3V6I - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PERIPHERAL STALK OF THERMUS THERMOPHILUS H+-ATPASE/SYNTHASE AT 2.25 A RESOLUTION

Authors :   A. G. Stewart, L. K. Lee, M. Donohoe, J. J. Chaston, D. Stock

Date :   19 Dec 11 (Deposition) - 22 Feb 12 (Release) - 07 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Peripheral Stator Stalk, Right Handed Coiled-Coil, Atpase/Synthase, Atp Binding, Membrane, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Stewart, L. K. Lee, M. Donohoe, J. J. Chaston, D. Stock
The Dynamic Stator Stalk Of Rotary Atpases
Nat Commun V. 3 687 2012
PubMed-ID: 22353718 | Reference-DOI: 10.1038/NCOMMS1693

Molecule 1 - V-TYPE ATP SYNTHASE SUBUNIT E
	Chains	:	A, Y
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET DUET-1 MCS2
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ATPE, TTHA1276, VATE
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	V-ATPASE SUBUNIT E

Molecule 2 - V-TYPE ATP SYNTHASE, SUBUNIT (VAPC-THERM)
	Chains	:	B, X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET DUET-1 MCS1
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINALLY TRUNCATED, UNP RESIDUES 17-120
	Gene	:	TTHA1279
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2	3	4
Asymmetric Unit	:	A	B	X	Y
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	5	Ligand/Ion	CALCIUM ION
2	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:13 , GLN A:17 , CA A:204 , HOH A:334 , HOH A:336 , ASP B:108 , HOH B:308	BINDING SITE FOR RESIDUE CA A 201
2	AC2	SOFTWARE	GLU A:13 , CA A:204 , HOH A:335 , ALA B:105 , HOH B:308	BINDING SITE FOR RESIDUE CA A 202
3	AC3	SOFTWARE	GLU A:22 , GLU A:113 , HOH A:319 , HOH A:330 , HOH A:340 , HOH Y:305 , HOH Y:307	BINDING SITE FOR RESIDUE CA A 203
4	AC4	SOFTWARE	GLN A:10 , CA A:201 , CA A:202 , ALA B:105	BINDING SITE FOR RESIDUE CA A 204
5	AC5	SOFTWARE	GLU B:117 , GLU Y:61 , HOH Y:304	BINDING SITE FOR RESIDUE CA B 201
6	AC6	SOFTWARE	HOH A:309 , GLU X:117 , HOH X:313	BINDING SITE FOR RESIDUE NA X 201
7	AC7	SOFTWARE	GLU X:38 , GLU X:90 , GLU X:93 , HOH X:315 , HOH X:316	BINDING SITE FOR RESIDUE NA X 202
8	AC8	SOFTWARE	HOH A:333 , GLU Y:22 , GLU Y:113 , HOH Y:312 , HOH Y:317	BINDING SITE FOR RESIDUE NA Y 201

(no "SS Bond" information available for 3V6I)

(no "Cis Peptide Bond" information available for 3V6I)

(no "SAP(SNP)/Variant" information available for 3V6I)

(no "PROSITE Motif" information available for 3V6I)

(no "Exon" information available for 3V6I)

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:187
 aligned with VATE_THET8 | P74901 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
           VATE_THET8     2 SKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG 188
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.eeee......eeeee......eeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6i A   2 SKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with Q5SIT5_THET8 | Q5SIT5 from UniProtKB/TrEMBL  Length:120

    Alignment length:101
                                    29        39        49        59        69        79        89        99       109       119 
         Q5SIT5_THET8    20 LGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP 120
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3v6i B  20 LGLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP 120
                                    29        39        49        59        69        79        89        99       109       119

Chain X from PDB  Type:PROTEIN  Length:99
 aligned with Q5SIT5_THET8 | Q5SIT5 from UniProtKB/TrEMBL  Length:120

    Alignment length:99
                                    31        41        51        61        71        81        91       101       111         
         Q5SIT5_THET8    22 LIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP 120
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3v6i X  22 LIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP 120
                                    31        41        51        61        71        81        91       101       111

Chain Y from PDB  Type:PROTEIN  Length:187
 aligned with VATE_THET8 | P74901 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
           VATE_THET8     2 SKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG 188
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh.eeee......eeeee......eeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v6i Y   2 SKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

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 '\|'

(no "SCOP Domain" information available for 3V6I)

(no "CATH Domain" information available for 3V6I)

(no "Pfam Domain" information available for 3V6I)

Asymmetric Unit(hide GO term definitions)

Chain A,Y (VATE_THET8 | P74901)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046933	proton-transporting ATP synthase activity, rotational mechanism	Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ADP + H2O + phosphate + H+(in) = ATP + H+(out), by a rotational mechanism.
	GO:0046961	proton-transporting ATPase activity, rotational mechanism	Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
biological process
	GO:0006754	ATP biosynthetic process	The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0015991	ATP hydrolysis coupled proton transport	The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0042777	plasma membrane ATP synthesis coupled proton transport	The transport of protons across the plasma membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
	GO:0015992	proton transport	The directed movement of protons (hydrogen ions) 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:0033178	proton-transporting two-sector ATPase complex, catalytic domain	A protein complex that forms part of a proton-transporting two-sector ATPase complex and catalyzes ATP hydrolysis or synthesis. The catalytic domain (F1, V1, or A1) comprises a hexameric catalytic core and a central stalk, and is peripherally associated with the membrane when the two-sector ATPase is assembled.

Chain B,X (Q5SIT5_THET8 | Q5SIT5)

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	Cis Peptide Bonds
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	VATE_THET8 \| P74901	:	3j0j 3k5b 5gar 5gas 5tsj
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	Q5SIT5_THET8 \| Q5SIT5	:	3j0j 3k5b 5gar 5gas 5tsj

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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