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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5

Authors :   S. Terzyan, X. Zhang

Date :   30 Mar 01 (Deposition) - 19 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: B (1x),C (1x)

Keywords :   Cytochrome, X-Ray Diffraction, Heme, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Altuve, S. Silchenko, K. H. Lee, K. Kuczera, S. Terzyan, X. Zhang, D. R. Benson, M. Rivera
Probing The Differences Between Rat Liver Outer Mitochondrial Membrane Cytochrome B5 And Microsomal Cytochromes B5.
Biochemistry V. 40 9469 2001
PubMed-ID: 11583146 | Reference-DOI: 10.1021/BI010636I
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
	Cell	:	HEPATOCYTE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET 11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	WATER SOLUBLE DOMAIN
	Mutation	:	YES
	Organ	:	LIVER
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:		B (1x)	C (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 1)

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

Biological Unit 5 (1, 1)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:202 , HOH B:202 , HOH B:203 , HOH C:202 , HOH C:203 , HOH C:204	BINDING SITE FOR RESIDUE MG A 88
2	AC2	SOFTWARE	HOH A:203 , HOH A:204 , GLU C:69 , HOH C:205 , HOH C:206 , HOH D:202 , HOH D:203	BINDING SITE FOR RESIDUE MG C 88
3	AC3	SOFTWARE	HOH A:205 , HOH A:206 , HOH A:207 , HOH A:208 , HOH A:209 , HOH A:210	BINDING SITE FOR RESIDUE MG A 89
4	AC4	SOFTWARE	ASP A:1 , PRO A:2 , MET A:23 , PHE A:35 , HIS A:39 , PRO A:40 , GLY A:41 , VAL A:45 , LEU A:46 , PHE A:58 , VAL A:61 , HIS A:63 , SER A:64 , MET A:70 , LEU A:71 , HOH A:227	BINDING SITE FOR RESIDUE HEM A 201
5	AC5	SOFTWARE	PHE B:35 , HIS B:39 , PRO B:40 , GLY B:41 , VAL B:45 , LEU B:46 , PHE B:58 , VAL B:61 , HIS B:63 , SER B:64 , ALA B:67 , MET B:70 , LEU B:71 , SER C:57 , HEM C:201	BINDING SITE FOR RESIDUE HEM B 201
6	AC6	SOFTWARE	PRO B:40 , GLY B:42 , GLU B:43 , GLU B:44 , HEM B:201 , MET C:23 , ILE C:25 , PHE C:35 , HIS C:39 , PRO C:40 , GLY C:41 , VAL C:45 , LEU C:46 , PHE C:58 , VAL C:61 , HIS C:63 , SER C:64 , ALA C:67 , MET C:70 , LEU C:71 , HOH C:207 , HOH C:219 , HOH C:225	BINDING SITE FOR RESIDUE HEM C 201
7	AC7	SOFTWARE	PHE D:35 , HIS D:39 , PRO D:40 , GLY D:41 , VAL D:45 , LEU D:46 , GLN D:49 , PHE D:58 , VAL D:61 , HIS D:63 , SER D:64 , ALA D:67 , MET D:70 , LEU D:71 , HOH D:244	BINDING SITE FOR RESIDUE HEM D 201

(no "SS Bond" information available for 1ICC)

(no "Cis Peptide Bond" information available for 1ICC)

(no "SAP(SNP)/Variant" information available for 1ICC)

Asymmetric Unit (2, 8)

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

Biological Unit 3 (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	- - C:4-80 -
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5B_RAT	51-58	1	- - C:35-42 -

Biological Unit 4 (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	- - - D:4-80
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5B_RAT	51-58	1	- - - D:35-42

Biological Unit 5 (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	- B:4-80 C:4-80 -
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5B_RAT	51-58	2	- B:35-42 C:35-42 -

Asymmetric Unit (3, 12)

