3W5V - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CROSS-LINKED COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ REDUCTASE

Authors :   Y. Kimata-Ariga, H. Kubota-Kawai, N. Muraki, T. Hase, G. Kurisu

Date :   06 Feb 13 (Deposition) - 19 Jun 13 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.81

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

Keywords :   Electron Transfer Complex, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kimata-Ariga, H. Kubota-Kawai, Y. -H. Lee, N. Muraki, T. Ikegami, G. Kurisu, T. Hase
Concentration-Dependent Oligomerization Of Cross-Linked Complexes Between Ferredoxin And Ferredoxin-Nadp(+) Reductase
Biochem. Biophys. Res. Commun. V. 434 867 2013
PubMed-ID: 23618857 | Reference-DOI: 10.1016/J.BBRC.2013.04.033

Molecule 1 - FERREDOXIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 42-355
	Gene	:	L-FNRI, ZEAMMB73_343560
	Mutation	:	YES
	Organism Common	:	MAIZE
	Organism Scientific	:	ZEA MAYS
	Organism Taxid	:	4577
	Synonym	:	FERREDOXIN--NADP REDUCTASE, LEAF ISOZYME, FERREDOXINFERREDOXIN--NADP REDUCTASE, LEAF ISOZYME, UNCHARACTERIZED PROTEIN

Molecule 2 - FERREDOXIN-1, CHLOROPLASTIC
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 53-150
	Gene	:	FDX1, PFD1
	Mutation	:	YES
	Organism Common	:	MAIZE
	Organism Scientific	:	ZEA MAYS
	Organism Taxid	:	4577
	Synonym	:	FERREDOXIN I, FD I

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:93 , LEU A:94 , TYR A:95 , SER A:96 , CYS A:114 , LYS A:116 , LEU A:118 , TYR A:120 , GLY A:130 , VAL A:131 , CYS A:132 , SER A:133 , THR A:172 , TYR A:314 , SER B:38	BINDING SITE FOR RESIDUE FAD A 401
2	AC2	SOFTWARE	SER B:38 , CYS B:39 , ARG B:40 , GLY B:42 , SER B:43 , CYS B:44 , CYS B:47 , LEU B:75 , CYS B:77	BINDING SITE FOR RESIDUE FES B 101
3	AC3	SOFTWARE	GLY A:242 , ARG A:244 , ARG C:93 , LEU C:94 , TYR C:95 , SER C:96 , CYS C:114 , VAL C:115 , LYS C:116 , LEU C:118 , TYR C:120 , GLY C:130 , VAL C:131 , CYS C:132 , SER C:133 , THR C:172 , TYR C:314	BINDING SITE FOR RESIDUE FAD C 401
4	AC4	SOFTWARE	SER D:38 , CYS D:39 , ARG D:40 , GLY D:42 , SER D:43 , CYS D:44 , CYS D:47 , LEU D:75 , CYS D:77	BINDING SITE FOR RESIDUE FES D 101

Asymmetric Unit

No.	Residues
1	A:19	-	D:70
2	B:70	-	C:19

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Pro A:150
2	Gly C:149	-	Pro C:150

(no "SAP(SNP)/Variant" information available for 3W5V)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER1_MAIZE	55-145	2	B:3-93 D:3-93
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	FER1_MAIZE	91-99	2	B:39-47 D:39-47

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER1_MAIZE	55-145	1	- D:3-93
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	FER1_MAIZE	91-99	1	- D:39-47

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	FER1_MAIZE	55-145	1	B:3-93 -
2	2FE2S_FER_1	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.	FER1_MAIZE	91-99	1	B:39-47 -

(no "Exon" information available for 3W5V)

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:297
 aligned with Q9SLP6_MAIZE | Q9SLP6 from UniProtKB/TrEMBL  Length:355

    Alignment length:297
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       
         Q9SLP6_MAIZE    59 KESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 355
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeee...ee.........eeeeeee...........eeeee.............eeee.............eeeeeee..eee.....eeehhhhhhhhh.....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.......hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w5v A  18 KCSKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 314
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with FER1_MAIZE | P27787 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:96
                                    62        72        82        92       102       112       122       132       142      
           FER1_MAIZE    53 ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELT 148
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhh................eeeeee..ee.......hhhhhh..eee.hhhee...eeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: B:3-93 UniProt: 55-145                                                   --- PROSITE (1)
                PROSITE (2) --------------------------------------2FE2S_FER------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3w5v B   1 ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQICDGWVLTCHAYPTSDVVIETHKEEELT  96
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:297
 aligned with Q9SLP6_MAIZE | Q9SLP6 from UniProtKB/TrEMBL  Length:355

    Alignment length:297
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       
         Q9SLP6_MAIZE    59 KESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 355
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeee...ee.........eeeeeee...........eeeee.............eeee.............eeeeeee..eee.....eeehhhhhhhhh.....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.......hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w5v C  18 KCSKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 314
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307

Chain D from PDB  Type:PROTEIN  Length:96
 aligned with FER1_MAIZE | P27787 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:96
                                    62        72        82        92       102       112       122       132       142      
           FER1_MAIZE    53 ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELT 148
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhh................eeeeee..ee.......hhhhhhh.eee.hhhee...eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: D:3-93 UniProt: 55-145                                                   --- PROSITE (1)
                PROSITE (2) --------------------------------------2FE2S_FER------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3w5v D   1 ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQICDGWVLTCHAYPTSDVVIETHKEEELT  96
                                    10        20        30        40        50        60        70        80        90

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 3W5V)

(no "CATH Domain" information available for 3W5V)

(no "Pfam Domain" information available for 3W5V)

Asymmetric Unit(hide GO term definitions)

Chain A,C (Q9SLP6_MAIZE | Q9SLP6)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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.

Chain B,D (FER1_MAIZE | P27787)

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.
biological process
	GO:0022900	electron transport chain	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: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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:149 - Pro A:150	[ RasMol ]
		Gly C:149 - Pro C:150	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3w5v
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	FER1_MAIZE \| P27787
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	Q9SLP6_MAIZE \| Q9SLP6
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UniProtKB/Swiss-Prot
	FER1_MAIZE \| P27787	:	1gaq 3b2f 3w5u 5h8y 5h92
UniProtKB/TrEMBL
	Q9SLP6_MAIZE \| Q9SLP6	:	1gaq 1gaw 3w5u

1gaw	FERREDOXIN-NADP+ REDUCTASE
3b2f	FERREDOXIN
3w5u	SIMILAR COMPLEX WITH A DISTINCT CROSS-LINKAGE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (10, 11)

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