3CVB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   REGULATION OF PROTEIN FUNCTION: CRYSTAL PACKING INTERFACES AND CONFORMATIONAL DIMERIZATION

Authors :   P. B. Crowley, P. M. Matias, H. Mi, S. J. Firbank, M. J. Banfield, C. Dennison

Date :   18 Apr 08 (Deposition) - 08 Jul 08 (Release) - 21 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Cupredoxin, Self Assembly, Copper, Electron Transport, Metal-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. B. Crowley, P. M. Matias, H. Mi, S. J. Firbank, M. J. Banfield, C. Dennison
Regulation Of Protein Function: Crystal Packing Interfaces And Conformational Dimerization.
Biochemistry V. 47 6583 2008
PubMed-ID: 18479147 | Reference-DOI: 10.1021/BI800125H
(for further references see the PDB file header)

Molecule 1 - PLASTOCYANIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	PETE
	Organism Scientific	:	PHORMIDIUM LAMINOSUM
	Organism Taxid	:	32059

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CU1	2	Ligand/Ion	COPPER (I) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CU1	1	Ligand/Ion	COPPER (I) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CU1	1	Ligand/Ion	COPPER (I) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:39 , CYS A:89 , HIS A:92 , MET A:97	BINDING SITE FOR RESIDUE CU1 A 106
2	AC2	SOFTWARE	HIS B:39 , CYS B:89 , HIS B:92 , MET B:97	BINDING SITE FOR RESIDUE CU1 B 106

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

Asymmetric Unit

No.	Residues
1	Glu A:17	-	Pro A:18
2	Pro A:37	-	Pro A:38
3	Glu B:17	-	Pro B:18
4	Pro B:37	-	Pro B:38

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_PHOLA	116-131	2	A:82-97 B:82-97

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_PHOLA	116-131	1	A:82-97 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_PHOLA	116-131	1	- B:82-97

(no "Exon" information available for 3CVB)

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:105
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:105
                                    44        54        64        74        84        94       104       114       124       134     
           PLAS_PHOLA    35 ETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d3cvba_ A: Plastocyanin                                                                                   SCOP domains
               CATH domains 3cvbA00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........ee..eeee...eeeeeee.....eeeee....hhhhhhhhhhhhheeeee.....eeeeee......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3cvb A   1 ETFTVKMGADSGLFQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:105
                                    44        54        64        74        84        94       104       114       124       134     
           PLAS_PHOLA    35 ETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d3cvbb_ B: Plastocyanin                                                                                   SCOP domains
               CATH domains 3cvbB00 B:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........ee..eeee....eeeeee.....eeeee.hhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3cvb B   1 ETFTVKMGADSGLFQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                    10        20        30        40        50        60        70        80        90       100

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 beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Plastocyanin (56)

Phormidium laminosum [TaxId: 32059] (8)

1a	d3cvba_	A:
1b	d3cvbb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Phormidium laminosum. Organism_taxid: 32059. (3)

1a	3cvbA00	A:1-105
1b	3cvbB00	B:1-105

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PLAS_PHOLA | Q51883)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

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		Glu B:17 - Pro B:18	[ RasMol ]
		Pro A:37 - Pro A:38	[ RasMol ]
		Pro B:37 - Pro B:38	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	PLAS_PHOLA \| Q51883	:	1baw 2q5b 2w88 2w8c 3bqv 3cvc 3cvd 4r0o

Description

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