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- PDB-3l4b: Crystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Rin... -

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Basic information

Entry
Database: PDB / ID: 3l4b
TitleCrystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Ring Gating Assembly, TM1088A:TM1088B, from Thermotoga maritima
Components
  • TrkA K+ Channel protein TM1088A
  • TrkA K+ Channel protein TM1088B
KeywordsTRANSPORT PROTEIN / Potassium Channel / Ring-Gating Complex / TrkA / Structural Genomics / PSI-2-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


potassium ion transmembrane transporter activity / nucleotide binding / plasma membrane
Similarity search - Function
Potassium uptake protein TrkA / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain ...Potassium uptake protein TrkA / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TrkA K+ Channel protien TM1088A / Trk system potassium uptake protein TrkA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.45 Å
AuthorsDeller, M.C. / Johnson, H.A. / Miller, M. / Spraggon, G. / Wilson, I.A. / Lesley, S.A. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Ring Gating Assembly, TM1088A:TM1088B, from Thermotoga maritima
Authors: Deller, M.C. / Johnson, H.A. / Miller, M. / Spraggon, G. / Lesley, S.A.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 2, 2020Group: Derived calculations / Structure summary / Category: entity / struct / struct_site
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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
Item: _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: TrkA K+ Channel protein TM1088A
B: TrkA K+ Channel protein TM1088A
C: TrkA K+ Channel protein TM1088B
D: TrkA K+ Channel protein TM1088B
E: TrkA K+ Channel protein TM1088A
F: TrkA K+ Channel protein TM1088A
G: TrkA K+ Channel protein TM1088B
H: TrkA K+ Channel protein TM1088B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,85913
Polymers160,4708
Non-polymers1,3895
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20660 Å2
ΔGint-162 kcal/mol
Surface area56420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.778, 96.778, 305.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31E
41F
12C
22D
32G
42H
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
TrkA K+ Channel protein TM1088A


Mass: 16051.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1088 / Production host: Escherichia coli (E. coli) / References: UniProt: D3KFX7*PLUS
#2: Protein
TrkA K+ Channel protein TM1088B


Mass: 24066.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1088 / Production host: Escherichia coli (E. coli) / References: UniProt: D3KFX8*PLUS
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Magnesium Chloride, 15% PEG 4000, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2007
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→48.39 Å / Num. all: 22866 / Num. obs: 22866 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.45→3.57 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: 2G1U

2g1u


Resolution: 3.45→48.39 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.836 / SU B: 74.088 / SU ML: 0.559 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.703 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3) STRUCTURE BASED ON HIGH RESOLUTION STRUCTURE OF INDIVIDUAL COMPONENTS. (4) ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3) STRUCTURE BASED ON HIGH RESOLUTION STRUCTURE OF INDIVIDUAL COMPONENTS. (4) UNKNOWN ION MODELLED AS UNX NEXT TO ADENINE MOIETY OF AMP. (5) 12 TLS GROUPS SELECTED ACCORDING TO PROTEIN DOMAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30827 1164 5.1 %RANDOM
Rwork0.25893 ---
all0.26134 21497 --
obs0.26134 21497 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.705 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 3.45→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8952 0 93 0 9045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0219192
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.95412588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.35851350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57724.503302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32915978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6931532
X-RAY DIFFRACTIONr_chiral_restr0.0650.21519
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217161
X-RAY DIFFRACTIONr_mcbond_it0.53736732
X-RAY DIFFRACTIONr_mcangle_it1.192510378
X-RAY DIFFRACTIONr_scbond_it2.69682460
X-RAY DIFFRACTIONr_scangle_it4.513112210
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A762tight positional0.030.05
11B762tight positional0.030.05
11E762tight positional0.020.05
11F762tight positional0.020.05
22C1194tight positional0.020.05
22D1194tight positional0.030.05
22G1194tight positional0.020.05
22H1194tight positional0.020.05
11A762tight thermal0.040.5
11B762tight thermal0.040.5
11E762tight thermal0.030.5
11F762tight thermal0.030.5
22C1194tight thermal0.040.5
22D1194tight thermal0.040.5
22G1194tight thermal0.030.5
22H1194tight thermal0.030.5
LS refinement shellResolution: 3.45→3.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 84 -
Rwork0.281 1532 -
obs-1532 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)
13.65810.7221-0.372210.84320.26943.8831-0.1179-0.2240.46891.201-0.0620.2854-0.7623-0.20070.17990.35470.11210.05130.26330.00630.1591-18.8822.285836.7588
27.5054-2.2947-1.40065.1375-0.20835.5628-0.03510.046-0.5335-0.3206-0.0887-0.18580.53990.31390.12380.13380.1105-0.00020.13540.01310.12137.864-22.497416.1612
35.5623.45273.302716.29417.8834.81530.1852-0.1061-0.47194.21710.0426-0.94592.06520.6209-0.22781.0910.2789-0.21140.8210.14060.30330.106-12.177930.7982
49.3152-0.58451.31045.2450.446.22250.00410.25380.4881-0.3783-0.04330.0672-0.66020.17730.03920.5107-0.07920.10640.0743-0.03930.32351.486133.924218.7349
52.6311-0.3911-0.90934.82660.20057.31530.03870.1331-0.0686-0.3344-0.2662-0.0454-0.6560.06530.22750.03270.0355-0.07490.17430.01630.0374-16.86311.903719.0757
63.6918-0.84610.0333.42610.51994.7697-0.1881-0.4698-0.21990.42270.29760.1030.35540.2965-0.10950.06930.0580.03870.20370.10170.0432-9.3108-11.265433.3592
72.3131-0.0403-0.6936.10481.48667.58030.19510.08380.0432-0.47160.0072-0.0539-0.10590.3261-0.20230.0468-0.11730.04210.50450.00680.209126.61339.494916.2662
85.5053-1.7559-1.12253.39890.66223.09280.2182-0.6640.37710.53920.0583-0.5537-0.66590.2446-0.27650.4345-0.3072-0.05060.5535-0.12650.179520.90921.575232.7262
95.32042.5351-1.76690.5348-1.440420.6333-0.0685-0.33640.30850.36071.14160.56592.5232-1.5486-1.07310.4993-0.2738-0.32930.60020.1431.6543-36.6427-22.110934.1886
108.12752.45260.85466.6563-1.90819.79510.40640.6879-0.6266-0.7496-0.37220.62470.1727-0.8761-0.03420.22530.0423-0.12250.4616-0.16711.1884-39.263-16.790916.4462
1111.95714.29552.795-1.8788-2.53869.317-0.7926-0.7414-0.35990.4837-0.5635-1.3639-1.42921.51521.3560.734-0.3927-0.08140.9510.01362.000248.962531.403230.7963
1211.233110.2613-5.74489.256-4.885512.2274-0.72981.0698-0.3166-1.35530.0107-2.2397-0.49610.50460.71920.6143-0.30390.45981.1248-0.36442.047148.613128.90113.6492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 137
2X-RAY DIFFRACTION2B7 - 135
3X-RAY DIFFRACTION3E9 - 138
4X-RAY DIFFRACTION4F8 - 135
5X-RAY DIFFRACTION5C1 - 134
6X-RAY DIFFRACTION6D1 - 134
7X-RAY DIFFRACTION7G1 - 134
8X-RAY DIFFRACTION8H1 - 134
9X-RAY DIFFRACTION9C135 - 216
10X-RAY DIFFRACTION10D135 - 216
11X-RAY DIFFRACTION11G135 - 216
12X-RAY DIFFRACTION12H135 - 214

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