1B5B - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Title :   RAT FERROCYTOCHROME B5 B CONFORMATION, NMR, 1 STRUCTURE

Authors :   B. Dangi, S. Sarma, C. Yan, D. Banville, R. D. Guiles

Date :   06 Apr 98 (Deposition) - 17 Jun 98 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

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

Reference :   B. Dangi, S. Sarma, C. Yan, D. L. Banville, R. D. Guiles
The Origin Of Differences In The Physical Properties Of The Equilibrium Forms Of Cytochrome B5 Revealed Through High-Resolution Nmr Structures And Backbone Dynamic Analyses.
Biochemistry V. 37 8289 1998
PubMed-ID: 9622481 | Reference-DOI: 10.1021/BI9801964
(for further references see the PDB file header)

Molecule 1 - FERROCYTOCHROME B5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21
	Expression System Plasmid	:	PET3C
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	HEME AS PROSTHETIC GROUP, WITH H63 AND H39 AS AXIAL LIGANDS


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

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

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:23 , PHE A:35 , HIS A:39 , PRO A:40 , GLY A:41 , VAL A:45 , LEU A:46 , ALA A:54 , ASN A:57 , VAL A:61 , HIS A:63 , SER A:64 , SER A:71	BINDING SITE FOR RESIDUE HEM A 95

(no "SS Bond" information available for 1B5B)

(no "Cis Peptide Bond" information available for 1B5B)

(no "SAP(SNP)/Variant" information available for 1B5B)

NMR Structure (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.	CYB5_RAT	9-85	1	A:4-80
2	CYTOCHROME_B5_1	PS00191	Cytochrome b5 family, heme-binding domain signature.	CYB5_RAT	40-47	1	A:35-42

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000020446	1	ENSRNOE00000145553	chr18:81415962-81416156	195	CYB5_RAT	1-43	43	1	A:1-38	38
1.2	ENSRNOT00000020446	2	ENSRNOE00000218963	chr18:81434867-81434995	129	CYB5_RAT	44-86	43	1	A:39-81	43
1.3	ENSRNOT00000020446	3	ENSRNOE00000145848	chr18:81436683-81436712	30	CYB5_RAT	87-96	10	1	A:82-91	10
1.5	ENSRNOT00000020446	5	ENSRNOE00000145949	chr18:81449591-81449625	35	CYB5_RAT	97-108	12	1	A:92-94	3
1.6	ENSRNOT00000020446	6	ENSRNOE00000145993	chr18:81452246-81452606	361	CYB5_RAT	108-134	27	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:94
 aligned with CYB5_RAT | P00173 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:94
                                    15        25        35        45        55        65        75        85        95    
              CYB5_RAT    6 DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELHPDDRSKIAKPSETL 99
               SCOP domains d1b5ba_ A: Cytochrome b5                                                                       SCOP domains
               CATH domains 1b5bA00 A:1-94 Flavocytochrome B2, subunit A, domain 1                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ....eee.hhhh........eeeee.eeeeeehhhhhh.....hhhh...--hhhhhhhh....hhhhhhh..eeeeeeehhhhhh........ Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------eeee---------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYTOCHROME_B5_2  PDB: A:4-80 UniProt: 9-85                                   -------------- PROSITE (1)
                PROSITE (2) ----------------------------------CYTOCHRO---------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-38 UniProt: 1-43   Exon 1.2  PDB: A:39-81 UniProt: 44-86      Exon 1.3  1.5 Transcript 1
                  1b5b A  1 DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELHPDDRSKIAKPSETL 94
                                    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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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)

d1b5ba_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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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)

1b5bA00

A:1-94

(no "Pfam Domain" information available for 1B5B)

NMR Structure(hide GO term definitions)

Chain A (CYB5_RAT | P00173)

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:0019899	enzyme binding	Interacting selectively and non-covalently with any 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.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
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:0046686	response to cadmium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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: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:0031090	organelle membrane	A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

NMR Structure
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	CYB5_RAT \| P00173	:	1aqa 1aw3 1axx 1b5a 1bfx 1blv 1i87 1i8c 1ib7 1iet 1ieu 1jex 1mny 2axx

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