1WP0 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   HUMAN SCO1

Authors :   J. C. Williams, C. Sue, G. S. Banting, H. Yang, D. M. Glerum, W. A. Hendrickson, E. A. Schon

Date :   27 Aug 04 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Cu-Binding Protein, Mitochondrial Assembly Factor, Redox, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Williams, C. Sue, G. S. Banting, H. Yang, D. M. Glerum, W. A. Hendrickson, E. A. Schon
Crystal Structure Of Human Sco1: Implications For Redox Signaling By A Mitochondrial Cytochrome C Oxidase "Assembly" Protein
J. Biol. Chem. V. 280 15202 2005
PubMed-ID: 15659396 | Reference-DOI: 10.1074/JBC.M410705200
(for further references see the PDB file header)

Molecule 1 - SCO1 PROTEIN HOMOLOG
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24D
	Expression System Strain	:	BL21-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	IMS FRAGMENT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HSCO1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 11)

No.	Name	Count	Type	Full Name
1	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1WP0)

(no "SS Bond" information available for 1WP0)

(no "Cis Peptide Bond" information available for 1WP0)

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012109	P	174	L	SCO1_HUMAN	Disease (MT-C4D)	104894630	A/B/C	P	174	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012109	P	174	L	SCO1_HUMAN	Disease (MT-C4D)	104894630	A	P	174	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012109	P	174	L	SCO1_HUMAN	Disease (MT-C4D)	104894630	B	P	174	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012109	P	174	L	SCO1_HUMAN	Disease (MT-C4D)	104894630	C	P	174	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1WP0)

Asymmetric Unit (4, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000255390	1a	ENSE00001523689	chr17:10600885-10600552	334	SCO1_HUMAN	1-91	91	0	-	-
1.2	ENST00000255390	2	ENSE00000907744	chr17:10599148-10599058	91	SCO1_HUMAN	92-122	31	0	-	-
1.3b	ENST00000255390	3b	ENSE00000907743	chr17:10596278-10596081	198	SCO1_HUMAN	122-188	67	3	A:138-188 B:137-188 (gaps) C:137-188 (gaps)	51 53 53
1.4	ENST00000255390	4	ENSE00000907742	chr17:10595281-10595189	93	SCO1_HUMAN	188-219	32	3	A:188-219 B:188-219 C:188-219	32 32 32
1.5	ENST00000255390	5	ENSE00000907741	chr17:10590159-10590044	116	SCO1_HUMAN	219-257	39	3	A:219-257 B:219-257 C:219-257	39 39 39
1.6b	ENST00000255390	6b	ENSE00001830664	chr17:10584570-10583654	917	SCO1_HUMAN	258-301	44	3	A:258-297 B:258-297 C:258-297	40 40 40

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:160
 aligned with SCO1_HUMAN | O75880 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:160
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
           SCO1_HUMAN   138 GPFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKMIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKRKGEIAASIATHMRPY 297
               SCOP domains d1wp0a1 A:138-297 Thioredoxin-like protein Sco1 (YpmQ), soluble domain                                                                                           SCOP domains
               CATH domains 1wp0A00 A:138-297 Glutaredoxin                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhh.....eeee.hhhhhhhhhhhh...eee...hhhhh..eee..eeeee.....eeeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------L--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:138-188 UniProt: 122-188         ------------------------------Exon 1.5  PDB: A:219-257               Exon 1.6b  PDB: A:258-297 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.4  PDB: A:188-219        ------------------------------------------------------------------------------ Transcript 1 (2)
                 1wp0 A 138 GPFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKmIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIImYLIGPDGEFLDYFGQNKRKGEIAASIATHmRPY 297
                                   147       157       167       177  |    187       197       207       217       227       237       247       257      |267       277       287      |297
                                                                    180-MSE                                                                             264-MSE                       294-MSE

