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Title :   2A RESOLUTION STRUCTURE OF RAT TYPE B CYTOCHROME B5

Authors :   S. Terzyan, X. Zhang, D. R. Benson

Date :   03 May 10 (Deposition) - 13 Apr 11 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Cytochrome B5, Heme, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Parthasarathy, A. Altuve, S. Terzyan, X. Zhang, K. Kuczera, M. Rivera, D. R. Benson
Accommodating A Non-Conservative Internal Mutation By Water-Mediated Hydrogen-Bonding Between Beta-Sheet Strands: A Comparison Of Human And Rat Type B (Mitochondrial) Cytochrome B5
Biochemistry V. 50 5544 2011
PubMed-ID: 21574570 | Reference-DOI: 10.1021/BI2004729

Molecule 1 - CYTOCHROME B5 TYPE B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 17-102
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

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:32 , PHE A:35 , HIS A:39 , PRO A:40 , GLY A:41 , LEU A:46 , SER A:57 , VAL A:61 , HIS A:63 , SER A:64 , ALA A:67 , LEU A:71 , HOH A:128 , SER B:64 , PRO B:65 , ARG B:68	BINDING SITE FOR RESIDUE HEM A 201
2	AC2	SOFTWARE	ILE B:32 , ARG B:34 , PHE B:35 , HIS B:39 , PRO B:40 , VAL B:45 , LEU B:46 , VAL B:61 , HIS B:63 , SER B:64 , ALA B:67 , LEU B:71 , HOH B:88 , HOH B:162 , HOH B:169	BINDING SITE FOR RESIDUE HEM B 201

(no "SS Bond" information available for 3MUS)

(no "Cis Peptide Bond" information available for 3MUS)

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

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.	CYB5B_RAT	20-96	2	A:4-80 B:4-80
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5B_RAT	51-58	2	A:35-42 B:35-42

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.	CYB5B_RAT	20-96	1	A:4-80 -
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5B_RAT	51-58	1	A:35-42 -

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.	CYB5B_RAT	20-96	1	- B:4-80
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5B_RAT	51-58	1	- B:35-42

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000015006	1	ENSRNOE00000104782	chr19:37016959-37017126	168	CYB5B_RAT	1-54	54	2	A:2-38 B:1-38	37 38
1.2	ENSRNOT00000015006	2	ENSRNOE00000105131	chr19:37036324-37036452	129	CYB5B_RAT	55-97	43	2	A:39-81 B:39-81	43 43
1.3	ENSRNOT00000015006	3	ENSRNOE00000105523	chr19:37036904-37036933	30	CYB5B_RAT	98-107	10	2	A:82-86 B:82-87	5 6
1.4	ENSRNOT00000015006	4	ENSRNOE00000105590	chr19:37045457-37045485	29	CYB5B_RAT	108-117	10	0	-	-
1.5	ENSRNOT00000015006	5	ENSRNOE00000295386	chr19:37048353-37050718	2366	CYB5B_RAT	117-146	30	0	-	-

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:85
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:85
                                    27        37        47        57        67        77        87        97     
            CYB5B_RAT    18 PAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKP 102
               SCOP domains d3musa_ A: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhh..ee..eeeeee..eeee.hhhh......hhhhhh.....hhhhhhhhh.hhhhhhhhh..eeeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CYTOCHROME_B5_2  PDB: A:4-80 UniProt: 20-96                                  ------ PROSITE (1)
                PROSITE (2) ---------------------------------CYTOCHRO-------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-38 UniProt: 1-54  Exon 1.2  PDB: A:39-81 UniProt: 55-97      1.3   Transcript 1
                 3mus A   2 PAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKP  86
                                    11        21        31        41        51        61        71        81

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:87
                                    26        36        46        56        66        76        86        96       
            CYB5B_RAT    17 DPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK 103
               SCOP domains d3musb_ B: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Cyt-b5-3musB01 B:6-80                                                      ------- Pfam domains (1)
           Pfam domains (2) -----Cyt-b5-3musB02 B:6-80                                                      ------- Pfam domains (2)
         Sec.struct. author .....eehhhhhhh.ee..eeeeee..eeee.hhhhhhh...hhhhhhh....hhhhhhhhh.hhhhhhhhh..eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYTOCHROME_B5_2  PDB: B:4-80 UniProt: 20-96                                  ------- PROSITE (1)
                PROSITE (2) ----------------------------------CYTOCHRO--------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:1-38 UniProt: 1-54   Exon 1.2  PDB: B:39-81 UniProt: 55-97      1.3    Transcript 1
                 3mus B   1 DPAVTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPA  87
                                    10        20        30        40        50        60        70        80

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cytochrome b5-like heme/steroid binding domain (64)

Superfamily: Cytochrome b5-like heme/steroid binding domain (64)

Family: Cytochrome b5 (57)

Protein domain: automated matches (10)

Norway rat (Rattus norvegicus) [TaxId: 10116] (3)

1a	d3musa_	A:
1b	d3musb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Cyt-b5 (29)

Rattus norvegicus (Rat) (4)

1a	Cyt-b5-3musB01	B:6-80
1b	Cyt-b5-3musB02	B:6-80

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYB5B_RAT | P04166)

molecular function
	GO:0045153	electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity	Enables the directed movement of electrons within the CoQH2-cytochrome c reductase complex.
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	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.
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:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer 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.

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	CYB5B_RAT \| P04166	:	1awp 1b5m 1eue 1icc 1lj0 2i89 4hil

1icc	RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 TRIPLE MUTANT
1ljo	STRUCTURE OF QUINTUPLE MUTANT OF THE RAT OUTER MITOCONDRIAL CYTOCHROME B5.
2i89	STRUCTURE OF SEPTUPLE MUTANT OF RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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