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- PDB-2q0a: Structure and rearrangements in the carboxy-terminal region of Sp... -

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Basic information

Entry
Database: PDB / ID: 2q0a
TitleStructure and rearrangements in the carboxy-terminal region of SpIH channels
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN / HCN2 / ion channel / cyclic nucleotide binding domain / C-linker / cGMP
Function / homology
Function and homology information


HCN channels / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma 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 ...HCN channels / HCN channel complex / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma 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 / cAMP binding / cellular response to cAMP / somatodendritic compartment / potassium ion transmembrane transport / dendrite membrane / regulation of membrane potential / dendritic shaft / PDZ domain binding / molecular adaptor activity / axon / dendrite / neuronal cell body / protein-containing complex binding / membrane / 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
CYCLIC GUANOSINE MONOPHOSPHATE / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFlynn, G.E. / Black, K.D. / Islas, L.D. / Sankaran, B. / Zagotta, W.N.
CitationJournal: Structure / Year: 2007
Title: Structure and rearrangements in the carboxy-terminal region of SpIH channels.
Authors: Flynn, G.E. / Black, K.D. / Islas, L.D. / Sankaran, B. / Zagotta, W.N.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5464
Polymers46,8552
Non-polymers6902
Water3,873215
1
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0928
Polymers93,7114
Non-polymers1,3814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area11870 Å2
ΔGint-47 kcal/mol
Surface area38190 Å2
MethodPISA, PQS
2
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7732
Polymers23,4281
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,18416
Polymers187,4228
Non-polymers2,7628
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_555x+1/2,y+1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-y+1/2,x+1/2,z+1/21
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Buried area28350 Å2
ΔGint-126 kcal/mol
Surface area71350 Å2
MethodPISA
4
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules

B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0928
Polymers93,7114
Non-polymers1,3814
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
MethodPQS
Unit cell
Length a, b, c (Å)94.734, 94.734, 124.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer generated from a single monomer chain A in the asymmetric unit by the operations: x,y,z (1_555) -y+1,x,z (3_655) y,-x+1,z (4_565) -x+1,-y+1,z (2_665) or From monomer chain B in the asymmetric unit by the operations: x,y,z (1_555) y,-x,z (4_555) -y,x,z (3_555) -x,-y,z (2_555)

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Components

#1: Protein 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: 23427.734 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (residues 443-640) / Mutation: I636D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hcn2, Bcng2, Hac1 / Plasmid: pHMalc2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: O88703
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10 % w/v PEG 8000, 0.5 M NaCl, 15 % Glycerol, 0.1 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -k,-h,-l / Fraction: 0.43
ReflectionResolution: 2.2→40 Å / Num. all: 27611 / Num. obs: 27611 / % possible obs: 100 % / Redundancy: 7.4 % / Rsym value: 0.043 / Χ2: 1.115 / Net I/σ(I): 45
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 2764 / Rsym value: 0.241 / Χ2: 1.551 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q5o.pdb

1q5o


Resolution: 2.25→40 Å / Cross valid method: THROUGHOUT / σ(F): 83
Details: Coordinates from twinned data minimization refinement, twinning operator= -k,-h,-l twinning fraction= 0.43. The densities of loop region 566-570 in both monomers are not well determined.
RfactorNum. reflection% reflection
Rfree0.261 2349 9.1 %
Rwork0.209 --
obs-25720 99.1 %
Solvent computationBsol: 36.52 Å2
Displacement parametersBiso mean: 38.234 Å2
Baniso -1Baniso -2Baniso -3
1--7.711 Å20 Å20 Å2
2---7.711 Å20 Å2
3---15.423 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 46 215 3467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.849
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ligand.param

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