1TU2 - JenaLib

Title :   THE COMPLEX OF NOSTOC CYTOCHROME F AND PLASTOCYANIN DETERMIN WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES

Authors :   I. Diaz-Moreno, A. Diaz-Quintana, M. A. De La Rosa, M. Ubbink

Date :   24 Jun 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)
NMR Structure *: A,B  (1x)

Keywords :   Electron Transport, Paramagnetic, Chemical Shift, Complex Formation, Dynamic Complex, Photosynthesis, Pseudocontact Shift, Electron Transport Proteins Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Diaz-Moreno, A. Diaz-Quintana, M. A. De La Rosa, M. Ubbink
Structure Of The Complex Between Plastocyanin And Cytochrom F From The Cyanobacterium Nostoc Sp. Pcc 7119 As Determined By Paramagnetic Nmr. The Balance Between Electrostatic And Hydrophobic Interactions Within The Transient Complex Determines The Relative Orientation Of The Two Proteins.
J. Biol. Chem. V. 280 18908 2005
PubMed-ID: 15705583 | Reference-DOI: 10.1074/JBC.M413298200
(for further references see the PDB file header)

Compounds

Molecule 1 - PLASTOCYANIN
	Cellular Location	:	THYLAKOID LUMEN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	PERIPLASM
	Expression System Plasmid	:	PEAP-WT
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PETE
	Organelle	:	THYLACOID
	Organism Scientific	:	NOSTOC SP.
	Organism Taxid	:	1168
	Strain	:	PCC 7119

Molecule 2 - APOCYTOCHROME F
	Cellular Location	:	THYLAKOID MEMBRANE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	PERIPLASM
	Expression System Plasmid	:	PEAF-WT
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SOLUBLE DOMAIN
	Gene	:	PETA
	Organelle	:	THYLACOID
	Organism Scientific	:	NOSTOC SP.
	Organism Taxid	:	1168
	Strain	:	PCC 7119

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 30)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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_NOSS1 | P46444 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:105
                                    44        54        64        74        84        94       104       114       124       134     
           PLAS_NOSS1    35 ETYTVKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKSADLAKSLSHKQLLMSPGQSTSTTFPADAPAGEYTFYCEPHRGAGMVGKITVAG 139
               SCOP domains d1tu2a1 A:1-105 Plastocyanin                                                                              SCOP domains
               CATH domains 1tu2A00 A:1-105 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --Copper-bind-1tu2A01 A:3-104                                                                           - Pfam domains
         Sec.struct. author ...ee........................eee........eee........hhhhh..............eee.........eeeeeee.hhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1tu2 A   1 ETYTVKLGSDKGLLVFEPAKLTIKPGDTVEFLNNKVPPHNVVFDAALNPAKSADLAKSLSHKQLLMSPGQSTSTTFPADAPAGEYTFYCEPHRGAGMVGKITVAG 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with CYF_NOSS1 | Q93SW9 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:254
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294    
            CYF_NOSS1    45 YPFWAQQTYPETPREPTGRIVCANCHLAAKPTEVEVPQSVLPDTVFKAVVKIPYDTSVQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEELKEEIGDVYFQPYGEDKDNIVIVGPLPGEQYQEIVFPVLSPNPANDKNIHFGKYSVHVGGNRGRGQVYPTGEKSNNNLYSAAATGTISKIAKQEGEDGSVKYLVDIKTESGEVVSDTIPAGPELIVSEGQAVTAGDALTNNPNVGGFGQLDAEIVLQDANR 298
               SCOP domains d1tu2b1 B:1-169,B:236-254 Cytochrome f, large domain                                                                                                                     d1tu2b2 B:170-235 Cytochrome f, small domain                      d1tu2b1             SCOP domains
               CATH domains 1tu2B01 B:1-171,B:234-252  [code=2.60.40.830, no name defined]                                                                                                             1tu2B02 B:172-233  [code=2.40.50.100, no name defined]        1tu2B01            -- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------Apocytochr_F_C-1tu2B01 B:168-254                                                        Pfam domains
         Sec.struct. author hhhhhhhhh...........hhhhhh......eee...ee....eeeeeee........ee.....ee..eeeeeee........hhhhhhhhhhhhh.....ee.......eeeeeeeehhhhheeeeeee..hhhhh......eeeeeeeeee......................eeeeeeeeee....eeeeeeeee....eee..ee............ee.............eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tu2 B   1 YPFWAQQTYPETPREPTGRIVCANCHLAAKPTEVEVPQSVLPDTVFKAVVKIPYDTSVQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEELKEEIGDVYFQPYGEDKDNIVIVGPLPGEQYQEIVFPVLSPNPANDKNIHFGKYSVHVGGNRGRGQVYPTGEKSNNNLYSAAATGTISKIAKQEGEDGSVKYLVDIKTESGEVVSDTIPAGPELIVSEGQAVTAGDALTNNPNVGGFGQLDAEIVLQDANR 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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 (3, 3)

CATH Domains (3, 3)

Pfam Domains (2, 2)

Gene Ontology (12, 18)

NMR Structure(hide GO term definitions)

Chain A (PLAS_NOSS1 | P46444)

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.

Chain B (CYF_NOSS1 | Q93SW9)

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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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: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:0031361	integral component of thylakoid membrane	The component of the thylakoid membrane consisting of the gene products 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: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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