PDB file header)

Compounds

Molecule 1 - CYTOCHROME C
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	SO4	2	Ligand/Ion	SULFATE ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:2 , ALA A:3 , LYS A:4 , SER A:47 , LYS A:73 , HOH A:177	BINDING SITE FOR RESIDUE SO4 A 117
2	AC2	SOFTWARE	ARG A:13 , CYS A:14 , CYS A:17 , HIS A:18 , GLY A:23 , VAL A:28 , 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 , THR A:78 , LYS A:79 , MET A:80 , PHE A:82 , LEU A:98 , HOH A:134 , HOH A:181	BINDING SITE FOR RESIDUE HEM A 118

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC1_YEAST	7-108	1	A:1-102

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC1_YEAST	7-108	2	A:1-102

Exons (1, 1)

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJR048W	1	YJR048W.1	X:526327-526656	330	CYC1_YEAST	1-109	109	1	A:-5-103	108

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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 A from PDB  Type:PROTEIN  Length:108
 aligned with CYC1_YEAST | P00044 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
           CYC1_YEAST     2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
               SCOP domains d1ycca_ A: Mitochondrial cytochrome c                                                                        SCOP domains
               CATH domains 1yccA00 A:-5-103 Cytochrome c                                                                                CATH domains
               Pfam domains -------Cytochrom_C-1yccA01 A:3-101                                                                        -- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh......................eeee........hhhhhhh.eeehhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----CYTC  PDB: A:1-102 UniProt: 7-108                                                                     - PROSITE
               Transcript 1 Exon 1.1  PDB: A:-5-103 UniProt: 1-109 [INCOMPLETE]                                                          Transcript 1
                 1ycc A  -5 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPkKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 103
                                ||   5        15        25        35        45        55        65      | 75        85        95        
                               -1|                                                                     72-M3L                           
                                 1

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, 1)

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)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (49)

d1ycca_

CATH Domains (1, 1)

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)

Baker's yeast (Saccharomyces cerevisiae) (49)

1yccA00

A:-5-103

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cytochrome-c (108)

Family: Cytochrom_C (54)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (18)

Cytochrom_C-1yccA01

A:3-101

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (CYC1_YEAST | P00044)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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	1ycc
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	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 1yfc 1yic 2b0z 2b10 2b11 2b12 2bcn 2gb8 2hv4 2jqr 2jti 2lir 2lit 2mhm 2n18 2orl 2pcc 2ycc 3cx5 3tyi 4mu8 4n0k 4p4q 4q5p 4qao 4ye1 5cib 5cic 5cid 5cie 5cif 5cig 5cih 5kke 5klu 5kpf 5lft 5lyc 5t7h

Related Entries Specified in the PDB File

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