3VH4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ATG7CTD-ATG8-MGATP COMPLEX

Authors :   N. N. Noda, K. Satoo, F. Inagaki

Date :   23 Aug 11 (Deposition) - 21 Sep 11 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   Autophagy, E1, Zinc Binding, Metal Binding Protein-Protein Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. N. Noda, K. Satoo, Y. Fujioka, H. Kumeta, K. Ogura, H. Nakatogawa, Y. Ohsumi, F. Inagaki
Structural Basis Of Atg8 Activation By A Homodimeric E1, Atg7.
Mol. Cell V. 44 462 2011
PubMed-ID: 22055191 | Reference-DOI: 10.1016/J.MOLCEL.2011.08.035

Molecule 1 - UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME ATG7
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN (UNP RESIDUES 295-630)
	Gene	:	ATG7, APG7, CVT2, YHR171W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C
	Synonym	:	ATG12-ACTIVATING ENZYME E1 ATG7, AUTOPHAGY-RELATED PROTEIN 7, CYTOPLASM TO VACUOLE TARGETING PROTEIN 2

Molecule 2 - AUTOPHAGY-RELATED PROTEIN 8
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C
	Synonym	:	AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER ATG8, CYTOPLASM TO VACUOLE TARGETING PROTEIN 5

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:485 , CYS A:488 , CYS A:569 , CYS A:572	BINDING SITE FOR RESIDUE ZN A 701
2	AC2	SOFTWARE	GLY A:333 , THR A:334 , ASP A:355 , ASN A:356 , GLY A:357 , ASN A:363 , GLN A:367 , LYS A:379 , LEU A:401 , ILE A:403 , ASP A:438 , MG A:703 , GLY B:116	BINDING SITE FOR RESIDUE ATP A 702
3	AC3	SOFTWARE	ASP A:438 , ATP A:702	BINDING SITE FOR RESIDUE MG A 703

(no "SS Bond" information available for 3VH4)

(no "Cis Peptide Bond" information available for 3VH4)

(no "SAP(SNP)/Variant" information available for 3VH4)

(no "PROSITE Motif" information available for 3VH4)

(no "Exon" information available for 3VH4)

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:320
 aligned with ATG7_YEAST | P38862 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:320
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613
           ATG7_YEAST   294 PLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGTVSYSNPVRQALYNFEDCGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNRDEQSSKQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYLEEISGLSVIKQEVER 613
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.....hhhhhhhheeeee..hhhhhhhhhhhhhhh..eeeee................hhhhh..hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh..eeeeeee...eeeeee.............hhhhhh....................hhhhhhhhhhhhhhhhhhhh........ee..ee...eeeee....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vh4 A 294 MLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGTVSYSNPVRQALYNFEDCGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNRDEQSSKQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYLEEISGLSVIKQEVER 613
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with ATG8_YEAST | P38182 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:113
                                    13        23        33        43        53        63        73        83        93       103       113   
           ATG8_YEAST     4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGENTFG 116
               SCOP domains d3vh4b_ B: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh.......eeee..........hhhhhhhhhh.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3vh4 B   4 TFKSEYPFEKRKAESERIADRFPNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGENTFG 116
                                    13        23        33        43        53        63        73        83        93       103       113

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: GABARAP-like (33)

Protein domain: automated matches (22)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292] (4)

d3vh4b_

(no "CATH Domain" information available for 3VH4)

(no "Pfam Domain" information available for 3VH4)

Asymmetric Unit(hide GO term definitions)

Chain A (ATG7_YEAST | P38862)

molecular function
	GO:0019778	Atg12 activating enzyme activity	Catalysis of the activation of the small ubiquitin-related modifier APG12, through the formation of an ATP-dependent high-energy thiolester bond.
	GO:0019779	Atg8 activating enzyme activity	Catalysis of the activation of the small ubiquitin-related modifier APG8, through the formation of an ATP-dependent high-energy thiolester bond.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008641	small protein activating enzyme activity	Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
biological process
	GO:0006501	C-terminal protein lipidation	The covalent attachment of a lipid group to the carboxy terminus of a protein.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0000422	autophagy of mitochondrion	The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
	GO:0006995	cellular response to nitrogen starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.
	GO:0044805	late nucleophagy	A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.
	GO:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	GO:0034727	piecemeal microautophagy of nucleus	Degradation of a cell nucleus by lysosomal microautophagy.
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0032258	protein localization by the CVT pathway	A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
	GO:0032446	protein modification by small protein conjugation	A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to a target protein.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0097632	extrinsic component of pre-autophagosomal structure membrane	The component of the pre-autophagosomal structure membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000407	pre-autophagosomal structure	Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.

Chain B (ATG8_YEAST | P38182)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0000045	autophagosome assembly	The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0000422	autophagy of mitochondrion	The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
	GO:0034629	cellular protein complex localization	A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell.
	GO:0006995	cellular response to nitrogen starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.
	GO:0044805	late nucleophagy	A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.
	GO:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0034727	piecemeal microautophagy of nucleus	Degradation of a cell nucleus by lysosomal microautophagy.
	GO:0032258	protein localization by the CVT pathway	A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
	GO:0071211	protein targeting to vacuole involved in autophagy	The process of directing proteins towards the vacuole using signals contained within the protein, occurring as part of autophagy, the process in which cells digest parts of their own cytoplasm.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0061709	reticulophagy	The autophagic process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0033110	Cvt vesicle membrane	Either of the two lipid bilayers surrounding a Cvt vesicle, a vesicle that functions in the cytoplasm-to-vacuole targeting (Cvt) pathway.
	GO:0005776	autophagosome	A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
	GO:0000421	autophagosome membrane	The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0000329	fungal-type vacuole membrane	The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000407	pre-autophagosomal structure	Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.
	GO:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vh4)

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	3vh4
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3vh1	THE SAME PROTEIN AS A FREE FORM.
3vh2	THE SAME PROTEIN AS A FREE FORM.
3vh3	THE SAME PROTEIN COMPLEX WITHOUT MGATP.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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