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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPHERAL STALK OF THERMUS THERMOPHILUS H+-ATPASE/SYNTHASE
 
Authors :  L. K. Lee, A. G. Stewart, M. Donohoe, R. A. Bernal, D. Stock
Date :  07 Oct 09  (Deposition) - 23 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,E,G
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  E,G  (1x)
Keywords :  Right Handed Coiled Coil, Vacuolar Atpase/Synthase, V-Type Atpase/Synthase, A-Type Atpase/Synthase, Peripheral Stator, Peripheral Stalk, Atp Synthesis, Hydrogen Ion Transport, Ion Transport, Transport, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. K. Lee, A. G. Stewart, M. Donohoe, R. A. Bernal, D. Stock
The Structure Of The Peripheral Stalk Of Thermus Thermophilus H(+)-Atpase/Synthase.
Nat. Struct. Mol. Biol. V. 17 373 2010
PubMed-ID: 20173764  |  Reference-DOI: 10.1038/NSMB.1761

(-) Compounds

Molecule 1 - V-TYPE ATP SYNTHASE, SUBUNIT (VAPC-THERM)
    Chains: G, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 55981248, TTHA1279
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
 
Molecule 2 - V-TYPE ATP SYNTHASE SUBUNIT E
    Chains: E, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 55981245, ATPE, TTHA1276, VATE
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: V-ATPASE SUBUNIT E

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABEG
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   EG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3K5B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K5B)

(-) Exons   (0, 0)

(no "Exon" information available for 3K5B)

(-) Sequences/Alignments

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:185
 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 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhh.........--..eeeee........eeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5b A   2 SKLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEAmARERGVELQAEP--RLGVRAVGAEGKTQVENSLLARmDRAWDAmSSKVAQALWG 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  |    141    |  151       161       171      |181       
                                                                                                                                                              134-MSE     146  |                   171-MSE  |          
                                                                                                                                                                             149                          178-MSE      


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with Q5SIT5_THET8 | Q5SIT5 from UniProtKB/TrEMBL  Length:120

    Alignment length:100
                                    30        40        50        60        70        80        90       100       110       120
         Q5SIT5_THET8    21 GLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP 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
                 3k5b B  21 GLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAmARLDEAVALVLKEVLP 120
                                    30        40        50        60        70        80        90       100   |   110       120
                                                                                                             104-MSE            


Chain E from PDB  Type:PROTEIN  Length:184
 aligned with VATE_THET8 | P74901 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           VATE_THET8     3 KLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEALARERGVELQAEPALRLGVRAVGAEGKTQVENSLLARLDRAWDALSSKVAQALWG 188
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----vATP-synt_E-3k5bE01 E:7-187                                                                                                                                                          - Pfam domains (1)
           Pfam domains (2) ----vATP-synt_E-3k5bE02 E:7-187                                                                                                                                                          - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eee....................--......eeeee.......eeeehhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k5b E   3 KLEAILSQEVEAEIQALLQEAEAKAEAVKREAEEKAKALLQARERALEAQYRAALRRAESAGELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPEVVRKLALEALEALPGAKALVANPEDLPHLEAmARERGVEL--EPALRLGVRAVGAEGKTQVENSLLARmDRAWDAmSSKVAQALWG 188
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 |     142  |    152       162       172     | 182      
                                                                                                                                                             134-MSE 142  |                       171-MSE  |          
                                                                                                                                                                        145                              178-MSE      


Chain G from PDB  Type:PROTEIN  Length:100
 aligned with Q5SIT5_THET8 | Q5SIT5 from UniProtKB/TrEMBL  Length:120

    Alignment length:100
                                    30        40        50        60        70        80        90       100       110       120
         Q5SIT5_THET8    21 GLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAMARLDEAVALVLKEVLP 120
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3k5b G  21 GLIKSLAEKEKQLLERLEAAKKEAEERVKRAEAEAKALLEEAEAKAKALEAQYRERERAETEALLARYRERAEAEAKAVREKAmARLDEAVALVLKEVLP 120
                                    30        40        50        60        70        80        90       100   |   110       120
                                                                                                             104-MSE
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3K5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K5B)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: ATP_synthase (9)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,E   (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,G   (Q5SIT5_THET8 | Q5SIT5)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VATE_THET8 | P74901: 3j0j 3v6i 5gar 5gas 5tsj
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        Q5SIT5_THET8 | Q5SIT5: 3j0j 3v6i 5gar 5gas 5tsj

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