2B7J - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YEAST SCO1 WITH COPPER BOUND

Authors :   C. Abajian, A. C. Rosenzweig

Date :   04 Oct 05 (Deposition) - 11 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Metallochaperone, Cytochrome C Oxidase, Sco, Sco1, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Abajian, A. C. Rosenzweig
Crystal Structure Of Yeast Sco1.
J. Biol. Inorg. Chem. V. 11 459 2006
PubMed-ID: 16570183 | Reference-DOI: 10.1007/S00775-006-0096-7
(for further references see the PDB file header)

Molecule 1 - SCO1 PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3A
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 96-295
	Gene	:	SCO1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CU	6	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:181 , CYS A:216 , CU A:297 , CU A:298	BINDING SITE FOR RESIDUE CU A 296
2	AC2	SOFTWARE	CYS C:181 , HIS C:239 , CU C:297	BINDING SITE FOR RESIDUE CU C 296
3	AC3	SOFTWARE	CYS C:181 , CYS C:216 , CU C:296 , CU C:298	BINDING SITE FOR RESIDUE CU C 297
4	AC4	SOFTWARE	CYS A:181 , HIS A:239 , CU A:296	BINDING SITE FOR RESIDUE CU A 297
5	AC5	SOFTWARE	CYS C:216 , CU C:297	BINDING SITE FOR RESIDUE CU C 298
6	AC6	SOFTWARE	CYS A:216 , CU A:296	BINDING SITE FOR RESIDUE CU A 298

Asymmetric Unit

No.	Residues
1	A:148	-	A:152
2	B:148	-	B:152
3	C:148	-	C:152
4	D:148	-	D:152

(no "Cis Peptide Bond" information available for 2B7J)

(no "SAP(SNP)/Variant" information available for 2B7J)

(no "PROSITE Motif" information available for 2B7J)

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR037C	1	YBR037C.1	II:311451-310564	888	SCO1_YEAST	1-295	295	4	A:111-282 (gaps) B:113-293 C:111-282 (gaps) D:113-293	172 181 172 181

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:158
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:172
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           SCO1_YEAST   111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQR 282
               SCOP domains d2b7ja1 A:111-282 Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                       SCOP domains
               CATH domains 2b7jA00 A:111-282 Glutaredoxin                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh....eeee.hhhhhhhhhhhh...--------------......eeee.....eeeee......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:111-282 (gaps) UniProt: 1-295 [INCOMPLETE]                                                                                                                  Transcript 1
                 2b7j A 111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVY--------------VDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQR 282
                                   120       130       140       150       160       170       180       190       200       210       220 |       -      |240       250       260       270       280  
                                                                                                                                         222            237

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:181
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
           SCO1_YEAST   113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQRAKQKEAWYSFL 293
               SCOP domains d2b7jb_ B: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                                       SCOP domains
               CATH domains ------2b7jB01 B:119-285 Glutaredoxin                                                                                                                                         -------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh.......................eeee.....eeeee....hhhhhhhhhhhhhhh...hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:113-293 UniProt: 1-295 [INCOMPLETE]                                                                                                                                  Transcript 1
                 2b7j B 113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQRAKQKEAWYSFL 293
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:172
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           SCO1_YEAST   111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQR 282
               SCOP domains d2b7jc_ C: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                              SCOP domains
               CATH domains 2b7jC00 C:111-282 Glutaredoxin                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh...--------------......eeee.....eeeee......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:111-282 (gaps) UniProt: 1-295 [INCOMPLETE]                                                                                                                  Transcript 1
                 2b7j C 111 GKPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVY--------------VDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQR 282
                                   120       130       140       150       160       170       180       190       200       210       220 |       -      |240       250       260       270       280  
                                                                                                                                         222            237

Chain D from PDB  Type:PROTEIN  Length:181
 aligned with SCO1_YEAST | P23833 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:181
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
           SCO1_YEAST   113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQRAKQKEAWYSFL 293
               SCOP domains d2b7jd_ D: Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                                                       SCOP domains
               CATH domains ------2b7jD01 D:119-285 Glutaredoxin                                                                                                                                         -------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhh......eeee.hhhhhhhhhhhh.......................eeee.....eeeee....hhhhhhhhhhhhhhh...hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:113-293 UniProt: 1-295 [INCOMPLETE]                                                                                                                                  Transcript 1
                 2b7j D 113 PSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNTLSSKYGITLQPLFITCDPARDSPAVLKEYLSDFHPSILGLTGTFDEVKNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVKSYVPAEQRAKQKEAWYSFL 293
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

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: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione peroxidase-like (136)

Protein domain: Thioredoxin-like protein Sco1 (YpmQ), soluble domain (6)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d2b7ja1	A:111-282
1b	d2b7jb_	B:
1c	d2b7jc_	C:
1d	d2b7jd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Baker's yeast (Saccharomyces cerevisiae) (19)

1a	2b7jA00	A:111-282
1b	2b7jC00	C:111-282
1c	2b7jB01	B:119-285
1d	2b7jD01	D:119-285

(no "Pfam Domain" information available for 2B7J)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SCO1_YEAST | P23833)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008379	thioredoxin peroxidase activity	Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
	GO:0006878	cellular copper ion homeostasis	Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0006825	copper ion transport	The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0008535	respiratory chain complex IV assembly	The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase), the terminal member of the respiratory chain of the mitochondrion and some aerobic bacteria. Cytochrome c oxidases are multi-subunit enzymes containing from 13 subunits in the mammalian mitochondrial form to 3-4 subunits in the bacterial forms.
	GO:0051775	response to redox state	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	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.

Asymmetric Unit
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	2b7j
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	SCO1_YEAST \| P23833	:	2b7k

2b7k	CRYSTAL STRUCTURE OF YEAST SCO1

Description

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Ligands, Modified Residues, Ions (1, 6)

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SS Bonds (4, 4)

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