1EFV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THREE-DIMENSIONAL STRUCTURE OF HUMAN ELECTRON TRANSFER FLAVOPROTEIN TO 2.1 A RESOLUTION

Authors :   D. L. Roberts, F. E. Frerman, J. J. P. Kim

Date :   16 Oct 96 (Deposition) - 03 Dec 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Electron Transport, Flavoprotein, Glutaric Acidemia Type Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. L. Roberts, F. E. Frerman, J. J. Kim
Three-Dimensional Structure Of Human Electron Transfer Flavoprotein To 2. 1-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 93 14355 1996
PubMed-ID: 8962055 | Reference-DOI: 10.1073/PNAS.93.25.14355
(for further references see the PDB file header)

Molecule 1 - ELECTRON TRANSFER FLAVOPROTEIN
	Cellular Location	:	MITOCHONDRIA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBLUESCRIPT SK+
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	COFACTORS FAD 1 AND AMP 1 ARE NON- COVALENTLY BOUND
	Synonym	:	ETF, HETF, ELECTRON TRANSFERRING FLAVOPROTEIN

Molecule 2 - ELECTRON TRANSFER FLAVOPROTEIN
	Cellular Location	:	MITOCHONDRIA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBLUESCRIPT SK+
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	COFACTORS FAD 1 AND AMP 1 ARE NON- COVALENTLY BOUND
	Synonym	:	ETF, HETF, ELECTRON TRANSFERRING FLAVOPROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:222 , ARG A:223 , GLY A:224 , LYS A:226 , SER A:248 , ARG A:249 , ALA A:250 , GLN A:262 , VAL A:263 , GLY A:264 , GLN A:265 , THR A:266 , GLY A:267 , GLY A:279 , ILE A:280 , SER A:281 , GLN A:285 , HIS A:286 , ASN A:300 , LYS A:301 , ASP A:302 , ALA A:317 , ASP A:318 , LEU A:319 , PHE A:320 , HOH A:1001 , HOH A:1102 , HOH A:1103 , HOH A:1166 , HOH A:1206 , HOH A:1251 , TYR B:16	BINDING SITE FOR RESIDUE FAD A 599
2	AC2	SOFTWARE	ALA B:9 , VAL B:10 , LYS B:11 , ASN B:39 , CYS B:42 , CYS B:66 , VAL B:104 , LEU B:122 , GLY B:123 , GLN B:125 , ALA B:126 , ASP B:129 , CYS B:131 , ASN B:132 , GLN B:133 , THR B:134 , HOH B:1017	BINDING SITE FOR RESIDUE AMP B 600

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

Asymmetric/Biological Unit

No.	Residues
1	Leu B:177	-	Pro B:178

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002366	G	116	R	ETFA_HUMAN	Disease (GA2A)	119458971	A	G	116	R
2	UniProt	VAR_025804	D	128	N	ETFB_HUMAN	Disease (GA2B)	104894678	B	D	128	N
3	UniProt	VAR_008548	T	154	M	ETFB_HUMAN	Polymorphism	1130426	B	T	154	M
4	UniProt	VAR_002367	V	157	G	ETFA_HUMAN	Disease (GA2A)	119458969	A	V	157	G
5	UniProt	VAR_002369	R	164	Q	ETFB_HUMAN	Disease (GA2B)	104894677	B	R	164	Q
6	UniProt	VAR_008547	T	171	I	ETFA_HUMAN	Polymorphism	1801591	A	T	171	I
7	UniProt	VAR_002368	T	266	M	ETFA_HUMAN	Disease (GA2A)	119458970	A	T	266	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETF_BETA	PS01065	Electron transfer flavoprotein beta-subunit signature.	ETFB_HUMAN	162-182	1	B:162-182
2	ETF_ALPHA	PS00696	Electron transfer flavoprotein alpha-subunit signature.	ETFA_HUMAN	274-300	1	A:274-300

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000309244	1	ENSE00001384271	chr19:51869672-51869524	149	ETFB_HUMAN	1-19	19	1	B:4-19	16
1.2b	ENST00000309244	2b	ENSE00001225639	chr19:51857562-51857404	159	ETFB_HUMAN	20-72	53	1	B:20-72	53
1.3	ENST00000309244	3	ENSE00000722381	chr19:51856544-51856386	159	ETFB_HUMAN	73-125	53	1	B:73-125	53
1.4	ENST00000309244	4	ENSE00000722391	chr19:51853645-51853583	63	ETFB_HUMAN	126-146	21	1	B:126-146	21
1.5	ENST00000309244	5	ENSE00000722401	chr19:51850312-51850154	159	ETFB_HUMAN	147-199	53	1	B:147-199	53
1.6	ENST00000309244	6	ENSE00001471664	chr19:51848635-51848410	226	ETFB_HUMAN	200-255	56	1	B:200-255	56

