3KS0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HEME DOMAIN OF FLAVOCYTOCHROME B2 IN COMPLEX WITH FAB B2B4

Authors :   B. Golinelli-Pimpaneau, F. Lederer, K. H. D. Le

Date :   20 Nov 09 (Deposition) - 26 May 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,H,J,K,L
Biol. Unit 1: A,J,K  (1x)
Biol. Unit 2: B,H,L  (1x)

Keywords :   Electron Transfer, Epitope, Domain Mobility, Flavocytochrome B2, Antibody, Fab, Heme Domain, Electron Transport, Flavoprotein, Fmn, Heme, Metal-Binding, Mitochondrion, Oxidoreductase, Respiratory Chain, Transit Peptide, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Diep Le, F. Lederer, B. Golinelli-Pimpaneau
Structural Evidence For The Functional Importance Of The Heme Domain Mobility In Flavocytochrome B2.
J. Mol. Biol. V. 400 518 2010
PubMed-ID: 20546754 | Reference-DOI: 10.1016/J.JMB.2010.05.035
(for further references see the PDB file header)

Molecule 1 - HEME DOMAIN OF FLAVOCYTOCHROME B2
	Chains	:	L, J
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - FRAGMENT ANTIGEN BINDING B2B4
	Chains	:	H, K
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - CYTOCHROME B2, MITOCHONDRIAL
	Chains	:	A, B
	EC Number	:	1.1.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CYB2, YML054C, YM9958.08C
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	L-LACTATE DEHYDROGENASE [CYTOCHROME], L-LACTATE FERRICYTOCHROME C OXIDOREDUCTASE, L-LCR

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	H	J	K	L
Biological Unit 1 (1x)	:	A			J	K
Biological Unit 2 (1x)	:		B	H			L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:29 , PHE A:39 , HIS A:43 , PRO A:44 , VAL A:49 , VAL A:58 , PHE A:62 , LEU A:65 , HIS A:66 , ILE A:71 , TYR A:74 , ILE A:75 , HOH A:276 , SER K:52 , TYR K:53 , LYS L:152 , GLY L:155	BINDING SITE FOR RESIDUE HEM A 101
2	AC2	SOFTWARE	ILE B:29 , PHE B:39 , HIS B:43 , PRO B:44 , GLY B:45 , VAL B:49 , VAL B:58 , PHE B:62 , LEU B:65 , HIS B:66 , TYR B:74 , ILE B:75 , HOH B:325 , TYR H:33 , SER H:52 , TYR H:53 , GLY H:54 , SER H:56 , LYS J:152 , GLY J:155	BINDING SITE FOR RESIDUE HEM B 101

Asymmetric Unit

No.	Residues
1	H:22	-	H:95
2	H:144	-	H:199
3	J:22	-	J:90
4	J:137	-	J:196
5	K:22	-	K:95
6	K:144	-	K:199
7	L:22	-	L:90
8	L:137	-	L:196

Asymmetric Unit

No.	Residues
1	Tyr L:143	-	Pro L:144
2	Phe H:150	-	Pro H:151
3	Glu H:152	-	Pro H:153
4	Trp H:192	-	Pro H:193
5	Tyr J:143	-	Pro J:144
6	Phe K:150	-	Pro K:151
7	Glu K:152	-	Pro K:153
8	Trp K:192	-	Pro K:193
9	Cys K:219	-	Gly K:220

(no "SAP(SNP)/Variant" information available for 3KS0)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_B5_2	PS50255	Cytochrome b5 family, heme-binding domain profile.	CYB2_YEAST	88-165	2	A:8-85 B:8-85
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB2_YEAST	119-126	2	A:39-46 B:39-46

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_B5_2	PS50255	Cytochrome b5 family, heme-binding domain profile.	CYB2_YEAST	88-165	1	A:8-85 -
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB2_YEAST	119-126	1	A:39-46 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_B5_2	PS50255	Cytochrome b5 family, heme-binding domain profile.	CYB2_YEAST	88-165	1	- B:8-85
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB2_YEAST	119-126	1	- B:39-46

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YML054C	1	YML054C.1	XIII:167308-165533	1776	CYB2_YEAST	1-591	591	2	A:6-97 B:6-97	92 92

