[English] 日本語
Yorodumi
- PDB-4wb6: Crystal structure of a L205R mutant of human cAMP-dependent prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wb6
TitleCrystal structure of a L205R mutant of human cAMP-dependent protein kinase A (catalytic alpha subunit)
Components
  • (cAMP-dependent protein kinase catalytic subunit ...CAMP-dependent pathway) x 2
  • PKI (5-24)
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Cushing's syndrome / protein kinase / phosphorylation / mutant / adenosine triphosphate / catalysis / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / regulation of cardiac conduction / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / sperm flagellum / Mitochondrial protein degradation / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / Recruitment of NuMA to mitotic centrosomes / cellular response to epinephrine stimulus / calcium channel complex / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / Regulation of insulin secretion / neural tube closure / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / cellular response to heat / manganese ion binding / Factors involved in megakaryocyte development and platelet production / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle
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
ADENOSINE-5'-TRIPHOSPHATE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural insights into mis-regulation of protein kinase A in human tumors.
Authors: Cheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Robine, N. / Darnell, R.B. / Hendrickson, W.A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
J: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16710
Polymers86,0564
Non-polymers1,1126
Water3,549197
1
A: cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5845
Polymers43,0282
Non-polymers5563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area16210 Å2
MethodPISA
2
B: cAMP-dependent protein kinase catalytic subunit alpha
J: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5845
Polymers43,0282
Non-polymers5563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-26 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.169, 90.193, 90.377
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
CAMP-dependent protein kinase catalytic subunit ... , 2 types, 2 molecules AB

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / PKA C-alpha


Mass: 40801.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / PKA C-alpha


Mass: 40801.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase

-
Protein/peptide , 1 types, 2 molecules IJ

#3: Protein/peptide PKI (5-24)


Mass: 2226.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925*PLUS

-
Non-polymers , 3 types, 203 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000, 0.1M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 52562 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/av σ(I): 20.8 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.85 / % possible all: 99.3

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WB8

4wb8


Resolution: 2.1→40.492 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2572 4.94 %RANDOM
Rwork0.1878 ---
obs0.1903 52060 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→40.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 66 197 6203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086156
X-RAY DIFFRACTIONf_angle_d1.0578320
X-RAY DIFFRACTIONf_dihedral_angle_d14.9662302
X-RAY DIFFRACTIONf_chiral_restr0.044865
X-RAY DIFFRACTIONf_plane_restr0.0051052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13460.36261270.28162566X-RAY DIFFRACTION93
2.1346-2.17820.34111350.27862753X-RAY DIFFRACTION99
2.1782-2.22550.32971210.28332789X-RAY DIFFRACTION100
2.2255-2.27730.54651260.48392468X-RAY DIFFRACTION89
2.2773-2.33430.34191550.26442771X-RAY DIFFRACTION100
2.3343-2.39740.33051400.23072734X-RAY DIFFRACTION99
2.3974-2.46790.30411580.23432755X-RAY DIFFRACTION99
2.4679-2.54750.29721580.23262728X-RAY DIFFRACTION99
2.5475-2.63860.30881200.22722772X-RAY DIFFRACTION100
2.6386-2.74420.31321510.23732775X-RAY DIFFRACTION100
2.7442-2.86910.25281740.22142753X-RAY DIFFRACTION100
2.8691-3.02030.29021340.22262795X-RAY DIFFRACTION100
3.0203-3.20940.30461510.21092789X-RAY DIFFRACTION100
3.2094-3.45710.23061510.20882754X-RAY DIFFRACTION100
3.4571-3.80480.25231620.18252791X-RAY DIFFRACTION100
3.8048-4.35480.171550.14362788X-RAY DIFFRACTION100
4.3548-5.48440.16871220.12412825X-RAY DIFFRACTION100
5.4844-40.50.14041320.13292882X-RAY DIFFRACTION100
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)
12.87430.9709-0.01533.4282-1.11074.4393-0.13940.0579-0.0661-0.10350.1471-0.5212-0.23710.70740.00080.395-0.03060.03550.4823-0.09440.33991.8356-17.6062-23.3619
21.51140.1563-0.36862.36350.50584.4214-0.08810.1167-0.1483-0.1170.0942-0.22390.13080.364-0.02290.2679-0.0210.00420.3546-0.05480.3714-4.0296-22.8688-31.8832
33.5844-0.1231-0.82051.44640.09399.4483-0.10990.3079-0.0639-0.30030.04210.2359-0.2319-1.43370.04750.4134-0.0409-0.00560.5023-0.07430.4062-19.2493-23.538-34.1244
43.57680.4685-0.44861.89810.03545.5672-0.28020.584-0.4735-0.46740.2670.08040.9509-0.46180.01250.7916-0.14110.03320.5008-0.14470.4808-12.9159-36.7777-41.7507
52.91430.2308-2.0015.81752.46162.9350.1386-0.01290.1473-0.41480.1379-0.3151-1.0640.9993-0.33260.5066-0.0442-0.03150.59660.01640.42920.2522-7.0667-27.8508
64.53620.2629-0.22683.4166-0.20334.54810.1604-0.1308-0.318-0.0901-0.14060.05870.6342-0.9606-0.03360.5192-0.0717-0.01220.51160.07010.3029-21.7296-34.08852.9681
72.30990.83430.69142.98670.04257.27290.0351-0.1124-0.16390.1182-0.046-0.00570.2432-1.16620.00060.3123-0.0070.01190.45420.02050.3352-23.5292-28.76016.7371
82.24130.57450.20992.4041-0.14225.91950.1023-0.32050.20710.2697-0.171-0.066-0.9502-0.02760.05780.55750.0089-0.02360.35350.03440.3439-11.612-18.958215.1544
93.19570.5061-0.05212.2848-0.89187.0767-0.0995-0.1879-0.0931-0.00540.11880.35670.3601-1.6044-0.00790.58320.00780.02780.9178-0.02860.5144-35.124-29.36343.1746
109.7731-0.64893.70732.43273.78398.208-0.41982.06680.1535-1.8772-0.97420.9155-0.9931-0.79981.29170.82520.0519-0.09711.0588-0.04550.5456-19.5859-15.7819-53.5762
115.00894.28583.41236.84021.35133.1682-0.0529-0.16830.56970.7932-0.42270.8832-1.3701-1.39250.53510.65010.07610.03340.6262-0.10060.532-14.8524-12.0254-39.5553
126.73580.7902-2.20293.182-2.58732.47621.3777-0.83981.01071.0295-0.20010.1453-1.76430.4483-1.04151.28560.15890.15971.1038-0.12620.6912-24.5271-8.763528.4152
135.6613-0.091-3.77284.46513.15535.45980.2672-0.42680.828-0.1372-0.38981.1798-2.0339-1.41490.08410.88390.3550.02610.8589-0.12060.6248-28.9227-12.619115.11
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 179 )
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 350 )
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 316 )
9X-RAY DIFFRACTION9chain 'B' and (resid 317 through 350 )
10X-RAY DIFFRACTION10chain 'I' and (resid 5 through 13 )
11X-RAY DIFFRACTION11chain 'I' and (resid 14 through 23 )
12X-RAY DIFFRACTION12chain 'J' and (resid 5 through 11 )
13X-RAY DIFFRACTION13chain 'J' and (resid 12 through 24 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more