Asymmetric/Biological 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:312
 aligned with ETFA_HUMAN | P13804 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:312
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329  
           ETFA_HUMAN    20 QSTLVIAEHANDSLAPITLNTITAATRLGGEVSCLVAGTKCDKVAQDLCKVAGIAKVLVAQHDVYKGLLPEELTPLILATQKQFNYTHICAGASAFGKNLLPRVAAKLEVAPISDIIAIKSPDTFVRTIYAGNALCTVKCDEKVKVFSVRGTSFDAAATSGGSASSEKASSTSPVEISEWLDQKLTKSDRPELTGAKVVVSGGRGLKSGENFKLLYDLADQLHAAVGASRAAVDAGFVPNDMQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKTIVAINKDPEAPIFQVADYGIVADLFKVVPEMTEILK 331
               SCOP domains d1efva1 A:20-207 Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain                                                                                             d1efva2 A:208-331 C-terminal domain of the electron transfer flavoprotein alpha subunit                                      SCOP domains
               CATH domains 1efvA02 A:20-204 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                   1efvA01 A:205-331 TPP-binding domain                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.........hhhhhhhhhhhhh..eeeeeeee...hhhhhhhhh.....eeeeee.hhh....hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh.........eeee..eeeeee....eeeeeee....eeeee.hhh...........eeee.........eeeeeeee.......hhh..eeeee.hhh...hhhhhhhhhhhhh..eeee.hhhhh.....hhh............eeeee.....hhhhhh.....eeeeee.....hhhh...eeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------R----------------------------------------G-------------I----------------------------------------------------------------------------------------------M----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_ALPHA  PDB: A:274-300  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1efv A  20 QSTLVIAEHANDSLAPITLNTITAATRLGGEVSCLVAGTKCDKVAQDLCKVAGIAKVLVAQHDVYKGLLPEELTPLILATQKQFNYTHICAGASAFGKNLLPRVAAKLEVAPISDIIAIKSPDTFVRTIYAGNALCTVKCDEKVKVFSVRGTSFDAAATSGGSASSEKASSTSPVEISEWLDQKLTKSDRPELTGAKVVVSGGRGLKSGENFKLLYDLADQLHAAVGASRAAVDAGFVPNDMQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKTIVAINKDPEAPIFQVADYGIVADLFKVVPEMTEILK 331
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with ETFB_HUMAN | P38117 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:252
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
           ETFB_HUMAN     4 LRVLVAVKRVIDYAVKIRVKPDRTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSCGPAQCQETIRTALAMGADRGIHVEVPPAEAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDCNQTGQMTAGFLDWPQGTFASQVTLEGDKLKVEREIDGGLETLRLKLPAVVTADLRLNEPRYATLPNIMKAKKKKIEVIKPGDLGVDLTSKLSVISVEDPPQRTAGVKVETTEDLVAKLKEIGRI 255
               SCOP domains d1efvb_ B: Small, beta subunit of electron transfer flavoprotein ETFP                                                                                                                                                                                        SCOP domains
               CATH domains 1efvB00 B:4-255 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eee.....................eee.hhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhh...eeeeee..hhhhhh..hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhh..eee..eeeeeee..eeeeeeee..eeeeeeee..eeeee.hhh.......hhhhhhhhh..eeeeehhhh.......eeeeeee.............hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------N-------------------------M---------Q------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_BETA             ------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1        Exon 1.2b  PDB: B:20-72 UniProt: 20-72               Exon 1.3  PDB: B:73-125 UniProt: 73-125              Exon 1.4             Exon 1.5  PDB: B:147-199 UniProt: 147-199            Exon 1.6  PDB: B:200-255 UniProt: 200-255                Transcript 1
                 1efv B   4 LRVLVAVKRVIDYAVKIRVKPDRTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSCGPAQCQETIRTALAMGADRGIHVEVPPAEAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDCNQTGQMTAGFLDWPQGTFASQVTLEGDKLKVEREIDGGLETLRLKLPAVVTADLRLNEPRYATLPNIMKAKKKKIEVIKPGDLGVDLTSKLSVISVEDPPQRTAGVKVETTEDLVAKLKEIGRI 255
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Human (Homo sapiens) (9)

1efvA01

A:205-331

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Human (Homo sapiens) (27)

2a	1efvA02	A:20-204
2b	1efvB00	B:4-255

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ETFA_HUMAN | P13804)

molecular function
	GO:0003995	acyl-CoA dehydrogenase activity	Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
	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:0000062	fatty-acyl-CoA binding	Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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.
	GO:0052890	oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a flavin.
biological process
	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
	GO:0055088	lipid homeostasis	Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
	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:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	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.

Chain B (ETFB_HUMAN | P38117)

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.
biological process
	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
	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:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	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: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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	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.

Asymmetric/Biological Unit
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	1efv
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	ETFA_HUMAN \| P13804	:	1t9g 2a1t 2a1u
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(no "Related Entries Specified in the PDB File" available for 1EFV)

Description

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