4IX9 - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SUBUNIT F OF V-ATPASE FROM S. CEREVISIAE

Authors :   S. Basak, A. M. Balakrishna, M. S. S. Manimekalai, G. Gruber

Date :   24 Jan 13 (Deposition) - 20 Mar 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.33

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)

Keywords :   V-Atpase, Stalk Subunit, Subunit F, Rossmann Fold, Regulatory, Coupling, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Basak, J. Lim, M. S. S. Manimekalai, A. M. Balakrishna, G. Gruber
Crystal And Nmr Structures Give Insights Into The Role And Dynamics Of Subunit F Of The Eukaryotic V-Atpase From Saccharomyces Cerevisiae
J. Biol. Chem. V. 288 11930 2013
PubMed-ID: 23476018 | Reference-DOI: 10.1074/JBC.M113.461533

Molecule 1 - V-TYPE PROTON ATPASE SUBUNIT F
	Chains	:	A, B, C, D
	EC Number	:	3.6.3.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9D
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	COUPLING AND REGULATORY SUBUNIT F, UNP RESIDUES 1-94
	Gene	:	VMA7, YGR020C
	Mutation	:	YES
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	V-ATPASE SUBUNIT F, V-ATPASE 14 KDA SUBUNIT, VACUOLAR PROTON PUMP SUBUNIT F

		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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	TRS	4	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:7 , ILE A:8 , GLY A:24 , ILE A:25 , GLY A:26 , GLN A:27 , ASN A:36 , HOH A:219	BINDING SITE FOR RESIDUE TRS A 101
2	AC2	SOFTWARE	TYR A:40 , GLU A:42 , HIS A:72 , ASN A:76 , HOH A:213	BINDING SITE FOR RESIDUE TRS A 102
3	AC3	SOFTWARE	GLN B:41 , GLU B:42 , HOH B:212 , HOH B:222 , HOH B:264 , GLU C:48 , GLU C:75 , HOH C:239 , HOH C:264	BINDING SITE FOR RESIDUE GOL B 101
4	AC4	SOFTWARE	LEU B:7 , ILE B:8 , GLY B:24 , GLY B:26 , GLN B:27 , ASN B:36 , HOH B:259	BINDING SITE FOR RESIDUE GOL B 102
5	AC5	SOFTWARE	LYS B:47 , GLU B:75 , ASN B:76 , ILE B:77 , ARG B:78 , ALA B:79 , ARG B:80 , HOH B:269	BINDING SITE FOR RESIDUE GOL B 103
6	AC6	SOFTWARE	TYR B:40 , GLU B:42 , HIS B:72 , ASN B:76 , HOH B:234 , TYR C:40 , GLU C:42 , HIS C:72 , ASN C:76 , HOH C:269	BINDING SITE FOR RESIDUE TRS B 104
7	AC7	SOFTWARE	ASP B:13 , THR B:16 , ASN B:70 , HIS B:72 , HOH B:223 , HOH B:231 , HOH B:233 , HOH B:238 , HOH B:241 , GLN C:71 , HIS C:72	BINDING SITE FOR RESIDUE GOL B 105
8	AC8	SOFTWARE	ILE C:8 , GLY C:24 , ILE C:25 , GLY C:26 , GLN C:27 , ASN C:36 , HOH C:212	BINDING SITE FOR RESIDUE GOL C 101
9	AC9	SOFTWARE	ILE D:8 , GLY D:24 , ILE D:25 , GLY D:26 , GLN D:27 , HOH D:201 , HOH D:213 , HOH D:226	BINDING SITE FOR RESIDUE TRS D 101

(no "SS Bond" information available for 4IX9)

Asymmetric Unit

No.	Residues
1	Phe A:88	-	Pro A:89
2	Phe B:88	-	Pro B:89
3	Phe C:88	-	Pro C:89
4	Phe D:88	-	Pro D:89

(no "SAP(SNP)/Variant" information available for 4IX9)

(no "PROSITE Motif" information available for 4IX9)

(no "Exon" information available for 4IX9)

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
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Chain A from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeehhhhhhhhhh.............eeee.....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4ix9 A  3 EKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLmNQHIAENIRARVDSFTNAFPAILEI 94
                                    12        22        32        42        52        62      | 72        82        92  
                                                                                             69-MSE

Chain B from PDB  Type:PROTEIN  Length:93
                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhhhhhh.............eee......hhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhh.....eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  4ix9 B  2 AEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLmNQHIAENIRARVDSFTNAFPAILEI 94
                                    11        21        31        41        51        61       |71        81        91   
                                                                                              69-MSE

Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeehhhhhhhhhh.............eeee.....hhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhh......eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4ix9 C  3 EKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLmNQHIAENIRARVDSFTNAFPAILEI 94
                                    12        22        32        42        52        62      | 72        82        92  
                                                                                             69-MSE

Chain D from PDB  Type:PROTEIN  Length:90
                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhh.............eee......hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  4ix9 D  5 RTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLmNQHIAENIRARVDSFTNAFPAILEI 94
                                    14        24        34        44        54        64    |   74        84        94
                                                                                           69-MSE

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	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 4IX9)

(no "CATH Domain" information available for 4IX9)

(no "Pfam Domain" information available for 4IX9)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:88 - Pro A:89	[ RasMol ]
		Phe B:88 - Pro B:89	[ RasMol ]
		Phe C:88 - Pro C:89	[ RasMol ]
		Phe D:88 - Pro D:89	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 13)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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