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- PDB-4j9v: Crystal Structure of the TrkA Gating ring bound to ATP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 4j9v
TitleCrystal Structure of the TrkA Gating ring bound to ATP-gamma-S
ComponentsPotassium uptake protein TrkA
KeywordsTRANSPORT PROTEIN / RCK domain / nucleotide binding / potassium transport / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Trk system potassium uptake protein TrkA
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.051 Å
AuthorsHuang, H. / Levin, E.J. / Jin, X. / Cao, Y. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nature / Year: 2013
Title: Gating of the TrkH ion channel by its associated RCK protein TrkA.
Authors: Cao, Y. / Pan, Y. / Huang, H. / Jin, X. / Levin, E.J. / Kloss, B. / Zhou, M.
History
DepositionFeb 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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: Potassium uptake protein TrkA
B: Potassium uptake protein TrkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6249
Polymers100,3862
Non-polymers2,2387
Water19811
1
A: Potassium uptake protein TrkA
B: Potassium uptake protein TrkA
hetero molecules

A: Potassium uptake protein TrkA
B: Potassium uptake protein TrkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,24818
Polymers200,7724
Non-polymers4,47514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area14150 Å2
ΔGint-99 kcal/mol
Surface area74200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.324, 109.324, 337.656
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Potassium uptake protein TrkA


Mass: 50193.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP3045 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87KD2
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30% PEG 400, 100 mM Glycine, 200 mM MgSO4, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 23765 / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.103 / Χ2: 0.847 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.05-3.112.10.88911420.7021100
3.1-3.16120.78111470.7341100
3.16-3.22120.6411720.7611100
3.22-3.29120.52811410.6761100
3.29-3.36120.42611430.8111100
3.36-3.43120.34311710.7021100
3.43-3.5211.90.28611710.7021100
3.52-3.62120.24811540.871100
3.62-3.7211.90.24311570.7781100
3.72-3.8411.90.18911720.9341100
3.84-3.9811.70.16911720.5531100
3.98-4.1411.90.11711730.9891100
4.14-4.3311.80.09811871.0431100
4.33-4.5611.60.08511941.031100
4.56-4.8411.80.07711721.0471100
4.84-5.2111.50.08112121.0011100
5.21-5.7411.40.08412110.981199.9
5.74-6.5711.20.08112221.0461100
6.57-8.2710.70.05312600.843199.9
8.27-5010.10.03613920.7291100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.051→49.17 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7752 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1200 5.07 %RANDOM
Rwork0.2114 ---
obs0.2144 23674 99.92 %-
all-23677 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 338.58 Å2 / Biso mean: 85.7532 Å2 / Biso min: 22.72 Å2
Refinement stepCycle: LAST / Resolution: 3.051→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6990 0 131 11 7132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067224
X-RAY DIFFRACTIONf_angle_d1.0219830
X-RAY DIFFRACTIONf_chiral_restr0.0561156
X-RAY DIFFRACTIONf_plane_restr0.0041272
X-RAY DIFFRACTIONf_dihedral_angle_d15.1552697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0513-3.17350.32411210.27742415253699
3.1735-3.31790.33421320.26424452577100
3.3179-3.49280.32551400.236324072547100
3.4928-3.71150.28841410.225824482589100
3.7115-3.9980.31191240.213124612585100
3.998-4.40010.26921300.181425032633100
4.4001-5.03620.25591510.173324812632100
5.0362-6.3430.24921390.226925532692100
6.343-49.17630.24211220.208427612883100
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)
15.6235-3.0814-0.2982.68941.71280.7459-0.4777-0.6335-0.44860.7550.29810.02220.17170.22380.22780.72750.13890.01550.65750.21570.374-40.4599-27.9082-4.136
21.24790.29760.72173.8353-1.49686.07090.09880.2456-0.1988-0.2823-0.3048-1.96470.7491.76710.10840.51440.1647-0.01441.10880.04591.1915-11.9747-42.4778-13.1842
35.4764-0.61510.41621.15490.08052.8048-0.65110.31430.7951-0.11370.13010.0499-0.75260.12060.39890.8441-0.0272-0.18850.28650.11520.5714-58.3258-6.3592-15.5469
41.5452-0.16551.70847.8198-4.03956.4227-0.24560.1730.2277-0.3399-0.17151.0532-0.1659-1.11630.56430.56960.1299-0.02230.7852-0.27470.9288-90.56281.6252-16.7555
57.51270.6977-1.075.53680.5974.0775-0.11410.5738-0.72670.0032-0.35110.38620.9024-0.4470.3520.91050.03390.04260.5278-0.16070.4881-80.8588-20.5258-11.5939
610.07841.41310.55329.57470.04983.59650.24840.1412-0.2179-1.9353-0.162-0.6461-0.26520.4317-0.0321.01250.062-0.06850.43860.09330.6439-72.802314.5716-20.9804
74.06650.14921.28974.4385-0.23516.9177-0.14670.58090.3884-0.74210.0925-0.4514-0.7680.2413-0.0710.51660.0120.0870.73210.08780.513-27.4543-29.9305-26.868
82.47230.67141.04782.8498-0.72657.96670.1355-0.284-0.12220.8917-0.0441-0.7212-0.07160.698-0.07380.79170.1094-0.32940.60010.09480.7176-21.3759-42.21167.4151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 152 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 241)A0
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 152 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 153 through 241 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 242 through 364 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 365 through 455 )B0
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 364 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 365 through 455 )A0

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