- PDB-4hpt: Crystal structure of the catalytic subunit of cAMP-dependent prot... -
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Basic information
Entry
Database: PDB / ID: 4hpt
Title
Crystal structure of the catalytic subunit of cAMP-dependent protein kinase displaying complete phosphoryl transfer of AMP-PNP onto a substrate peptide
Components
cAMP-dependent protein kinase catalytic subunit alpha
spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / regulation of synaptic transmission, glutamatergic / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha Similarity search - Component
Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal grow
Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein buffer: 50 mM Bicine, 150 mM Ammonium Acetate, 10 mM DTT, ~7-10 mg/mL protein Well Solution: 1 mL of 2% MPD, 80 uL methanol added to the well immediately before sealing 8 uL drops of ...Details: Protein buffer: 50 mM Bicine, 150 mM Ammonium Acetate, 10 mM DTT, ~7-10 mg/mL protein Well Solution: 1 mL of 2% MPD, 80 uL methanol added to the well immediately before sealing 8 uL drops of 1:1 protein:well were used., VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 8.0
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.15→44.35 Å / Num. obs: 21475 / % possible obs: 85.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shell
Resolution: 2.15→2.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.8 / % possible all: 66.2
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0110
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→44.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.412 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22797
1076
5.1 %
RANDOM
Rwork
0.18709
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-
-
obs
0.18907
20161
83.81 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 35.324 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.14 Å2
0 Å2
0 Å2
2-
-
1.98 Å2
0 Å2
3-
-
-
-1.84 Å2
Refinement step
Cycle: LAST / Resolution: 2.15→44.35 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2908
0
29
177
3114
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
3018
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.155
1.965
4089
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.512
5
358
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.923
23.878
147
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.545
15.057
522
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.757
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
433
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2280
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.497
1.5
1776
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.936
2
2864
X-RAY DIFFRACTION
r_scbond_it
1.344
3
1242
X-RAY DIFFRACTION
r_scangle_it
2.201
4.5
1223
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.15→2.206 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.27
59
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Rwork
0.258
1098
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obs
-
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63.16 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.2947
-0.2414
0.0375
0.6288
0.2677
0.9711
0.001
0.0076
0.0208
-0.0103
-0.0145
0.0125
-0.0151
0.1377
0.0135
0.0041
-0.0093
-0.0023
0.0602
0.018
0.0196
27.0983
-2.5511
-2.5763
2
1.7121
-0.9867
-0.5716
1.6413
1.8433
2.739
-0.082
-0.0896
-0.0985
-0.0646
0.0218
0.092
-0.0125
-0.1422
0.0602
0.0611
-0.0223
0.0065
0.0606
0.0157
0.0209
13.729
1.1935
9.2946
3
3.8988
-10.3884
-0.8459
27.6818
2.2533
0.1838
-0.1716
-0.0718
0.2778
0.492
0.2211
-0.7315
0.0411
0.0094
-0.0495
0.0242
-0.0277
-0.004
0.1567
0.0525
0.0884
26.593
-10.1383
2.5248
4
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.055
-0.0254
0.0036
0.0781
0.0605
0.0585
22.4696
-7.2082
0.528
5
0.6696
-0.3965
-0.1794
0.3291
0.3962
1.0758
-0.0213
0.0114
-0.002
0.0056
0.0035
0.0176
0.0174
0.0808
0.0178
0.041
0.0097
0.0002
0.0465
0.026
0.0573
25.5477
-2.2906
-1.3541
6
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0.1232
-0.0718
0.0368
0.2109
0.1783
0.247
21.0937
-8.5463
-3.391
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
E
14 - 350
2
X-RAY DIFFRACTION
2
I
5 - 23
3
X-RAY DIFFRACTION
3
E
401
4
X-RAY DIFFRACTION
4
E
402
5
X-RAY DIFFRACTION
5
E
501 - 659
6
X-RAY DIFFRACTION
5
I
101 - 118
7
X-RAY DIFFRACTION
6
E
403
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