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(-) Description

Title :  TETRAMERIZATION DYNAMICS OF THE C-TERMINUS UNDERLIES ISOFORM-SPECIFIC CAMP-GATING IN HCN CHANNELS
 
Authors :  M. Lolicato, M. Nardini, S. Gazzarrini, S. Moller, D. Bertinetti, F. W. M. Bolognesi, H. Martin, M. Fasolini, J. A. Bertrand, C. Arrigoni, G. T A. Moroni
Date :  29 Sep 11  (Deposition) - 26 Oct 11  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Lolicato, M. Nardini, S. Gazzarrini, S. Moller, D. Bertinetti, F. W. Herberg, M. Bolognesi, H. Martin, M. Fasolini, J. A. Bertrand, C. Arrigoni, G. Thiel, A. Moroni
Tetramerization Dynamics Of C-Terminal Domain Underlies Isoform-Specific Camp Gating In Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels.
J. Biol. Chem. V. 286 44811 2011
PubMed-ID: 22006928  |  Reference-DOI: 10.1074/JBC.M111.297606

(-) Compounds

Molecule 1 - POTASSIUM/SODIUM HYPERPOLARIZATION-ACTIVATED CYCLIC NUCLEOTIDE-GATED CHANNEL 4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-24 MODIFIED WITH THE LIC CLONING CASSETTE
    Expression System StrainK12 ROSETTA CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN (UNP RESIDUES 521-723)
    GeneHCN4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)A 
Biological Unit 2 (4x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL5Ligand/IonGLYCEROL
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL20Ligand/IonGLYCEROL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL-1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:649 , THR A:650 , PHE A:658 , GLY A:659 , GLU A:660 , ILE A:661 , CYS A:662 , ARG A:669 , THR A:670 , ALA A:671 , ARG A:710 , ARG A:713BINDING SITE FOR RESIDUE CMP A 846
2AC2SOFTWARELEU A:543 , PRO A:544 , PRO A:545 , ARG A:548 , PRO B:594 , LEU B:595 , ALA B:599 , ASP B:600BINDING SITE FOR RESIDUE GOL A 724
3AC3SOFTWARELYS A:651BINDING SITE FOR RESIDUE GOL A 725
4AC4SOFTWAREASN A:583 , PHE A:596 , ALA A:599 , PRO A:601 , VAL A:604 , THR A:605BINDING SITE FOR RESIDUE GOL A 726
5AC5SOFTWAREHOH A:149 , HOH A:157 , GLU A:625 , GLY A:626BINDING SITE FOR RESIDUE GOL A 727
6AC6SOFTWARELEU A:652 , SER A:656 , ASP A:709 , ARG A:710 , ARG A:713BINDING SITE FOR RESIDUE GOL A 728
7AC7SOFTWAREVAL B:642 , THR B:650 , PHE B:658 , GLY B:659 , GLU B:660 , ILE B:661 , CYS B:662 , ARG B:669 , THR B:670 , ALA B:671 , ARG B:710 , ILE B:714BINDING SITE FOR RESIDUE CMP B 846

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U11)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U11)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026534D553NHCN4_HUMANDisease (SSS2)104894485A/BD553N
2UniProtVAR_026535S672RHCN4_HUMANDisease (SSS2)104894488A/BS672R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026534D553NHCN4_HUMANDisease (SSS2)104894485AD553N
2UniProtVAR_026535S672RHCN4_HUMANDisease (SSS2)104894488AS672R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026534D553NHCN4_HUMANDisease (SSS2)104894485BD553N
2UniProtVAR_026535S672RHCN4_HUMANDisease (SSS2)104894488BS672R

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.HCN4_HUMAN595-710
 
  2A:595-710
B:595-710
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.HCN4_HUMAN622-638
 
  2A:622-638
B:622-638
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.HCN4_HUMAN595-710
 
  4A:595-710
-
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.HCN4_HUMAN622-638
 
  4A:622-638
-
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.HCN4_HUMAN595-710
 
  4-
B:595-710
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.HCN4_HUMAN622-638
 
  4-
B:622-638

(-) Exons   (0, 0)

(no "Exon" information available for 3U11)

(-) 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:198
 aligned with HCN4_HUMAN | Q9Y3Q4 from UniProtKB/Swiss-Prot  Length:1203

    Alignment length:198
                                   530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710        
           HCN4_HUMAN   521 DSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVALDRLDRIGKKN 718
               SCOP domains d3u11a_ A: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeee....eee.......eeeeeee.eeeeee..eeeeeee...eehhhhhhhh.....eeee...eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------N----------------------------------------------------------------------------------------------------------------------R---------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------CNMP_BINDING_3  PDB: A:595-710 UniProt: 595-710                                                                     -------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------CNMP_BINDING_1   -------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3u11 A 521 DSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNcRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVALDRLDRIGKKN 718
                                   530       540       550       560       570       580     | 590       600       610       620       630       640       650       660       670       680       690       700       710        
                                                                                           586-CSO                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with HCN4_HUMAN | Q9Y3Q4 from UniProtKB/Swiss-Prot  Length:1203

    Alignment length:202
                                   530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720  
           HCN4_HUMAN   521 DSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILL 722
               SCOP domains d3u11b_ B: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.eeeee....eee.......eeeeeee..eeeee..eeeeee....eehhhhhhhh.....eeee...eeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------N----------------------------------------------------------------------------------------------------------------------R-------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------CNMP_BINDING_3  PDB: B:595-710 UniProt: 595-710                                                                     ------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------CNMP_BINDING_1   ------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u11 B 521 DSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNcRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILL 722
                                   530       540       550       560       570       580     | 590       600       610       620       630       640       650       660       670       680       690       700       710       720  
                                                                                           586-CSO                                                                                                                                    

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U11)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U11)

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HCN4_HUMAN | Q9Y3Q4)
molecular function
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005222    intracellular cAMP activated cation channel activity    Enables the transmembrane transfer of a cation by a channel that opens when intracellular cAMP has been bound by the channel complex or one of its constituent parts.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    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:0005267    potassium channel activity    Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005272    sodium channel activity    Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
    GO:0005249    voltage-gated potassium channel activity    Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
    GO:0005248    voltage-gated sodium channel activity    Enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0086015    SA node cell action potential    An action potential that occurs in a sinoatrial node cardiac muscle cell.
    GO:0008015    blood circulation    The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0071321    cellular response to cGMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cGMP (cyclic GMP, guanosine 3',5'-cyclophosphate) stimulus.
    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:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0071805    potassium ion transmembrane transport    A process in which a potassium ion is transported from one side of a membrane to the other.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055117    regulation of cardiac muscle contraction    Any process that modulates the frequency, rate or extent of cardiac muscle contraction.
    GO:0002027    regulation of heart rate    Any process that modulates the frequency or rate of heart contraction.
    GO:0086091    regulation of heart rate by cardiac conduction    A cardiac conduction process that modulates the frequency or rate of heart contraction.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0003254    regulation of membrane depolarization    Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
    GO:0042391    regulation of membrane potential    Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0060078    regulation of postsynaptic membrane potential    Any process that modulates the potential difference across a post-synaptic membrane.
    GO:0035725    sodium ion transmembrane transport    A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006814    sodium ion transport    The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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: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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HCN4_HUMAN | Q9Y3Q42mng 3otf 4hbn 4kl1 4nvp

(-) Related Entries Specified in the PDB File

1q43 HCN2 CNBD
3otf HCN4 CNBD
3u0z HCN1 CNBD
3u10 HCN2 CNBD