[English] 日本語
Yorodumi
- PDB-3u11: Tetramerization dynamics of the C-terminus underlies isoform-spec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u11
TitleTetramerization dynamics of the C-terminus underlies isoform-specific cAMP-gating in HCN channels
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / HCN channel complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / membrane depolarization during SA node cell action potential / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / membrane depolarization during cardiac muscle cell action potential ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / HCN channel complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / membrane depolarization during SA node cell action potential / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / regulation of heart rate by cardiac conduction / monoatomic cation transport / sodium ion transmembrane transport / regulation of cardiac muscle contraction / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of heart rate / regulation of membrane potential / muscle contraction / axon / dendrite / perinuclear region of cytoplasm / identical protein binding / plasma membrane
Similarity search - Function
Helix hairpin bin / Ion transport N-terminal / Ion transport protein N-terminal / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Helix hairpin bin / Ion transport N-terminal / Ion transport protein N-terminal / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. ...Lolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. / Arrigoni, C. / Thiel, G. / Moroni, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Tetramerization dynamics of C-terminal domain underlies isoform-specific cAMP gating in hyperpolarization-activated cyclic nucleotide-gated channels.
Authors: Lolicato, M. / Nardini, M. / Gazzarrini, S. / Moller, S. / Bertinetti, D. / Herberg, F.W. / Bolognesi, M. / Martin, H. / Fasolini, M. / Bertrand, J.A. / Arrigoni, C. / Thiel, G. / Moroni, A.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3719
Polymers49,2522
Non-polymers1,1197
Water2,648147
1
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,66328
Polymers98,5054
Non-polymers3,15924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15440 Å2
ΔGint-43 kcal/mol
Surface area38160 Å2
MethodPISA
2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8218
Polymers98,5054
Non-polymers1,3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area11790 Å2
ΔGint-45 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.310, 88.310, 57.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

-
Components

#1: Protein Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4


Mass: 24626.133 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 521-723)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN4 / Plasmid: pET-24 modified with the LIC cloning cassette / Production host: Escherichia coli (E. coli) / Strain (production host): K12 Rosetta codon plus / References: UniProt: Q9Y3Q4
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 5
Details: 25% PEG 3350, 0.4M Sodium Acetate buffer, pH 5.0, 0.5M dibasic Ammonium phosphate, VAPOR DIFFUSION, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97238 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97238 Å / Relative weight: 1
ReflectionResolution: 2.5→62.44 Å / Num. obs: 15615 / % possible obs: 100 % / Observed criterion σ(F): 10 / Observed criterion σ(I): 10 / Redundancy: 4.8 % / Rmerge(I) obs: 0.132
Reflection shellResolution: 2.5→2.64 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q43

1q43


Resolution: 2.5→62.44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.85 / SU B: 11.496 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27737 781 5 %RANDOM
Rwork0.19306 ---
all0.19727 14834 --
obs0.19727 14834 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→62.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 74 147 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223495
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9914697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2985.098410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72722.637182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16415643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4521540
X-RAY DIFFRACTIONr_chiral_restr0.1320.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212636
X-RAY DIFFRACTIONr_mcbond_it0.7381.52005
X-RAY DIFFRACTIONr_mcangle_it1.44523246
X-RAY DIFFRACTIONr_scbond_it2.30131490
X-RAY DIFFRACTIONr_scangle_it3.8224.51448
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 57 -
Rwork0.255 1087 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more