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- PDB-4ojk: Structure of the cGMP Dependent Protein Kinase II and Rab11b Complex -

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Basic information

Entry
Database: PDB / ID: 4ojk
TitleStructure of the cGMP Dependent Protein Kinase II and Rab11b Complex
Components
  • Ras-related protein Rab-11B
  • cGMP-dependent protein kinase 2
KeywordsHydrolase/Protein Binding / small gtpase / leucine zipper / trafficking / serine/threonine kinase / membrane associated / Hydrolase-Protein Binding complex
Function / homology
Function and homology information


constitutive secretory pathway / negative regulation of chloride transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / receptor recycling / cGMP effects / regulation of endocytic recycling / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / regulated exocytosis / amyloid-beta clearance by transcytosis ...constitutive secretory pathway / negative regulation of chloride transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / receptor recycling / cGMP effects / regulation of endocytic recycling / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / regulated exocytosis / amyloid-beta clearance by transcytosis / transferrin transport / negative regulation of cell volume / melanosome transport / cellular hypotonic response / regulation of protein localization to cell surface / cellular response to acidic pH / peptidyl-serine autophosphorylation / RAB geranylgeranylation / myosin V binding / endocytic recycling / establishment of protein localization to membrane / insulin secretion involved in cellular response to glucose stimulus / TBC/RABGAPs / cGMP binding / phagocytic vesicle / small monomeric GTPase / regulation of monoatomic anion transport / G protein activity / protein localization to plasma membrane / circadian regulation of gene expression / synaptic vesicle membrane / recycling endosome / circadian rhythm / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / synaptic vesicle / nuclear membrane / cadherin binding / apical plasma membrane / protein phosphorylation / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / small GTPase Rab1 family profile. / 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 ...cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / small GTPase Rab1 family profile. / 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 / Extension to Ser/Thr-type protein kinases / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / RmlC-like jelly roll fold / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11B / cGMP-dependent protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.657 Å
AuthorsReger, A.S. / Yang, M.P. / Guo, E. / Kim, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the cGMP-dependent Protein Kinase II Leucine Zipper and Rab11b Protein Complex Reveals Molecular Details of G-kinase-specific Interactions.
Authors: Reger, A.S. / Yang, M.P. / Koide-Yoshida, S. / Guo, E. / Mehta, S. / Yuasa, K. / Liu, A. / Casteel, D.E. / Kim, C.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Derived calculations
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 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 / 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 / _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: Ras-related protein Rab-11B
B: Ras-related protein Rab-11B
C: cGMP-dependent protein kinase 2
D: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4116
Polymers55,5244
Non-polymers8862
Water37821
1
A: Ras-related protein Rab-11B
C: cGMP-dependent protein kinase 2
hetero molecules

B: Ras-related protein Rab-11B
D: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4116
Polymers55,5244
Non-polymers8862
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_444-x-1/2,y-1/2,-z-1/41
Buried area6730 Å2
ΔGint-52 kcal/mol
Surface area18230 Å2
MethodPISA
2
A: Ras-related protein Rab-11B
C: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2053
Polymers27,7622
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-19 kcal/mol
Surface area10990 Å2
MethodPISA
3
B: Ras-related protein Rab-11B
D: cGMP-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2053
Polymers27,7622
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-16 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.007, 136.007, 76.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ras-related protein Rab-11B / GTP-binding protein YPT3


Mass: 22400.055 Da / Num. of mol.: 2 / Mutation: R184C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11B, YPT3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15907, small monomeric GTPase
#2: Protein/peptide cGMP-dependent protein kinase 2 / cGK 2 / cGK2 / cGMP-dependent protein kinase II / cGKII


Mass: 5362.073 Da / Num. of mol.: 2 / Fragment: UNP residues 40-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkg2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64595
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate dibasic, 10 mM ethylenediaminetetraacetic acid disodium salt dehydrate., pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 8, 2012
RadiationMonochromator: Kohzu HLD-4 Double Crystal Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.657→19.949 Å / Num. all: 21309 / Num. obs: 21139 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.66→2.8 Å / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 3.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Specdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F9L

2f9l


Resolution: 2.657→19.949 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1051 4.98 %Random
Rwork0.2013 ---
all0.2037 21309 --
obs0.2037 21125 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.657→19.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 56 21 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033184
X-RAY DIFFRACTIONf_angle_d0.6944330
X-RAY DIFFRACTIONf_dihedral_angle_d13.7951118
X-RAY DIFFRACTIONf_chiral_restr0.047518
X-RAY DIFFRACTIONf_plane_restr0.001539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6565-2.77710.38691250.33912454X-RAY DIFFRACTION99
2.7771-2.92310.40821290.30662464X-RAY DIFFRACTION99
2.9231-3.10560.33691270.28522468X-RAY DIFFRACTION99
3.1056-3.34440.36291290.2672485X-RAY DIFFRACTION99
3.3444-3.6790.25611330.20962500X-RAY DIFFRACTION99
3.679-4.2070.22281320.17082512X-RAY DIFFRACTION100
4.207-5.28410.1951350.15042547X-RAY DIFFRACTION99
5.2841-19.94980.23761410.19822644X-RAY DIFFRACTION98
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)
14.7804-1.72392.87655.9893-1.68615.31090.10910.443-0.3741-0.2991-0.3157-0.07830.51990.24860.20620.4054-0.00440.05790.27380.03670.4036-45.33624.5853-18.351
21.75082.2839-1.4966.614-4.14177.7717-0.05310.0894-0.163-0.1073-0.1837-0.5924-0.27350.1256-0.00990.47130.0131-0.02350.22160.05720.6179-41.6396-0.3697-12.2643
35.2725-0.83640.86734.142-0.00553.74090.1562-0.50140.09980.9478-0.4916-0.4223-0.21910.12210.30980.6314-0.1521-0.08080.33670.09340.4503-45.292914.2557-7.8417
47.8936-0.18672.95739.50890.42525.247-0.00530.11930.40090.1239-0.2662-0.45260.01260.31820.2490.4966-0.1455-0.00020.4515-0.02060.4701-32.588640.8765-7.158
56.64611.0267-1.05981.8049-2.28513.77410.6947-1.134-0.01980.4681-0.3068-0.03010.13580.078-0.4110.9278-0.1232-0.17050.5125-0.09930.3918-31.335638.76064.5921
64.46760.47980.12480.8518-2.06254.17110.771-0.95660.10771.4055-0.7163-0.96730.42650.2913-0.21281.1957-0.4021-0.32570.65030.10710.5605-33.184330.79126.7573
74.65070.8671-0.17145.16420.67381.52690.1978-0.326-0.1951.2075-0.4861-0.01540.5603-0.08720.17120.7994-0.1898-0.0590.4638-0.04390.409-40.872931.8836-0.943
82.99254.26642.8696.40932.34127.4253-0.148-0.37810.27990.0395-0.4731-0.39980.46610.47920.43390.41990.08590.01650.41680.16260.4936-40.0768-10.6545-11.3843
99.0962-0.60294.39712.78660.04556.0625-0.2655-2.23370.48061.5224-0.25810.92970.9133-0.81380.07340.6598-0.10990.3330.3639-0.1650.7973-31.599456.2862-0.6158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 179 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 66 )
5X-RAY DIFFRACTION5chain 'B' and (resid 67 through 95 )
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 178 )
8X-RAY DIFFRACTION8chain 'C' and (resid 47 through 83 )
9X-RAY DIFFRACTION9chain 'D' and (resid 49 through 81 )

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