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- PDB-5jon: Crystal structure of the unliganded form of HCN2 CNBD -

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Basic information

Entry
Database: PDB / ID: 5jon
TitleCrystal structure of the unliganded form of HCN2 CNBD
ComponentsMaltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
KeywordsTRANSPORT PROTEIN / HCN channels / cyclic nucleotide regulated channels / cyclic nucleotide binding domain
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 / maltose binding ...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 / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / sodium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / somatodendritic compartment / dendrite membrane / dendritic shaft / regulation of membrane potential / PDZ domain binding / outer membrane-bounded periplasmic space / molecular adaptor activity / axon / neuronal cell body / dendrite / protein-containing complex binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Cyclic nucleotide-binding domain superfamily / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
alpha-maltose / NITRATE ION / Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.042 Å
AuthorsKlenchin, V.A. / Chanda, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM084140 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS081293 United States
CitationJournal: Elife / Year: 2016
Title: Structure and dynamics underlying elementary ligand binding events in human pacemaking channels.
Authors: Goldschen-Ohm, M.P. / Klenchin, V.A. / White, D.S. / Cowgill, J.B. / Cui, Q. / Goldsmith, R.H. / Chanda, B.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
B: Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6997
Polymers114,8292
Non-polymers8715
Water6,648369
1
A: Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8193
Polymers57,4141
Non-polymers4042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8814
Polymers57,4141
Non-polymers4663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.517, 42.010, 198.376
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 / MBP / MMBP / Maltodextrin-binding protein / Brain cyclic nucleotide-gated channel 2 / BCNG-2 / ...MBP / MMBP / Maltodextrin-binding protein / Brain cyclic nucleotide-gated channel 2 / BCNG-2 / Hyperpolarization-activated cation channel 1 / HAC-1


Mass: 57414.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Mus musculus (house mouse)
Gene: malE, Z5632, ECs5017, Hcn2, Bcng2, Hac1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEY0, UniProt: O88703
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.24 Å3/Da / Density % sol: 44.89 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 34-36% dimethyl PEG 500, 240 mM potassium nitrate, 20 mM magnesium chloride, 100 mM BIS-TRIS, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.878
11-h,-k,l20.122
ReflectionResolution: 2.04→25 Å / Num. obs: 62519 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.115 / Net I/av σ(I): 9.9 / Net I/σ(I): 7.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.042→24.82 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.088 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22084 3134 5 %RANDOM
Rwork0.18036 ---
obs0.18237 59374 95.68 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.33 Å2
2---13.42 Å2-0 Å2
3---14.18 Å2
Refinement stepCycle: 1 / Resolution: 2.042→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7879 0 58 369 8306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028157
X-RAY DIFFRACTIONr_bond_other_d0.0020.027711
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.97111076
X-RAY DIFFRACTIONr_angle_other_deg1.005317819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83551027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01925.291361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.341151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6171528
X-RAY DIFFRACTIONr_chiral_restr0.0740.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021784
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5172.4554072
X-RAY DIFFRACTIONr_mcbond_other1.5172.4554071
X-RAY DIFFRACTIONr_mcangle_it2.57327.5555090
X-RAY DIFFRACTIONr_mcangle_other2.57327.5575091
X-RAY DIFFRACTIONr_scbond_it2.2062.8364085
X-RAY DIFFRACTIONr_scbond_other2.2062.8314076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.79630.515971
X-RAY DIFFRACTIONr_long_range_B_refined5.69361.1579329
X-RAY DIFFRACTIONr_long_range_B_other5.66160.5589230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 92 -
Rwork0.216 1941 -
obs--42.52 %
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)
11.03150.1090.04140.4027-0.36540.45490.0146-0.07680.06630.0371-0.0348-0.0571-0.09180.00270.02020.05210.00040.02470.05340.00260.03459.1542-7.6103-60.7679
20.2719-0.12880.05550.2765-0.30460.5260.02170.0319-0.0534-0.0056-0.03460.0175-0.0322-0.00310.01290.02890.00780.01640.0618-0.01290.0383-0.8348-6.9421-78.431
32.2387-0.28491.29710.44130.32761.3560.01280.0922-0.1545-0.11920.1327-0.0265-0.14770.2045-0.14550.0431-0.020.03410.09510.02560.075723.65532.3325-82.3066
40.9169-0.3044-0.80563.5099-0.69520.994-0.0278-0.30360.04250.406-0.0326-0.2452-0.070.3270.06040.06660.01950.00870.17140.04130.087432.151217.0542-66.5156
50.77980.1913-0.14483.3845-1.58590.773-0.0361-0.44880.17170.6501-0.1472-0.2792-0.24660.14040.18340.24760.08590.05590.3173-0.00720.216931.095214.0893-57.8702
61.27520.1411-0.00370.194-0.36410.7468-0.06380.1252-0.1693-0.02950.0122-0.03930.0618-0.00620.05160.0526-0.02110.03920.0648-0.02410.0427.45763.2802-38.6039
70.21130.13050.04040.2727-0.16360.35950.0127-0.01510.03560.0063-0.01780.00330.0283-0.01370.00510.0298-0.01160.02110.0676-0.00830.0288-2.66112.5923-20.7055
82.73380.0621-0.94350.83230.62130.828-0.08620.09880.1387-0.12180.1627-0.0329-0.05530.0636-0.07640.076-0.02440.01660.10130.04730.051121.8197-7.2329-16.5871
90.88930.82770.95822.67310.51732.5945-0.10210.1151-0.1439-0.1670.0778-0.0895-0.18780.40330.02430.0211-0.03720.0030.13820.01840.048130.1264-22.6267-32.4892
100.9165-1.4342.00473.0795-2.31255.44090.22130.35450.0087-0.757-0.2207-0.2548-0.0581.254-0.00060.341-0.1644-0.01440.36210.03820.274429.8445-12.4696-43.4118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-371 - -297
2X-RAY DIFFRACTION2A-296 - -17
3X-RAY DIFFRACTION3A-16 - 514
4X-RAY DIFFRACTION4A515 - 585
5X-RAY DIFFRACTION5A586 - 635
6X-RAY DIFFRACTION6B-371 - -297
7X-RAY DIFFRACTION7B-296 - -18
8X-RAY DIFFRACTION8B-17 - 514
9X-RAY DIFFRACTION9B515 - 600
10X-RAY DIFFRACTION10B601 - 635

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