3OTF - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR THE CAMP-DEPENDENT GATING IN HUMAN HCN4 CHANNEL

Authors :   X. Xu, Z. V. Vysotskaya, Q. Liu, L. Zhou

Date :   11 Sep 10 (Deposition) - 13 Oct 10 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Cyclic-Nucleotide Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xu, Z. V. Vysotskaya, Q. Liu, L. Zhou
Structural Basis For The Camp-Dependent Gating In The Human Hcn4 Channel.
J. Biol. Chem. V. 285 37082 2010
PubMed-ID: 20829353 | Reference-DOI: 10.1074/JBC.M110.152033

Molecule 1 - POTASSIUM/SODIUM HYPERPOLARIZATION-ACTIVATED CYCLIC NUCLEOTIDE-GATED CHANNEL 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSMT3
	Expression System Strain	:	BL21DE3(GOLD)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEOTIDE BINDING DOMAIN (CNBD, UNP RESIDUES 521-739)
	Gene	:	HCN4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CMP	1	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CMP	4	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:658 , GLY A:659 , GLU A:660 , ILE A:661 , CYS A:662 , ARG A:669 , THR A:670 , ARG A:710	BINDING SITE FOR RESIDUE CMP A 725

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

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

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_026534	D	553	N	HCN4_HUMAN	Disease (SSS2)	104894485	A	D	553	N
2	UniProt	VAR_026535	S	672	R	HCN4_HUMAN	Disease (SSS2)	104894488	A	S	672	R

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

Biological Unit 1 (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_026534	D	553	N	HCN4_HUMAN	Disease (SSS2)	104894485	A	D	553	N
2	UniProt	VAR_026535	S	672	R	HCN4_HUMAN	Disease (SSS2)	104894488	A	S	672	R

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	HCN4_HUMAN	595-710	1	A:595-710
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	HCN4_HUMAN	622-638	1	A:622-638

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	HCN4_HUMAN	595-710	4	A:595-710
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	HCN4_HUMAN	622-638	4	A:622-638

(no "Exon" information available for 3OTF)

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:197
 aligned with HCN4_HUMAN | Q9Y3Q4 from UniProtKB/Swiss-Prot  Length:1203

    Alignment length:197
                                   530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       
           HCN4_HUMAN   521 DSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVALDRLDRIGKK 717
               SCOP domains d3otfa_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------cNMP_binding-3otfA01 A:613-698                                                        ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeee....eee.......eeeeeee..eeee......eee....ee.hhhhhhh.....eeee...eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhh.... 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
                 3otf A 521 DSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVALDRLDRIGKK 717
                                   530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: cAMP-binding domain (78)

Protein domain: automated matches (22)

Human (Homo sapiens) [TaxId: 9606] (5)

d3otfa_

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: cNMP_binding] (41)

Family: cNMP_binding (41)

Homo sapiens (Human) (3)

cNMP_binding-3otfA01

A:613-698

Asymmetric Unit(hide GO term definitions)

Chain A (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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3otf)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3otf
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HCN4_HUMAN \| Q9Y3Q4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	163800
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HCN4_HUMAN \| Q9Y3Q4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HCN4_HUMAN \| Q9Y3Q4	:	2mng 3u11 4hbn 4kl1 4nvp

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (36, 36)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File