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- PDB-3swf: CNGA1 621-690 containing CLZ domain -

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Basic information

Entry
Database: PDB / ID: 3swf
TitleCNGA1 621-690 containing CLZ domain
ComponentscGMP-gated cation channel alpha-1
KeywordsTRANSPORT PROTEIN / Coiled-coil / Assembly domain
Function / homology
Function and homology information


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / transmembrane transporter complex / response to stimulus / monoatomic cation transmembrane transport / monoatomic cation transport / cGMP binding ...intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / transmembrane transporter complex / response to stimulus / monoatomic cation transmembrane transport / monoatomic cation transport / cGMP binding / photoreceptor outer segment / visual perception / protein-containing complex binding / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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. ...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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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
cGMP-gated cation channel alpha-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 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 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: cGMP-gated cation channel alpha-1
B: cGMP-gated cation channel alpha-1
C: cGMP-gated cation channel alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0505
Polymers24,9193
Non-polymers1312
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-91 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.010, 76.710, 113.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cGMP-gated cation channel alpha-1 / Cyclic nucleotide-gated cation channel 1 / Cyclic nucleotide-gated channel alpha-1 / CNG channel ...Cyclic nucleotide-gated cation channel 1 / Cyclic nucleotide-gated channel alpha-1 / CNG channel alpha-1 / CNG-1 / CNG1 / Cyclic nucleotide-gated channel / photoreceptor / Rod photoreceptor cGMP-gated channel subunit alpha


Mass: 8306.367 Da / Num. of mol.: 3 / Fragment: CLZ domain (UNP residues 621-690)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CNCG, CNCG1, CNGA1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q00194
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18.2% w/v PEG3350, 45 mM zinc acetate, 9 mM cobalt chloride, pH 7.5, 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: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.14→56.555 Å / Num. all: 16022 / Num. obs: 16022 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.15 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.14-2.264.80.7750.71060722000.77596.9
2.26-2.3960.5381.21298821700.53899.9
2.39-2.5670.3771.81439720530.377100
2.56-2.767.60.2722.51465019270.272100
2.76-3.037.60.1763.91339217710.176100
3.03-3.387.50.1444.81210316120.144100
3.38-3.917.30.1115.71068914570.111100
3.91-4.797.10.0916.7888412440.091100
4.79-6.776.70.1035.766209840.103100
6.77-56.5556.40.0744.438436040.07499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L36