	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	4	A:1-38 B:1-38 C:4-38 D:1-38	38 38 35 38
1.2	ENSRNOT00000015006	2	ENSRNOE00000105131	chr19:37036324-37036452	129	CYB5B_RAT	55-97	43	4	A:39-81 B:39-81 C:39-81 D:39-81	43 43 43 43
1.3	ENSRNOT00000015006	3	ENSRNOE00000105523	chr19:37036904-37036933	30	CYB5B_RAT	98-107	10	4	A:82-87 B:82-87 C:82-86 D:82-87	6 6 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: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 d1icca_ A: Cytochrome b5                                                                SCOP domains
               CATH domains 1iccA00 A:1-87 Flavocytochrome B2, subunit A, domain 1                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhh..ee..eeeeee..eeee...hhhhh...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:1-38 UniProt: 1-54   Exon 1.2  PDB: A:39-81 UniProt: 55-97      1.3    Transcript 1
                 1icc A   1 DPAVTYYRLEEVAKRNTSEETWMVIHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK  87
                                    10        20        30        40        50        60        70        80

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 d1iccb_ B: Cytochrome b5                                                                SCOP domains
               CATH domains 1iccB00 B:1-87 Flavocytochrome B2, subunit A, domain 1                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhh.......eeee..eeee...........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
                 1icc B   1 DPAVTYYRLEEVAKRNTSEETWMVIHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK  87
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:83
 aligned with CYB5B_RAT | P04166 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:83
                                    29        39        49        59        69        79        89        99   
            CYB5B_RAT    20 VTYYRLEEVAKRNTAEETWMVIHGRVYDITRFLSEHPGGEEVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKP 102
               SCOP domains d1iccc_ C: Cytochrome b5                                                            SCOP domains
               CATH domains 1iccC00 C:4-86 Flavocytochrome B2, subunit A, domain 1                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhh........eeee..eeee.hhhhhhh...hhhhhhh....hhhhhhhhh.hhhhhhhh...eeeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYTOCHROME_B5_2  PDB: C:4-80 UniProt: 20-96                                  ------ PROSITE (1)
                PROSITE (2) -------------------------------CYTOCHRO-------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:4-38 UniProt: 1-54Exon 1.2  PDB: C:39-81 UniProt: 55-97      1.3   Transcript 1
                 1icc C   4 VTYYRLEEVAKRNTSEETWMVIHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKP  86
                                    13        23        33        43        53        63        73        83

Chain D 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 d1iccd_ D: Cytochrome b5                                                                SCOP domains
               CATH domains 1iccD00 D:1-87 Flavocytochrome B2, subunit A, domain 1                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhee..eeeeee..eeee...........hhhhhhhh...hhhhhhhh..hhhhhhhhh..eeeee.hhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYTOCHROME_B5_2  PDB: D:4-80 UniProt: 20-96                                  ------- PROSITE (1)
                PROSITE (2) ----------------------------------CYTOCHRO--------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:1-38 UniProt: 1-54   Exon 1.2  PDB: D:39-81 UniProt: 55-97      1.3    Transcript 1
                 1icc D   1 DPAVTYYRLEEVAKRNTSEETWMVIHGRVYDLTRFLSEHPGGEEVLREQAGADATESFEDVGHSPDAREMLKQYYIGDVHPNDLKPK  87
                                    10        20        30        40        50        60        70        80

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	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: Cytochrome b5 (38)

Norway rat (Rattus norvegicus) [TaxId: 10116] (20)

1a	d1icca_	A:
1b	d1iccb_	B:
1c	d1iccc_	C:
1d	d1iccd_	D:

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)

Norway rat (Rattus norvegicus) (20)

1a	1iccA00	A:1-87
1b	1iccB00	B:1-87
1c	1iccD00	D:1-87
1d	1iccC00	C:4-86

(no "Pfam Domain" information available for 1ICC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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 1lj0 2i89 3mus 4hil

1awp	1AWP IS RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
1b5m	1B5M IS RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5

Description

Compounds

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Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

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