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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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

Authors :   M. Ubbink, M. Ejdeback, B. G. Karlsson, D. S. Bendall

Date :   22 Dec 97 (Deposition) - 08 Apr 98 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

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

Reference :   M. Ubbink, M. Ejdeback, B. G. Karlsson, D. S. Bendall
The Structure Of The Complex Of Plastocyanin And Cytochrome F, Determined By Paramagnetic Nmr And Restrained Rigid-Body Molecular Dynamics.
Structure V. 6 323 1998
PubMed-ID: 9551554 | Reference-DOI: 10.1016/S0969-2126(98)00035-5
(for further references see the PDB file header)

Molecule 1 - PLASTOCYANIN
	Cellular Location	:	THYLAKOID LUMEN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Cellular Location	:	PERIPLASM
	Expression System Gene	:	PETE
	Expression System Plasmid	:	PSY2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Gene	:	PETE
	Organelle	:	CHLOROPLAST
	Organism Common	:	SPINACH
	Organism Scientific	:	SPINACIA OLERACEA
	Organism Taxid	:	3562

Molecule 2 - CYTOCHROME F
	Cellular Location	:	THYLAKOID MEMBRANE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Gene	:	PETE
	Expression System Plasmid	:	PSY2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	SOLUBLE DOMAIN
	Gene	:	PETE
	Organelle	:	CHLOROPLAST
	Organism Scientific	:	BRASSICA RAPA
	Organism Taxid	:	3711


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 2)

No.	Name	Count	Type	Full Name
1	CU	1	Ligand/Ion	COPPER (II) ION
2	HEC	1	Ligand/Ion	HEME C

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:36 , HIS A:37 , CYS A:84 , HIS A:87 , MET A:92	BINDING SITE FOR RESIDUE CU A 100
2	AC2	SOFTWARE	SER A:85 , PRO A:86 , HIS A:87 , GLN A:88 , TYR B:1 , ALA B:5 , CYS B:21 , CYS B:24 , HIS B:25 , GLN B:59 , ASN B:70 , VAL B:71 , GLY B:72 , ASN B:153 , GLY B:155 , ARG B:156 , GLY B:157 , ILE B:159 , TYR B:160	BINDING SITE FOR RESIDUE HEC B 251

(no "SS Bond" information available for 2PCF)

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10	Leu A:15	-	Pro A:16
2	1, 2, 3, 4, 5, 6, 7, 8, 9, 10	Phe A:35	-	Pro A:36
3	1, 2, 3, 4, 5, 6, 7, 8, 9, 10	Gly B:116	-	Pro B:117

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_SPIOL	147-161	1	A:78-92

(no "Exon" information available for 2PCF)

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:99
 aligned with PLAS_SPIOL | P00289 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:99
                                    79        89        99       109       119       129       139       149       159         
           PLAS_SPIOL    70 VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN 168
               SCOP domains d2pcfa_ A: Cytochrome f-plastocyanin complex                                                        SCOP domains
               CATH domains 2pcfA00 A:1-99 Cupredoxins -  blue copper proteins                                                  CATH domains
               Pfam domains Copper-bind-2pcfA01 A:1-99                                                                          Pfam domains
         Sec.struct. author .eeee.............eee......eeee.......eee..........hhhh..........................eee...........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2pcf A   1 VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN  99
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with CYF_BRARR | P36438 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:250
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
            CYF_BRARR    36 YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR 285
               SCOP domains d2pcfb_ B: Cytochrome f-plastocyanin complex                                                                                                                                                                                                               SCOP domains
               CATH domains 2pcfB01 B:1-170,B:230-250  [code=2.60.40.830, no name defined]                                                                                                            2pcfB02 B:171-229  [code=2.40.50.100, no name defined]     2pcfB01               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.........hhhhhhh....eeeeeeeeee...eeeeeeeee.......eee...eee..eeeeeeee....eee.....hhhhhhhh.....eee.....eeeeeeee.....eeeeeeeee...........eeeeeeeeeeee..eee...eee.........eeee.eeeee...eeeeeeee....eeeeeeee..........eeee...........eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcf B   1 YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR 250
                                    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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Low resolution protein structures (283)

Fold: Electron transport chains (4)

Superfamily: Electron transport chains (4)

Family: Electron transport chains (4)

Protein domain: Cytochrome f-plastocyanin complex (2)

Plant (Spinacia oleracea) and (Brassica rapa) [TaxId: 3562] (1)

1a	d2pcfa_	A:
1b	d2pcfb_	B:

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Spinacia oleracea (Spinach) (5)

Copper-bind-2pcfA01

A:1-99

NMR Structure(hide GO term definitions)

Chain A (PLAS_SPIOL | P00289)

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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Chain B (CYF_BRARR | P36438)

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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	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: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.

NMR Structure
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	Cis Peptide Bonds
		Gly B:116 - Pro B:117	[ RasMol ]
		Leu A:15 - Pro A:16	[ RasMol ]
		Phe A:35 - Pro A:36	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 2PCF)

Description

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Ligands, Modified Residues, Ions (2, 2)

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