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- PDB-8xfy: The Crystal Structure of RSK2 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xfy
TitleThe Crystal Structure of RSK2 from Biortus.
ComponentsRibosomal protein S6 kinase alpha-3Ribosome
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / Cell cycle / Stress response / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / Recycling pathway of L1 / ERK/MAPK targets / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / Recycling pathway of L1 / ERK/MAPK targets / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / central nervous system development / skeletal system development / positive regulation of cell differentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Senescence-Associated Secretory Phenotype (SASP) / chemical synaptic transmission / positive regulation of cell growth / peptidyl-serine phosphorylation / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / synapse / nucleolus / negative regulation of apoptotic process / protein kinase binding / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Similarity search - Domain/homology
: / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Lin, D. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of RSK2 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Lin, D. / Pan, W.
History
DepositionDec 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-3
B: Ribosomal protein S6 kinase alpha-3
C: Ribosomal protein S6 kinase alpha-3
D: Ribosomal protein S6 kinase alpha-3
E: Ribosomal protein S6 kinase alpha-3
F: Ribosomal protein S6 kinase alpha-3
G: Ribosomal protein S6 kinase alpha-3
H: Ribosomal protein S6 kinase alpha-3
I: Ribosomal protein S6 kinase alpha-3
J: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,05120
Polymers369,36710
Non-polymers3,68410
Water3,099172
1
A: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Ribosomal protein S6 kinase alpha-3
hetero molecules


  • defined by author
  • 37.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,3052
Polymers36,9371
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.063, 273.373, 170.341
Angle α, β, γ (deg.)90.000, 92.135, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosomal protein S6 kinase alpha-3 / Ribosome


Mass: 36936.723 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA3 / Production host: unidentified baculovirus / References: UniProt: P51812
#2: Chemical
ChemComp-A1LU8 / 2,6-bis(fluoranyl)-4-[4-(4-morpholin-4-ylphenyl)pyridin-3-yl]phenol


Mass: 368.377 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C21H18F2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium malonate pH6.75, 18% PEG 3350 / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979514 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979514 Å / Relative weight: 1
ReflectionResolution: 3.2→48.213 Å / Num. obs: 50864 / % possible obs: 99.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 5.9
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.947 / Num. unique obs: 4397

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.213 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.856 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.206 / SU B: 35.418 / SU ML: 0.574 / Average fsc free: 0.9389 / Average fsc work: 0.9651 / Cross valid method: FREE R-VALUE / ESU R Free: 0.67
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3027 2573 5.063 %
Rwork0.2289 48250 -
all0.233 --
obs-50823 99.394 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.355 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å2-0 Å21.225 Å2
2--1.187 Å20 Å2
3---1.748 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21768 0 270 172 22210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01222573
X-RAY DIFFRACTIONr_bond_other_d0.0010.01621880
X-RAY DIFFRACTIONr_angle_refined_deg0.7371.65930360
X-RAY DIFFRACTIONr_angle_other_deg0.2511.5850468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60952654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.5259.369206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15104143
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.599101017
X-RAY DIFFRACTIONr_chiral_restr0.0350.23237
X-RAY DIFFRACTIONr_chiral_restr_other0.0140.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0225777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025253
X-RAY DIFFRACTIONr_nbd_refined0.1870.24389
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.221510
X-RAY DIFFRACTIONr_nbtor_refined0.1780.210844
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.211667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2525
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.274
X-RAY DIFFRACTIONr_nbd_other0.1340.2356
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_mcbond_it1.7395.37810706
X-RAY DIFFRACTIONr_mcbond_other1.7395.37810706
X-RAY DIFFRACTIONr_mcangle_it3.1679.65513330
X-RAY DIFFRACTIONr_mcangle_other3.1679.65513331
X-RAY DIFFRACTIONr_scbond_it1.2655.45811867
X-RAY DIFFRACTIONr_scbond_other1.2655.45811868
X-RAY DIFFRACTIONr_scangle_it2.4019.99217030
X-RAY DIFFRACTIONr_scangle_other2.4019.99217031
X-RAY DIFFRACTIONr_lrange_it5.74850.8724790
X-RAY DIFFRACTIONr_lrange_other5.74850.87424789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.2-3.2830.4121800.32335520.32737450.8780.92799.65290.294
3.283-3.3720.3281860.29235500.29437490.9270.94599.65320.262
3.372-3.470.3441750.28333600.28635400.9180.94899.85880.249
3.47-3.5760.3411600.26632130.2733800.9230.95499.79290.234
3.576-3.6920.2951620.25832330.2633990.9390.9699.88230.23
3.692-3.8210.3071770.23731220.24133110.940.96699.63760.214
3.821-3.9640.3161540.22828790.23230430.9380.96899.67140.206
3.964-4.1250.2581670.20828500.2130300.9610.97499.5710.189
4.125-4.3070.2751460.19628190.229780.9540.97899.56350.177
4.307-4.5160.2741180.18225320.18626640.9570.98199.47450.171
4.516-4.7570.2861460.19425320.19926940.9530.97999.40610.182
4.757-5.0430.2771500.17823100.18424680.9680.98399.67580.165
5.043-5.3870.3151010.22921600.23323200.9380.97297.45690.214
5.387-5.8130.299970.22421000.22822340.9370.97598.34380.206
5.813-6.3580.347850.21818950.22319810.9360.97699.94950.196
6.358-7.0930.312960.21117530.21618600.9580.97499.40860.193
7.093-8.1610.256990.19515140.19916210.9680.98199.50650.187
8.161-9.9240.273720.19312730.19613520.9570.98899.48230.195
9.924-13.7470.241580.20910050.21110880.9730.98397.70220.214
13.747-48.2130.42440.3675980.3716600.8710.93897.27270.372

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