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with SCO1_HUMAN | O75880 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:162
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
           SCO1_HUMAN   136 LGGPFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKMIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKRKGEIAASIATHMRPY 297
               SCOP domains d1 wp0b_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains -1 wp0B00 B:138-297 Glutaredoxin                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-..eeee....eee.hhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhh.....eeee.hhhhhhhhhhhh...eee..........eee...eeee.....eeeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------L--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:137-188 (gaps) UniProt: 122-188    ------------------------------Exon 1.5  PDB: B:219-257               Exon 1.6b  PDB: B:258-297 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.4  PDB: B:188-219        ------------------------------------------------------------------------------ Transcript 1 (2)
                 1wp0 B 137 mG-PFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKmIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIImYLIGPDGEFLDYFGQNKRKGEIAASIATHmRPY 297
                            || |   145       155       165       175    |  185       195       205       215       225       235       245       255       265       275       285       295  
                            || |                                      180-MSE                                                                             264-MSE                       294-MSE
                          137-MSE                                                                                                                                                             
                           138 |                                                                                                                                                              
                             139

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with SCO1_HUMAN | O75880 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:162
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
           SCO1_HUMAN   136 LGGPFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKMIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIIMYLIGPDGEFLDYFGQNKRKGEIAASIATHMRPY 297
               SCOP domains d1 wp0c_ C: automated matches                                                                                                                                      SCOP domains
               CATH domains -1 wp0C00 C:138-297 Glutaredoxin                                                                                                                                   CATH domains
           Pfam domains (1) ---SCO1-SenC-1wp0C01 C:139-282                                                                                                                     --------------- Pfam domains (1)
           Pfam domains (2) ---SCO1-SenC-1wp0C02 C:139-282                                                                                                                     --------------- Pfam domains (2)
           Pfam domains (3) ---SCO1-SenC-1wp0C03 C:139-282                                                                                                                     --------------- Pfam domains (3)
         Sec.struct. author ..-..eeee....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eee..........eee..eeeee.....eeeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------L--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: C:137-188 (gaps) UniProt: 122-188    ------------------------------Exon 1.5  PDB: C:219-257               Exon 1.6b  PDB: C:258-297 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.4  PDB: C:188-219        ------------------------------------------------------------------------------ Transcript 1 (2)
                 1wp0 C 137 mG-PFSLTTHTGERKTDKDYLGQWLLIYFGFTHCPDVCPEELEKmIQVVDEIDSITTLPDLTPLFISIDPERDTKEAIANYVKEFSPKLVGLTGTREEVDQVARAYRVYYSPGPKDEDEDYIVDHTIImYLIGPDGEFLDYFGQNKRKGEIAASIATHmRPY 297
                            || |   145       155       165       175    |  185       195       205       215       225       235       245       255       265       275       285       295  
                            || |                                      180-MSE                                                                             264-MSE                       294-MSE
                          137-MSE                                                                                                                                                             
                           138 |                                                                                                                                                              
                             139

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: automated matches (46)

Human (Homo sapiens) [TaxId: 9606] (16)

1a	d1wp0b_	B:
1b	d1wp0c_	C:

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

Human (Homo sapiens) [TaxId: 9606] (2)

d1wp0a1

A:138-297

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)

Human (Homo sapiens) (186)

1a	1wp0A00	A:138-297
1b	1wp0B00	B:138-297
1c	1wp0C00	C:138-297

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: SCO1-SenC (7)

Homo sapiens (Human) (2)

1a	SCO1-SenC-1wp0C01	C:139-282
1b	SCO1-SenC-1wp0C02	C:139-282
1c	SCO1-SenC-1wp0C03	C:139-282

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SCO1_HUMAN | O75880)

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: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: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: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:0006091	generation of precursor metabolites and energy	The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
	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.
cellular component
	GO:0072492	host cell mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the host cell mitochondrial envelope.
	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.
	GO:0030016	myofibril	The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.

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Ligands, Modified Residues, Ions (1, 11)

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