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(-) Description

Title :  CRYSTAL STRUCTURE OF AN EHD ATPASE INVOLVED IN MEMBRANE REMODELLING
 
Authors :  O. Daumke
Date :  25 Jul 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Protein-Nucleotide Complex, Membrane Protein, Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Daumke, R. Lundmark, Y. Vallis, S. Martens, P. J. Butler, H. T. Mcmahon
Architectural And Mechanistic Insights Into An Ehd Atpase Involved In Membrane Remodelling.
Nature V. 449 923 2007
PubMed-ID: 17914359  |  Reference-DOI: 10.1038/NATURE06173

(-) Compounds

Molecule 1 - EH DOMAIN-CONTAINING PROTEIN-2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB-LNB
    Expression System Strain: BL21DE3 ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EHD2
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CA1Ligand/IonCALCIUM ION
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CA-1Ligand/IonCALCIUM ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:72 , THR A:94 , ANP A:600BINDING SITE FOR RESIDUE MG A 700
2AC2SOFTWAREASP A:494 , ASP A:496 , ASP A:498 , MET A:500 , GLU A:505BINDING SITE FOR RESIDUE CA A 701
3AC3SOFTWARETYR A:67 , SER A:68 , THR A:69 , GLY A:70 , LYS A:71 , THR A:72 , SER A:73 , VAL A:88 , GLY A:89 , THR A:93 , THR A:94 , GLY A:156 , ASN A:219 , LYS A:220 , SER A:256 , PHE A:257 , TRP A:258 , MG A:700BINDING SITE FOR RESIDUE ANP A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QPT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QPT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QPT)

(-) PROSITE Motifs  (4, 4)

Asymmetric Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_DYNAMIN_2PS51718 Dynamin-type guanine nucleotide-binding (G) domain profile.EHD2_MOUSE55-286  1A:55-286
2EHPS50031 EH domain profile.EHD2_MOUSE449-537  1A:449-537
3EF_HAND_2PS50222 EF-hand calcium-binding domain profile.EHD2_MOUSE481-516  1A:481-516
4EF_HAND_1PS00018 EF-hand calcium-binding domain.EHD2_MOUSE494-506  1A:494-506
Biological Unit 1 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_DYNAMIN_2PS51718 Dynamin-type guanine nucleotide-binding (G) domain profile.EHD2_MOUSE55-286  2A:55-286
2EHPS50031 EH domain profile.EHD2_MOUSE449-537  2A:449-537
3EF_HAND_2PS50222 EF-hand calcium-binding domain profile.EHD2_MOUSE481-516  2A:481-516
4EF_HAND_1PS00018 EF-hand calcium-binding domain.EHD2_MOUSE494-506  2A:494-506

(-) Exons   (0, 0)

(no "Exon" information available for 2QPT)

(-) 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:476
 aligned with EHD2_MOUSE | Q8BH64 from UniProtKB/Swiss-Prot  Length:543

    Alignment length:520
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538
           EHD2_MOUSE    19 RTVTSSLKELYRTKLLPLEEHYRFGSFHSPALEDADFDGKPMVLVAGQYSTGKTSFIQYLLEQEVPGSRVGPEPTTDCFVAVMHGETEGTVPGNALVVDPEKPFRKLNPFGNTFLNRFMCAQLPNQVLESISIIDTPGILSGAKQRVSRGYDFPAVLRWFAERVDLIILLFDAHKLEISDEFSEAIGALRGHEDKIRVVLNKADMVETQQLMRVYGALMWALGKVVGTPEVLRVYIGSFWSQPLLVPDNRRLFELEEQDLFRDIQGLPRHAALRKLNDLVKRARLVRVHAYIISYLKKEMPTVFGKENKKKQLILKLPVIFAKIQLEHHISPGDFPDCQKMQELLMAHDFTKFHSLKPKLLEALDDMLAQDIAKLMPLLRQEELESVEAGVQGGAFEGTRMGPFVERGPDEAIEDGEEGSEDDAEWVVTKDKSKYDEIFYNLAPADGKLSGSKAKTWMVGTKLPNSVLGRIWKLSDVDRDGMLDDEEFALASHLIEAKLEGHGLPTNLPRRLVPPSKRRQ 538
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------Dynamin_N-2qptA02 A:61-221                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                   efhand_3-2qptA01 A:443-538                                                                       Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeee....hhhhhhhhhhh................eeeee.....eee..------------------......eeeee..hhhhhhheeee......-------...hhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhh..hhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh......eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh......hhhhhh...-------------------......hhhhhhhhhhhh.....eehhhhhhhhhhhh..hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhh.......hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------G_DYNAMIN_2  PDB: A:55-286 UniProt: 55-286                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------EH  PDB: A:449-537 UniProt: 449-537                                                      - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_2  PDB: A:481-516           ---------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    -------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qpt A  19 RTVTSSLKELYRTKLLPLEEHYRFGSFHSPALEDADFDGKPMVLVAGQYSTGKTSFIQYLLEQEVPGSRVGPEPTTDCFVAVMHGETEGTVPG------------------NTFLNRFMCAQLPNQVLESISIIDTPGILS-------RGYDFPAVLRWFAERVDLIILLFDAHKLEISDEFSEAIGALRGHEDKIRVVLNKADMVETQQLMRVYGALMWALGKVVGTPEVLRVYIGSFWSQPLLVPDNRRLFELEEQDLFRDIQGLPRHAALRKLNDLVKRARLVRVHAYIISYLKKEMPTVFGKENKKKQLILKLPVIFAKIQLEHHISPGDFPDCQKMQELLMAHDFTKFHSLKPKLLEALDDMLAQDIAKLMPLLRQEELESVEAGVAGGAFEGTRMGPFV-------------------EWVVTKDKSKYDEIFYNLAPADGKLSGSKAKTWMVGTKLPNSVLGRIWKLSDVDRDGMLDDEEFALASHLIEAKLEGHGLPTNLPRRLVPPSKRRQ 538
                                    28        38        48        58        68        78        88        98       108  |      -         - |     138       148       158|      168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418    |    -         -    |  448       458       468       478       488       498       508       518       528       538
                                                                                                                      111                130                          159     167                                                                                                                                                                                                                                                             423                 443                                                                                               

   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 2QPT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QPT)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (EHD2_MOUSE | Q8BH64)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0030866    cortical actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
    GO:0032456    endocytic recycling    The directed movement of membrane-bounded vesicles from recycling endosomes back to the plasma membrane where they are recycled for further rounds of transport.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0097320    plasma membrane tubulation    A membrane tubulation process occurring in a plasma membrane.
    GO:2001137    positive regulation of endocytic recycling    Any process that activates or increases the frequency, rate or extent of endocytic recycling.
    GO:1901741    positive regulation of myoblast fusion    Any process that activates or increases the frequency, rate or extent of myoblast fusion.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
cellular component
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.

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        EHD2_MOUSE | Q8BH64: 4cid

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