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- PDB-3swy: CNGA3 626-672 containing CLZ domain -

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Basic information

Entry
Database: PDB / ID: 3swy
TitleCNGA3 626-672 containing CLZ domain
ComponentsCyclic nucleotide-gated cation channel alpha-3
KeywordsTRANSPORT PROTEIN / Coiled-coil / Assembly domain
Function / homology
Function and homology information


inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / axon initial segment / transmembrane transporter complex / myosin binding / monoatomic cation transmembrane transport / glial cell projection / ligand-gated monoatomic ion channel activity ...inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / axon initial segment / transmembrane transporter complex / myosin binding / monoatomic cation transmembrane transport / glial cell projection / ligand-gated monoatomic ion channel activity / response to magnesium ion / monoatomic cation transport / cGMP binding / response to cAMP / visual perception / perikaryon / cadherin binding / dendrite / protein-containing complex binding / signal transduction / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Cyclic nucleotide-binding domain signature 2. / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Cyclic nucleotide-binding domain signature 2. / 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 / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclic nucleotide-gated cation channel alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsShuart, N.G. / Haitin, Y. / Camp, S.S. / Black, K.D. / Zagotta, W.N.
CitationJournal: Nat Commun / Year: 2011
Title: Molecular mechanism for 3:1 subunit stoichiometry of rod cyclic nucleotide-gated ion channels.
Authors: Shuart, N.G. / Haitin, Y. / Camp, S.S. / Black, K.D. / Zagotta, W.N.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: 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

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Assembly

Deposited unit
A: Cyclic nucleotide-gated cation channel alpha-3
B: Cyclic nucleotide-gated cation channel alpha-3
C: Cyclic nucleotide-gated cation channel alpha-3


Theoretical massNumber of molelcules
Total (without water)15,7413
Polymers15,7413
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-48 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.750, 37.650, 49.580
Angle α, β, γ (deg.)90.000, 110.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Cyclic nucleotide-gated cation channel alpha-3 / Cone photoreceptor cGMP-gated channel subunit alpha / Cyclic nucleotide-gated channel alpha-3 / CNG ...Cone photoreceptor cGMP-gated channel subunit alpha / Cyclic nucleotide-gated channel alpha-3 / CNG channel alpha-3 / CNG-3 / CNG3


Mass: 5246.968 Da / Num. of mol.: 3 / Fragment: CLZ domain (UNP residues 626-669)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNCG3, CNGA3 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16281
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% w/v PEG3350, 200 mM potassium acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.324 Å / Num. all: 10016 / Num. obs: 10016 / % possible obs: 98.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 27.698 Å2 / Rsym value: 0.05 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.10.2662.5277913430.26692
2-2.122.70.1633.5373013820.16399.8
2.12-2.273.10.1234.5406013180.123100
2.27-2.453.50.0689.3421312110.068100
2.45-2.693.50.05810391211320.058100
2.69-33.40.05111.5346510180.051100
3-3.473.40.04512.230759080.045100
3.47-4.253.30.03913.825077620.03999.2
4.25-6.013.10.0539.718515990.05399.6
6.01-46.3243.20.03612.610863430.03697.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZVB

1zvb


Resolution: 1.9→29.217 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7997 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 465 4.79 %RANDOM
Rwork0.1967 ---
obs0.1981 9704 95.57 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.858 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 117.37 Å2 / Biso mean: 31.3853 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.6448 Å20 Å2-8.6559 Å2
2--6.2406 Å2-0 Å2
3---6.0521 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 0 115 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141073
X-RAY DIFFRACTIONf_angle_d1.0581434
X-RAY DIFFRACTIONf_chiral_restr0.084171
X-RAY DIFFRACTIONf_plane_restr0.004184
X-RAY DIFFRACTIONf_dihedral_angle_d16.102415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.17490.33881280.22962854298289
2.1749-2.73990.2251560.18673157331399
2.7399-29.22050.20581810.19383228340999
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)
10.39440.32780.42430.6184-0.10240.9767-0.1802-0.09630.28640.0486-0.07640.0038-0.1614-0.10520.05510.11390.00380.0020.0633-0.01830.1623-15.733219.68843.7732
20.9130.25040.56850.27970.09570.7416-0.1090.27260.2176-0.02820.0068-0.04480.05910.19820.04760.13130.00670.0190.1357-0.00610.1334-11.220515.965838.3699
30.8064-0.17-0.07330.3652-0.11320.230.1163-0.0763-0.1406-0.0314-0.03130.03010.2722-0.0906-0.03140.1544-0.034-0.00430.09280.00940.1159-15.856311.2743.1086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A0
2X-RAY DIFFRACTION2chain 'B'B0
3X-RAY DIFFRACTION3chain 'C'C0

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