3l36


Resolution: 2.14→56.555 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8557 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 799 5 %RANDOM
Rwork0.2027 ---
obs0.2041 15965 99.37 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.637 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 90.2 Å2 / Biso mean: 29.3672 Å2 / Biso min: 6.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.042 Å20 Å20 Å2
2--9.249 Å2-0 Å2
3---0.3576 Å2
Refinement stepCycle: LAST / Resolution: 2.14→56.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 2 136 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071349
X-RAY DIFFRACTIONf_angle_d0.9531799
X-RAY DIFFRACTIONf_chiral_restr0.063213
X-RAY DIFFRACTIONf_plane_restr0.003223
X-RAY DIFFRACTIONf_dihedral_angle_d13.779539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.27410.31131390.25852392253196
2.2741-2.44970.23511160.220525042620100
2.4497-2.69620.27931350.196124972632100
2.6962-3.08630.22751440.193225022646100
3.0863-3.88830.21611200.174425762696100
3.8883-56.57470.20411450.211526952840100
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)
10.1471-0.07180.09230.64950.16290.12970.09060.0414-0.1076-0.1889-0.0448-0.12260.06690.01520.01680.2990.0633-0.00430.11660.0670.217527.652271.0589-1.7854
20.0005-0.0216-0.0350.11930.2340.459-0.12180.24440.0166-0.12870.08510.0129-0.102-0.1306-0.06180.0435-0.02860.00520.12160.02470.092931.183458.478911.0352
30.0283-0.0292-0.03380.0479-0.03690.3104-0.00870.010.0008-0.0118-0.0036-0.00920.0238-0.038-0.10940.09150.04320.030.21850.10820.153531.328145.699122.9248
40.0276-0.01570.00950.009-0.00570.0032-0.04310.0092-0.04670.00850.0095-0.01230.044-0.024-0.0810.14360.02780.11930.18660.10380.14330.930838.784425.5864
50.0173-0.00790.02450.1507-0.01240.03360.02390.04320.0241-0.039-0.0082-0.05370.0022-0.00040.11370.11790.02260.07510.21480.21810.198631.070331.202731.0954
60.1076-0.0236-0.07010.0060.01470.0467-0.03580.0342-0.0912-0.01490.06040.12280.0629-0.1130.01820.0926-0.00890.0180.14020.08120.195424.467619.360537.3356
70.00550.0021-0.00340.0011-0.00120.00270.04220.1361-0.0647-0.0777-0.0029-0.019-0.09770.03270.01750.5077-0.0560.0310.2689-0.08190.191326.735365.404-9.7037
80.00410.0199-0.00350.0883-0.03990.063-0.0536-0.0143-0.0322-0.03010.01590.05910.07610.03320.01350.2166-0.02060.03280.1955-0.0170.1223.20257.03250.2382
90.027-0.0108-0.0060.0065-0.00560.0327-0.0265-0.0010.01280.0086-0.0142-0.0318-0.03510.0362-0.05990.4937-0.0937-0.09960.27560.1410.127622.053547.254910.6338
100.25120.16970.06230.59820.00010.4665-0.03090.00420.02270.0601-0.0036-0.0349-0.00730.08940.0470.4449-0.0206-0.06740.30510.17120.289522.13940.980518.9714
110.03960.03670.03410.0698-0.02760.1284-0.0019-0.0044-0.0233-0.099-0.00780.0211-0.1877-0.02520.02570.3090.0272-0.02760.22160.18270.284719.81738.227226.0344
120.03220.0079-0.08730.0298-0.04650.2451-0.0575-0.0764-0.050.0540.09050.11010.0645-0.0714-0.08770.13580.07060.02430.16890.17950.217120.146431.388935.1618
130.02040.00050.02340.03380.01370.0305-0.05550.0035-0.0071-0.0049-0.0195-0.00070.0391-0.0065-0.2850.0728-0.01440.0330.16350.07430.116423.290827.686948.8845
140.0410.0073-0.0060.0367-0.01490.0060.0374-0.0521-0.00830.0509-0.0513-0.00520.08770.00440.00960.21610.07060.02870.24280.02260.086717.744468.232-2.8164
150.06370.06610.01520.1295-0.02570.0332-0.0094-0.07670.00580.02060.0262-0.1008-0.0273-0.04130.04320.06590.04330.01760.1216-0.01380.094218.638363.74027.1812
160.1701-0.0717-0.01940.05190.06570.1552-0.0540.0236-0.03410.0001-0.0405-0.09320.0110.0447-0.06660.0760.02650.01110.23030.02120.196420.431457.945817.7405
170.04040.09380.01370.4993-0.08620.05060.0018-0.0233-0.06380.0404-0.0887-0.069-0.0078-0.07780.01740.23140.10770.09430.26610.09720.189222.735848.536627.6772
180.30020.0227-0.09880.03210.02690.07240.0198-0.03380.00980.08730.01520.0052-0.0449-0.03490.04090.250.03980.06840.09210.15050.213926.709640.960437.2447
190.1563-0.18220.00140.211800.0001-0.1325-0.06510.11220.01610.0045-0.0246-0.12050.0458-0.03020.1280.0909-0.01820.24810.12410.230532.640932.692942.2608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:10)A2 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:28)A11 - 28
3X-RAY DIFFRACTION3(chain A and resid 29:33)A29 - 33
4X-RAY DIFFRACTION4(chain A and resid 34:38)A34 - 38
5X-RAY DIFFRACTION5(chain A and resid 39:46)A39 - 46
6X-RAY DIFFRACTION6(chain A and resid 47:58)A47 - 58
7X-RAY DIFFRACTION7(chain B and resid 1:8)B1 - 8
8X-RAY DIFFRACTION8(chain B and resid 9:20)B9 - 20
9X-RAY DIFFRACTION9(chain B and resid 21:28)B21 - 28
10X-RAY DIFFRACTION10(chain B and resid 29:33)B29 - 33
11X-RAY DIFFRACTION11(chain B and resid 34:38)B34 - 38
12X-RAY DIFFRACTION12(chain B and resid 39:48)B39 - 48
13X-RAY DIFFRACTION13(chain B and resid 49:61)B49 - 61
14X-RAY DIFFRACTION14(chain C and resid 3:9)C3 - 9
15X-RAY DIFFRACTION15(chain C and resid 10:19)C10 - 19
16X-RAY DIFFRACTION16(chain C and resid 20:25)C20 - 25
17X-RAY DIFFRACTION17(chain C and resid 26:37)C26 - 37
18X-RAY DIFFRACTION18(chain C and resid 38:43)C38 - 43
19X-RAY DIFFRACTION19(chain C and resid 44:52)C44 - 52

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