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- PDB-3ffq: HCN2I 443-640 apo-state -

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Basic information

Entry
Database: PDB / ID: 3ffq
TitleHCN2I 443-640 apo-state
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsMETAL TRANSPORT / Ion transport / Ion channel / Membrane / Nucleotide-binding / Potassium / Potassium channel / Sodium channel / Transmembrane / Voltage-gated channel / cAMP / cAMP-binding / Glycoprotein / Ionic channel / Phosphoprotein / Potassium transport / Sodium transport / Transport
Function / homology
Function and homology information


HCN channels / HCN channel complex / ammonium transmembrane transport / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / cAMP binding ...HCN channels / HCN channel complex / ammonium transmembrane transport / intracellularly cAMP-activated cation channel activity / cellular response to cGMP / sodium ion import across plasma membrane / voltage-gated sodium channel activity / potassium ion import across plasma membrane / voltage-gated potassium channel activity / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of membrane potential / identical protein binding / membrane / 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. ...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
BROMIDE ION / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOlivier, N.B.
CitationJournal: Nat.Methods / Year: 2009
Title: Mapping the structure and conformational movements of proteins with transition metal ion FRET.
Authors: Taraska, J.W. / Puljung, M.C. / Olivier, N.B. / Flynn, G.E. / Zagotta, W.N.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_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

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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)47,97511
Polymers47,2562
Non-polymers7199
Water1,27971
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)96,11024
Polymers94,5124
Non-polymers1,59820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area10440 Å2
ΔGint-55 kcal/mol
Surface area33980 Å2
MethodPISA
2
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)95,79120
Polymers94,5124
Non-polymers1,27816
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 area10850 Å2
ΔGint-63 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.285, 95.285, 123.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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: 23628.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcng2, bcng2 or hac1, Hac1, Hcn2 / Plasmid: pETGQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O88703
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 58.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Two uL protein (5-7 mg/mL) mixed with one uL reservoir solution composed of 0.4 M NaCl, 0.1 NaBr, 0.1 M MES, pH 6.0, 20% glycerol (v/v), and 20% PEG 8000 (w/v). Crystals grew within eight ...Details: Two uL protein (5-7 mg/mL) mixed with one uL reservoir solution composed of 0.4 M NaCl, 0.1 NaBr, 0.1 M MES, pH 6.0, 20% glycerol (v/v), and 20% PEG 8000 (w/v). Crystals grew within eight weeks and harvested an additional eight weeks after initial growth, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2003 / Details: Doubly focusing toroidal mirror
RadiationMonochromator: Channel-cut Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 21512 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 23.3
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5817 / Rsym value: 0.46 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Q43

1q43


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 19.255 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / ESU R: 0.342 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28292 1103 5.1 %RANDOM
Rwork0.24314 ---
all0.24517 20412 --
obs0.24517 20404 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.365 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å20 Å2
2--2.31 Å20 Å2
3----4.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 9 71 2906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0222889
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.9463904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.765364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.4522.826138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.79715437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.9061522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022258
X-RAY DIFFRACTIONr_nbd_refined0.2680.21297
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.26
X-RAY DIFFRACTIONr_mcbond_it0.9641.51856
X-RAY DIFFRACTIONr_mcangle_it1.49322863
X-RAY DIFFRACTIONr_scbond_it2.73131173
X-RAY DIFFRACTIONr_scangle_it3.8874.51041
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 73 -
Rwork0.28 1479 -
obs--100 %
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)
14.27092.11420.652530.53887.6828-0.35630.6438-0.2272-0.20240.2894-0.338-1.1085-0.61190.06690.18290.2689-0.1234-0.0018-0.0604-0.088234.246-34.0632-16.0823
23.61660.6039-0.74270.26650.55264.9665-0.25420.06740.1381-0.1210.0355-0.1162-1.5030.38670.21870.3337-0.1992-0.1095-0.10590.0866-0.030455.0479-25.478-1.8698
32.06150.31390.52721.50540.21794.66420.0526-0.0096-0.03890.1048-0.1414-0.0445-1.3513-0.5020.08880.34240.2393-0.0904-0.1737-0.0172-0.046239.817-23.80457.8283
42.15261.7310.41034.2717-0.15689.47070.1259-0.26930.18680.5497-0.30050.17950.74730.95220.17460.05230.22730.07910.18590.1401-0.106711.4847-15.55340.4559
50.0915-0.4293-0.48113.54341.07783.4384-0.0037-0.2850.08110.2437-0.21770.1645-0.34791.56970.2214-0.1571-0.0885-0.05260.38180.1219-0.024121.68052.9449-11.6065
61.19130.2863-0.07472.4098-0.48194.173-0.1530.09760.062-0.04620.10150.03040.46411.25680.0515-0.17480.25550.00960.410.1011-0.038223.8296-7.7858-24.4667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A444 - 485
2X-RAY DIFFRACTION2A486 - 524
3X-RAY DIFFRACTION3A525 - 628
4X-RAY DIFFRACTION4B443 - 474
5X-RAY DIFFRACTION5B475 - 524
6X-RAY DIFFRACTION6B525 - 629

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