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(-) Description

Title :  HUMAN AQUAPORIN 5 (AQP5) - HIGH RESOLUTION X-RAY STRUCTURE
 
Authors :  R. Horsefield, K. Norden, M. Fellert, A. Backmark, S. Tornroth- Horsefield, A. C. Terwisscha Van Scheltinga, J. Kvassman, P. Kjellbom, U. Johanson, R. Neutze
Date :  27 May 08  (Deposition) - 26 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aquaporin, Aqp, Aquaglyceroporin, Membrane Protein, Water Transport, X-Ray Diffraction, Lipid, Phosphatidylserine, Psf, Npa, Ar/R, Water Channel, Glycoprotein, Membrane, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Horsefield, K. Norden, M. Fellert, A. Backmark, S. Tornroth-Horsefield, A. C. Terwisscha Van Scheltinga, J. Kvassman, P. Kjellbom, U. Johanson, R. Neutze
High-Resolution X-Ray Structure Of Human Aquaporin 5
Proc. Natl. Acad. Sci. Usa V. 105 13327 2008
PubMed-ID: 18768791  |  Reference-DOI: 10.1073/PNAS.0801466105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AQUAPORIN-5
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZB
    Expression System StrainX33
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneAQP5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsEASYSELECT PICHIA EXPRESSION KIT (INVITROGEN)
    SynonymAQP-5

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PS61Ligand/IonO-[(S)-{[(2S)-2-(HEXANOYLOXY)-3-(TETRADECANOYLOXY)PROPYL]OXY}(HYDROXY)PHOSPHORYL]-D-SERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:47 , GLY A:159 , LEU A:163 , LEU B:47 , GLY B:159 , PRO C:157 , VAL C:158 , GLY C:159 , SER C:160 , LEU C:163 , SER D:156 , PRO D:157 , VAL D:158 , GLY D:159 , SER D:160 , LEU D:163BINDING SITE FOR RESIDUE PS6 D 266

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D9S)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:115 -Asn A:116
2Leu A:230 -Ser A:231
3Ser A:231 -Leu A:232
4Asn C:116 -Leu C:117
5Glu C:244 -Pro C:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 20)

Asymmetric/Biological Unit (5, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070442A38EAQP5_HUMANDisease (PPKB)398123054A/B/C/DA38E
2UniProtVAR_070443I45SAQP5_HUMANDisease (PPKB)398123055A/B/C/DI45S
3UniProtVAR_070444N123DAQP5_HUMANDisease (PPKB)398123057A/B/C/DN123D
4UniProtVAR_070445I177FAQP5_HUMANDisease (PPKB)398123056A/B/C/DI177F
5UniProtVAR_070446R188CAQP5_HUMANDisease (PPKB)368292687A/B/C/DR188C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIPPS00221 MIP family signature.AQP5_HUMAN67-75
 
 
 
  4A:67-75
B:67-75
C:67-75
D:67-75

(-) Exons   (0, 0)

(no "Exon" information available for 3D9S)

(-) Sequences/Alignments

Asymmetric/Biological 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:245
 aligned with AQP5_HUMAN | P55064 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           AQP5_HUMAN     1 MKKEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
               SCOP domains d3d9sa_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 3d9sA00 A:1-245 Glycerol uptake facilitator protein.                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------E------S-----------------------------------------------------------------------------D-----------------------------------------------------F----------C--------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------MIP      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d9s A   1 SKKEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with AQP5_HUMAN | P55064 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           AQP5_HUMAN     1 MKKEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
               SCOP domains d3d9sb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 3d9sB00 B:1-245 Glycerol uptake facilitator protein.                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------E------S-----------------------------------------------------------------------------D-----------------------------------------------------F----------C--------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------MIP      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d9s B   1 SKKEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     

Chain C from PDB  Type:PROTEIN  Length:243
 aligned with AQP5_HUMAN | P55064 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:243
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   
           AQP5_HUMAN     3 KEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
               SCOP domains d3d9sc_ C: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 3d9sC00 C:3-245 Glycerol uptake facilitator protein.                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------E------S-----------------------------------------------------------------------------D-----------------------------------------------------F----------C--------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------MIP      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d9s C   3 KEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   

Chain D from PDB  Type:PROTEIN  Length:245
 aligned with AQP5_HUMAN | P55064 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           AQP5_HUMAN     1 MKKEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
               SCOP domains d3d9sd_ D: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 3d9sD00 D:1-245 Glycerol uptake facilitator protein.                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------E------S-----------------------------------------------------------------------------D-----------------------------------------------------F----------C--------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------MIP      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d9s D   1 SKKEVCSVAFLKAVFAEFLATLIFVFFGLGSALKWPSALPTILQIALAFGLAIGTLAQALGPVSGGHINPAITLALLVGNQISLLRAFFYVAAQLVGAIAGAGILYGVAPLNARGNLAVNALNNNTTQGQAMVVELILTFQLALCIFASTDSRRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPAVVMNRFSPAHWVFWVGPIVGAVLAAILYFYLLFPNSLSLSERVAIIKGTYEP 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D9S)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (AQP5_HUMAN | P55064)
molecular function
    GO:0015254    glycerol channel activity    Enables the facilitated diffusion of glycerol (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    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:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
    GO:0015250    water channel activity    Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
biological process
    GO:0048593    camera-type eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0015670    carbon dioxide transport    The directed movement of carbon dioxide (CO2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0009992    cellular water homeostasis    Any process involved in the maintenance of an internal steady state of water within a cell.
    GO:0007588    excretion    The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
    GO:0015793    glycerol transport    The directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0042476    odontogenesis    The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
    GO:0030157    pancreatic juice secretion    The regulated release of pancreatic juice by the exocrine pancreas into the upper part of the intestine. Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach.
    GO:0046541    saliva secretion    The regulated release of saliva from the salivary glands. In man, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin.
    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.
    GO:0006833    water transport    The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0009925    basal plasma membrane    The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AQP5_HUMAN | P550645c5x 5dye

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3D9S)