[English] 日本語
Yorodumi
- PDB-3c0g: CASK CaM-Kinase Domain- 3'-AMP complex, P1 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c0g
TitleCASK CaM-Kinase Domain- 3'-AMP complex, P1 form
ComponentsPeripheral plasma membrane protein CASK
KeywordsTRANSFERASE / CASK / neurexin / Ca2+/calmodulin dependent protein kinase / Mg2+ / synaptic plasticity / pseudokinase / MAGUK / membrane-associated guanylate kinase / ATP-binding / Calmodulin-binding / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Serine/threonine-protein kinase / SH3 domain
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Nephrin family interactions ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / Assembly and cell surface presentation of NMDA receptors / calcium ion import / Nephrin family interactions / Sensory processing of sound by outer hair cells of the cochlea / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / ciliary membrane / regulation of synaptic vesicle exocytosis / negative regulation of cell-matrix adhesion / Syndecan interactions / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / protein localization / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / signaling receptor binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3AM / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsWahl, M.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: CASK Functions as a Mg2+-independent neurexin kinase
Authors: Mukherjee, K. / Sharma, M. / Urlaub, H. / Bourenkov, G.P. / Jahn, R. / Sudhof, T.C. / Wahl, M.C.
History
DepositionJan 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK
B: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2094
Polymers78,5142
Non-polymers6942
Water4,540252
1
A: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6042
Polymers39,2571
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6042
Polymers39,2571
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.328, 60.267, 60.553
Angle α, β, γ (deg.)90.00, 106.49, 105.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 6 - 304 / Label seq-ID: 20 - 318

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Lin-2 homolog


Mass: 39257.121 Da / Num. of mol.: 2 / Fragment: CaM-Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK / Plasmid: pGEX-6T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.19→30 Å / Num. obs: 32667 / % possible obs: 89.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 48 Å2 / Rsym value: 0.112 / Net I/σ(I): 12.4
Reflection shellResolution: 2.19→2.3 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 4046 / Rsym value: 0.427 / % possible all: 76.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rat CamKI

Resolution: 2.19→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.385 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.375 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26969 1576 4.9 %RANDOM
Rwork0.20754 ---
obs0.21074 30426 86.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.058 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20.42 Å20.57 Å2
2---1.04 Å20.06 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.19→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 46 252 5308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225237
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9767079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96622.739230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92315926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8181540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023927
X-RAY DIFFRACTIONr_nbd_refined0.1880.22443
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2325
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.215
X-RAY DIFFRACTIONr_mcbond_it3.03643245
X-RAY DIFFRACTIONr_mcangle_it4.17765097
X-RAY DIFFRACTIONr_scbond_it3.27242257
X-RAY DIFFRACTIONr_scangle_it4.28261982
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2388 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.290.5
medium thermal0.552
LS refinement shellResolution: 2.188→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 84 -
Rwork0.278 1414 -
obs--54.51 %
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)
11.46030.3329-0.97072.7703-1.55293.9810.0833-0.08330.13450.34360.01260.1193-0.4485-0.3284-0.0958-0.11310.0762-0.0155-0.1686-0.0356-0.15520.78911.9885-0.0971
21.7818-0.6148-1.45632.46411.29944.67290.19030.15550.0883-0.5479-0.0227-0.0564-0.69210.1087-0.1676-0.04410.0018-0.0172-0.21980.0331-0.180128.1734-21.0164-24.9295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 9520 - 109
2X-RAY DIFFRACTION1AA96 - 322110 - 336
3X-RAY DIFFRACTION2BB5 - 9519 - 109
4X-RAY DIFFRACTION2BB96 - 324110 - 338

+
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