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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   SOLUTION MODEL OF CROSSLINKED COMPLEX OF CYTOCHROME C AND ADRENODOXIN

Authors :   X. Xu, W. Reinle, F. Hannemann, P. V. Konarev, D. I. Svergun, R. Bernhardt, M. Ubbink

Date :   07 Jun 07 (Deposition) - 22 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Electron Transport, Cytochrome C, Adrenodoxin, Crosslinked Complex, 2Fe2S Ferredoxin, Pseudocontact Shift, Paramagnetic Relaxation Enhancement, Encounter Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xu, W. Reinle, F. Hannemann, P. V. Konarev, D. I. Svergun, R. Bernhardt, M. Ubbink
Dynamics In A Pure Encounter Complex Of Two Proteins Studied By Solution Scattering And Paramagnetic Nmr Spectroscopy
J. Am. Chem. Soc. V. 130 6395 2008
PubMed-ID: 18439013 | Reference-DOI: 10.1021/JA7101357
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME C ISO-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PUCCC
	Gene	:	CYC1
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - ADRENODOXIN, MITOCHONDRIAL
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector	:	PKKHC, PMIXT
	Fragment	:	2FE-2S FERREDOXIN-TYPE DOMAIN, RESIDUES 62-166
	Gene	:	FDX1, ADX
	Mutation	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	ADRENAL FERREDOXIN, FERREDOXIN- 1, HEPATO- FERREDOXIN


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 2)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	HEC	1	Ligand/Ion	HEME C

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:16 , LEU B:30 , GLY B:44 , ALA B:45 , CYS B:46 , GLY B:48 , THR B:49 , CYS B:55	BINDING SITE FOR RESIDUE FES B 109

NMR Structure

No.	Residues
1	A:28	-	B:80

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

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

NMR Structure (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CYC1_YEAST	7-108	1	A:1-101
2	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	ADX_BOVIN	65-169	1	B:7-108
3	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	ADX_BOVIN	104-114	1	B:46-56

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENSBTAT00000015660	2	ENSBTAE00000127216	chr15:18520776-18521119	344	ADX_BOVIN	1-64	64	1	B:6-6	1
1.3	ENSBTAT00000015660	3	ENSBTAE00000127236	chr15:18526683-18526807	125	ADX_BOVIN	64-106	43	1	B:6-48	43
1.4	ENSBTAT00000015660	4	ENSBTAE00000127241	chr15:18545168-18545297	130	ADX_BOVIN	106-149	44	1	B:48-91	44
1.5	ENSBTAT00000015660	5	ENSBTAE00000359886	chr15:18555251-18556187	937	ADX_BOVIN	149-190	42	1	B:91-108	18

2.1	YJR048W	1	YJR048W.1	X:526327-526656	330	CYC1_YEAST	1-109	109	1	A:-4-103	108

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:108
 aligned with CYC1_YEAST | P00044 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
           CYC1_YEAST     2 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE 109
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2jqrA00 A:-4-103 Cytochrome c                                                                                CATH domains
               Pfam domains -------Cytochrom_C-2jqrA01 A:3-101                                                                        -- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh..................................hhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----CYTC  PDB: A:1-101 UniProt: 7-108                                                                     - PROSITE
               Transcript 2 Exon 2.1  PDB: A:-4-103 UniProt: 1-109 [INCOMPLETE]                                                          Transcript 2
                 2jqr A  -4 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKCGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKATE 103
                                     5        15        25        35        45        55        65        75        85        95

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with ADX_BOVIN | P00257 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:103
                                    73        83        93       103       113       123       133       143       153       163   
            ADX_BOVIN    64 KITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVP 166
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2jqrB00 B:6-108  [code=3.10.20.30, no name defined]                                                     CATH domains
               Pfam domains ------Fer2-2jqrB01 B:12-97                                                                  ----------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....hhhhhhhhh...................eee.hhhhhh.....hhhhhhhhh........eee.hhh..hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -2FE2S_FER_2  PDB: B:7-108 UniProt: 65-169                                                              PROSITE (2)
                PROSITE (3) ----------------------------------------ADX        ---------------------------------------------------- PROSITE (3)
           Transcript 1 (1) 1-----------------------------------------Exon 1.4  PDB: B:48-91 UniProt: 106-149     ----------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: B:6-48 UniProt: 64-106      ------------------------------------------Exon 1.5           Transcript 1 (2)
                 2jqr B   6 KITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDCAYGLTDRSRLGCQISLTKAMDNMTVRVP 108
                                    15        25        35        45        55        65        75        85        95       105

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 '\|'

(no "SCOP Domain" information available for 2JQR)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Baker's yeast (Saccharomyces cerevisiae) (4)

2jqrB00

B:6-108

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Baker's yeast (Saccharomyces cerevisiae) (49)

2jqrA00

A:-4-103

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cytochrome-c (108)

Family: Cytochrom_C (54)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (18)

Cytochrom_C-2jqrA01

A:3-101

Clan: Fer2 (69)

Family: Fer2 (60)

Bos taurus (Bovine) (10)

Fer2-2jqrB01

B:12-97

NMR Structure(hide GO term definitions)

Chain A (CYC1_YEAST | P00044)

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: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:0006123	mitochondrial electron transport, cytochrome c to oxygen	The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
	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:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	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:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain B (ADX_BOVIN | P00257)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0042446	hormone biosynthetic process	The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	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.

NMR Structure
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1ayf	RELATED ID: 15301 RELATED DB: BMRB
1ycc

Description

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Ligands, Modified Residues, Ions (2, 2)

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SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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Exons (5, 5)

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