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:92
 aligned with CYB2_YEAST | P00175 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:92
                                    95       105       115       125       135       145       155       165       175  
           CYB2_YEAST    86 MNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPY 177
               SCOP domains d3ks0a_ A: automated matches                                                                 SCOP domains
               CATH domains 3ks0A00 A:6-97 Flavocytochrome B2, subunit A, domain 1                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh.ee..eeeeee..eeee...hhhhh...hhhhhhhh.eehhhhhhhhh...hhhhhhhhh.eeee.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CYTOCHROME_B5_2  PDB: A:8-85 UniProt: 88-165                                  ------------ PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO--------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:6-97 UniProt: 1-591 [INCOMPLETE]                                            Transcript 1
                 3ks0 A   6 MNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPY  97
                                    15        25        35        45        55        65        75        85        95

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with CYB2_YEAST | P00175 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:92
                                    95       105       115       125       135       145       155       165       175  
           CYB2_YEAST    86 MNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPY 177
               SCOP domains d3ks0b_ B: automated matches                                                                 SCOP domains
               CATH domains 3ks0B00 B:6-97 Flavocytochrome B2, subunit A, domain 1                                       CATH domains
           Pfam domains (1) ----Cyt-b5-3ks0B01 B:10-97                                                                   Pfam domains (1)
           Pfam domains (2) ----Cyt-b5-3ks0B02 B:10-97                                                                   Pfam domains (2)
         Sec.struct. author ......hhhhhh..ee..eeeeee..eeee.hhhhhhh...hhhhhhhh...hhhhhh......hhhhhhhhh.eeee.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CYTOCHROME_B5_2  PDB: B:8-85 UniProt: 88-165                                  ------------ PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO--------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:6-97 UniProt: 1-591 [INCOMPLETE]                                            Transcript 1
                 3ks0 B   6 MNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPY  97
                                    15        25        35        45        55        65        75        85        95

Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ks0H01 H:1-117 Immunoglobulins                                                                                      3ks0H02 H:118-213 Immunoglobulins                                                         ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeeee...eeeeeeeee....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee............eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks0 H   1 EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYGGSTYYNPSLESRISITRDTSKNQYYLQLNSVTTEDTATYFCARLFGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     146       156       166       176       186       196       206       216 
                                                                                                                                                            131|                                                                               
                                                                                                                                                             138

Chain J from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d3ks0j1 J:1-110 automated matches                                                                             d3ks0j2 J:111-212 automated matches                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhh...eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks0 J   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNKRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWDSNHLVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSPA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain K from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ks0K01 K:1-117 Immunoglobulins                                                                                      3ks0K02 K:118-213 Immunoglobulins                                                         ------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee............eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks0 K   1 EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYGGSTYYNPSLESRISITRDTSKNQYYLQLNSVTTEDTATYFCARLFGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     146       156       166       176       186       196       206       216    
                                                                                                                                                            131|                                                                                  
                                                                                                                                                             138

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d3ks0l1 L:1-110 automated matches                                                                             d3ks0l2 L:111-212 automated matches                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks0 L   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNKRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWDSNHLVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSPA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Flavocytochrome B2; Chain A, domain 1 (56)

Homologous Superfamily: Flavocytochrome B2, subunit A, domain 1 (56)

Mouse (Mus musculus) (1)

1a	3ks0A00	A:6-97
1b	3ks0B00	B:6-97

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

2a	3ks0H02	H:118-213
2b	3ks0K02	K:118-213
2c	3ks0H01	H:1-117
2d	3ks0K01	K:1-117

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Cyt-b5] (29)

Family: Cyt-b5 (29)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (9)

1a	Cyt-b5-3ks0B01	B:10-97
1b	Cyt-b5-3ks0B02	B:10-97

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYB2_YEAST | P00175)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0004460	L-lactate dehydrogenase (cytochrome) activity	Catalysis of the reaction: (S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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: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:0006089	lactate metabolic process	The chemical reactions and pathways involving lactate, the anion of lactic acid.
	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:0006626	protein targeting to mitochondrion	The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	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.

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	3ks0
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	CYB2_YEAST \| P00175
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	CYB2_YEAST \| P00175
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	CYB2_YEAST \| P00175	:	1fcb 1kbi 1kbj 1lco 1ldc 1ltd 1qcw 1sze 1szf 1szg 2oz0

1fcb	MOLECULAR STRUCTURE OF FLAVOCYTOCHROME B2 AT 2.4 ANGSTROMS RESOLUTION
1kbi	CRYSTALLOGRAPHIC STUDY OF THE RECOMBINANT FLAVIN-BINDING DOMAIN OF BAKER'S YEAST FLAVOCYTOCHROME B2: COMPARISON WITH THE INTACT WILD-TYPE ENZYME

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (8, 8)

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