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- PDB-4eqf: Trip8b-1a#206-567 interacting with the carboxy-terminal seven res... -

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Basic information

Entry
Database: PDB / ID: 4eqf
TitleTrip8b-1a#206-567 interacting with the carboxy-terminal seven residues of HCN2
Components
  • PEX5-related protein
  • Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsPROTEIN BINDING/TRANSPORT PROTEIN / Accessory protein / Tetratricopeptide repeat / TPR / Accessory Protein for HCN channels / HCN / PROTEIN BINDING-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


intracellularly cyclic nucleotide-activated monoatomic cation channel activity / peroxisome matrix targeting signal-1 binding / HCN channels / peroxisome targeting sequence binding / small GTPase binding => GO:0031267 / positive regulation of corticotropin secretion / protein import into peroxisome matrix, docking / HCN channel complex / intracellular cyclic nucleotide activated cation channel complex / regulated exocytosis ...intracellularly cyclic nucleotide-activated monoatomic cation channel activity / peroxisome matrix targeting signal-1 binding / HCN channels / peroxisome targeting sequence binding / small GTPase binding => GO:0031267 / positive regulation of corticotropin secretion / protein import into peroxisome matrix, docking / HCN channel complex / intracellular cyclic nucleotide activated cation channel complex / regulated exocytosis / cell tip / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / maintenance of protein location / sodium ion import across plasma membrane / peroxisomal membrane / voltage-gated sodium channel activity / regulation of membrane depolarization / potassium ion import across plasma membrane / voltage-gated potassium channel activity / sodium ion transmembrane transport / regulation of cAMP-mediated signaling / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / somatodendritic compartment / dendrite membrane / dendritic shaft / regulation of membrane potential / PDZ domain binding / small GTPase binding / molecular adaptor activity / receptor complex / axon / neuronal cell body / dendrite / protein-containing complex binding / perinuclear region of cytoplasm / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PEX5-related, vertebrates / PEX5/PEX5L / Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Tetratricopeptide repeat / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Tetratricopeptide repeat domain ...PEX5-related, vertebrates / PEX5/PEX5L / Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Tetratricopeptide repeat / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / RmlC-like jelly roll fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ion transport domain / Ion transport protein / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / PEX5-related protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBankston, J.R. / Camp, S.S. / Dimaio, F. / Lewis, A.S. / Chetkovich, D.M. / Zagotta, W.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization-activated cyclic nucleotide-gated channels.
Authors: Bankston, J.R. / Camp, S.S. / Dimaio, F. / Lewis, A.S. / Chetkovich, D.M. / Zagotta, W.N.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEX5-related protein
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2


Theoretical massNumber of molelcules
Total (without water)41,7472
Polymers41,7472
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-3 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.320, 72.320, 146.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PEX5-related protein / PEX2-related protein / PEX5-like protein / Peroxin-5-related protein / Pex5Rp


Mass: 40969.930 Da / Num. of mol.: 1 / Fragment: UNP residues 206-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pex5l, Pex2, Pex5r, Pxr2 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8C437
#2: Protein/peptide Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / Brain cyclic nucleotide-gated channel 2 / BCNG-2 / Hyperpolarization-activated cation channel 1 / HAC-1


Mass: 776.861 Da / Num. of mol.: 1 / Fragment: UNP residues 857-863 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: O88703

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 91mM MES, 91mM triSodium citrate, 3.63M NaCL, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3→48.91 Å / Num. all: 8364 / Num. obs: 8364 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 109.7 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIX(phenix.phaser-mr: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FCH

1fch


Resolution: 3→29.808 Å / SU ML: 1.03 / σ(F): 1.34 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 384 4.64 %Random
Rwork0.2268 ---
obs0.2293 8274 99.59 %-
all-8274 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 111.631 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.4907 Å2-0 Å20 Å2
2---18.4907 Å2-0 Å2
3---36.9814 Å2
Refinement stepCycle: LAST / Resolution: 3→29.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 0 0 2260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072302
X-RAY DIFFRACTIONf_angle_d1.1353120
X-RAY DIFFRACTIONf_dihedral_angle_d16.492839
X-RAY DIFFRACTIONf_chiral_restr0.074344
X-RAY DIFFRACTIONf_plane_restr0.004412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.43370.32511270.28882567X-RAY DIFFRACTION100
3.4337-4.3240.28931270.21182561X-RAY DIFFRACTION99
4.324-29.80970.26721300.22092762X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.74240.1357-2.1045.1431.0071.8531-0.07440.0633-0.13330.372-0.2103-0.0083-0.3229-0.17440.12361.1843-0.0762-0.48840.5560.09680.9683-17.93937.731511.3645
24.8881.66330.05266.07150.87244.92030.02460.9976-0.5329-0.88920.1971-1.16070.12340.709-0.09181.01080.1154-0.24870.7606-0.21130.9159-13.926119.8120.4873
36.2387-2.3748-1.6193.6534-2.36614.3042-0.17340.2513-1.44850.13510.57060.34590.9443-0.0766-0.30681.20530.0507-0.43690.6121-0.19940.8112-25.81511.211210.3857
43.65630.48740.55423.96031.83387.94170.0856-0.13850.06950.4431-0.16541.0615-0.4284-1.51250.05570.85620.3133-0.21831.13480.06171.3601-42.32224.72669.8015
54.13390.5227-3.01391.44120.05613.09460.6265-1.42692.55860.37781.10740.15320.732-1.6502-1.75861.63030.4023-0.29671.2575-0.07781.5445-46.855230.708212.7104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:34)
2X-RAY DIFFRACTION2(chain A and resid 35:165)
3X-RAY DIFFRACTION3(chain A and resid 166:251)
4X-RAY DIFFRACTION4(chain A and resid 252:299)
5X-RAY DIFFRACTION5(chain A and resid 300:318)

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