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Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6A FROM ARABIDOPSIS THALIANA

Authors :   H. Chida, T. Yokoyama, F. Kawai, A. Nakazawa, H. Akazaki, Y. Takayama, T K. Suruga, T. Satoh, S. Yamada, R. Kawachi, S. Unzai, T. Nishio, S. -Y. P

Date :   11 Mar 06 (Deposition) - 04 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)
Biol. Unit 5: C  (1x)
Biol. Unit 6: D  (1x)

Keywords :   Cytochrome C6A, Electron Transfer, Heme Exposure, Arabidopsis Thaliana, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Chida, T. Yokoyama, F. Kawai, A. Nakazawa, H. Akazaki, Y. Takayama, T. Hirano, K. Suruga, T. Satoh, S. Yamada, R. Kawachi, S. Unzai, T. Nishio, S. -Y. Park, T. Oku
Crystal Structure Of Oxidized Cytochrome C(6A) From Arabidopsis Thaliana
Febs Lett. V. 580 3763 2006
PubMed-ID: 16777100 | Reference-DOI: 10.1016/J.FEBSLET.2006.05.067

Molecule 1 - CYTOCHROME C6
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSTV28CCM-A-H
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Gene	:	ATC6
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	CYTOCHROME C6 LIKE PROTEIN, SOLUBLE CYTOCHROME F, CYTOCHROME C553, CYTOCHROME C-553, CYTOCHROME C-552, ATC6

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:		B
Biological Unit 5 (1x)	:			C
Biological Unit 6 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 6 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:74 , GLU A:159 , ASP C:74 , LYS C:155 , GLU C:159	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	ASP B:74 , GLU B:159 , ASP D:74 , LYS D:155 , GLU D:159	BINDING SITE FOR RESIDUE ZN B 1002
3	AC3	SOFTWARE	CYS A:86 , CYS A:89 , HIS A:90 , ASN A:95 , ALA A:101 , THR A:102 , LEU A:103 , ASP A:107 , LEU A:108 , ASN A:111 , THR A:123 , LYS A:127 , MET A:130 , HOH A:1005 , HOH A:1010 , HOH A:1025	BINDING SITE FOR RESIDUE HEM A 200
4	AC4	SOFTWARE	ALA B:85 , CYS B:86 , CYS B:89 , HIS B:90 , ASN B:95 , ILE B:97 , GLN B:98 , ALA B:101 , THR B:102 , LEU B:103 , ASP B:107 , LEU B:108 , ASN B:111 , VAL B:113 , THR B:123 , LYS B:127 , MET B:130 , PHE B:133 , HOH B:1009 , HOH B:1020	BINDING SITE FOR RESIDUE HEM B 200
5	AC5	SOFTWARE	ARG A:110 , HOH A:1002 , ALA C:85 , CYS C:86 , CYS C:89 , HIS C:90 , ASN C:95 , ALA C:101 , THR C:102 , LEU C:103 , ASP C:107 , LEU C:108 , ASN C:111 , VAL C:113 , THR C:123 , LYS C:127 , MET C:130 , PHE C:133 , HOH C:223 , GLY D:88 , ILE D:96	BINDING SITE FOR RESIDUE HEM C 200
6	AC6	SOFTWARE	ARG B:110 , HOH B:1012 , HOH B:1038 , ILE C:96 , ALA D:85 , CYS D:86 , CYS D:89 , HIS D:90 , ASN D:95 , ALA D:101 , THR D:102 , LEU D:103 , ASP D:107 , LEU D:108 , ASN D:111 , VAL D:113 , THR D:123 , LYS D:127 , MET D:130 , PHE D:133 , HOH D:207	BINDING SITE FOR RESIDUE HEM D 200

Asymmetric Unit

No.	Residues
1	A:137	-	A:143
2	B:137	-	B:143
3	C:137	-	C:143
4	D:137	-	D:143

Asymmetric Unit

No.	Residues
1	Thr A:138	-	Pro A:139
2	Thr B:138	-	Pro B:139
3	Thr C:138	-	Pro C:139
4	Thr D:138	-	Pro D:139

(no "SAP(SNP)/Variant" information available for 2DGE)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	4	A:73-165 B:73-165 C:73-165 D:73-165

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	4	A:73-165 B:73-165 C:73-165 D:73-165

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	4	A:73-165 B:73-165 C:73-165 D:73-165

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	1	A:73-165 - - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	1	- B:73-165 - -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	1	- - C:73-165 -

Biological Unit 6 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC6_ARATH	73-165	1	- - - D:73-165

(no "Exon" information available for 2DGE)

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:102
 aligned with CYC6_ARATH | Q93VA3 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:102
                                    80        90       100       110       120       130       140       150       160       170  
           CYC6_ARATH    71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPTV 172
               SCOP domains d2dgea_ A: automated matches                                                                           SCOP domains
               CATH domains 2dgeA00 A:71-172 Cytochrome c                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh..hhhhhhhhhhhh............hhhhh......hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --CYTC  PDB: A:73-165 UniProt: 73-165                                                          ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2dge A  71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPTV 172
                                    80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with CYC6_ARATH | Q93VA3 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:102
                                    80        90       100       110       120       130       140       150       160       170  
           CYC6_ARATH    71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPTV 172
               SCOP domains d2dgeb_ B: automated matches                                                                           SCOP domains
               CATH domains 2dgeB00 B:71-172 Cytochrome c                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhee..ee.......hhhhh......hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --CYTC  PDB: B:73-165 UniProt: 73-165                                                          ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2dge B  71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPTV 172
                                    80        90       100       110       120       130       140       150       160       170

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with CYC6_ARATH | Q93VA3 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:102
                                    80        90       100       110       120       130       140       150       160       170  
           CYC6_ARATH    71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPTV 172
               SCOP domains d2dgec_ C: automated matches                                                                           SCOP domains
               CATH domains 2dgeC00 C:71-172 Cytochrome c                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh............hhhhh......hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --CYTC  PDB: C:73-165 UniProt: 73-165                                                          ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2dge C  71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWPTV 172
                                    80        90       100       110       120       130       140       150       160       170

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with CYC6_ARATH | Q93VA3 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:100
                                    80        90       100       110       120       130       140       150       160       170
           CYC6_ARATH    71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWP 170
               SCOP domains d2dged_ D: automated matches                                                                         SCOP domains
               CATH domains 2dgeD00 D:71-170 Cytochrome c                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh............hhhhh......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CYTC  PDB: D:73-165 UniProt: 73-165                                                          ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2dge D  71 QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIYRVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWP 170
                                    80        90       100       110       120       130       140       150       160       170

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: automated matches (31)

Protein domain: automated matches (31)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (4)

1a	d2dgea_	A:
1b	d2dgeb_	B:
1c	d2dgec_	C:
1d	d2dged_	D:

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)

Thale cress (Arabidopsis thaliana) (1)

1a	2dgeA00	A:71-172
1b	2dgeB00	B:71-172
1c	2dgeC00	C:71-172
1d	2dgeD00	D:71-170

(no "Pfam Domain" information available for 2DGE)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CYC6_ARATH | Q93VA3)

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.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009543	chloroplast thylakoid lumen	The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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		Thr D:138 - Pro D:139	[ RasMol ]

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