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- PDB-6lnm: Crystal structure of CASK-CaMK in complex with Mint1-CID -

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Basic information

Entry
Database: PDB / ID: 6lnm
TitleCrystal structure of CASK-CaMK in complex with Mint1-CID
Components
  • Amyloid-beta A4 precursor protein-binding family A member 1
  • Peripheral plasma membrane protein CASK
KeywordsTRANSFERASE / CASK / Lin-2 / MAGUK / Mint1 / CaMK / calmodulin-dependent protein kinase
Function / homology
Function and homology information


podocyte foot / Dopamine Neurotransmitter Release Cycle / negative regulation of cellular response to growth factor stimulus / gamma-aminobutyric acid secretion / Neurexins and neuroligins / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / nuclear lamina / regulation of neurotransmitter secretion / negative regulation of wound healing ...podocyte foot / Dopamine Neurotransmitter Release Cycle / negative regulation of cellular response to growth factor stimulus / gamma-aminobutyric acid secretion / Neurexins and neuroligins / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / nuclear lamina / regulation of neurotransmitter secretion / negative regulation of wound healing / positive regulation of dendritic spine morphogenesis / apical dendrite / glutamate secretion / calcium ion import / ciliary membrane / regulation of synaptic vesicle exocytosis / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / presynaptic active zone membrane / phosphatidylinositol-4,5-bisphosphate binding / protein kinase C binding / locomotory behavior / synaptic membrane / PDZ domain binding / establishment of localization in cell / protein localization to plasma membrane / intracellular protein transport / multicellular organism growth / Schaffer collateral - CA1 synapse / positive regulation of insulin secretion / cerebral cortex development / nuclear matrix / cell-cell junction / synaptic vesicle / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / regulation of gene expression / basolateral plasma membrane / protein-containing complex assembly / in utero embryonic development / vesicle / dendritic spine / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Amyloid beta A4 precursor protein-binding family A member 1 / 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 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. ...Amyloid beta A4 precursor protein-binding family A member 1 / 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 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 / PH-like domain superfamily / 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
Amyloid-beta A4 precursor protein-binding family A member 1 / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCai, Q. / Zhang, M.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)AoE-M09-12 Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6004-17G Hong Kong
CitationJournal: Structure / Year: 2020
Title: Structural Basis for the High-Affinity Interaction between CASK and Mint1.
Authors: Wu, X. / Cai, Q. / Chen, Y. / Zhu, S. / Mi, J. / Wang, J. / Zhang, M.
History
DepositionDec 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK
B: Amyloid-beta A4 precursor protein-binding family A member 1
C: Peripheral plasma membrane protein CASK
D: Amyloid-beta A4 precursor protein-binding family A member 1
E: Peripheral plasma membrane protein CASK
F: Amyloid-beta A4 precursor protein-binding family A member 1


Theoretical massNumber of molelcules
Total (without water)135,7206
Polymers135,7206
Non-polymers00
Water3,009167
1
A: Peripheral plasma membrane protein CASK
B: Amyloid-beta A4 precursor protein-binding family A member 1


Theoretical massNumber of molelcules
Total (without water)45,2402
Polymers45,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-22 kcal/mol
Surface area17530 Å2
MethodPISA
2
C: Peripheral plasma membrane protein CASK
D: Amyloid-beta A4 precursor protein-binding family A member 1


Theoretical massNumber of molelcules
Total (without water)45,2402
Polymers45,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22 kcal/mol
Surface area17500 Å2
MethodPISA
3
E: Peripheral plasma membrane protein CASK
F: Amyloid-beta A4 precursor protein-binding family A member 1


Theoretical massNumber of molelcules
Total (without water)45,2402
Polymers45,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-23 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.417, 151.417, 49.455
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALPROPROAA6 - 33512 - 341
221VALVALPROPROCC6 - 33512 - 341
132VALVALPROPROAA6 - 33512 - 341
242VALVALPROPROEE6 - 33512 - 341
153GLYGLYGLNGLNBB347 - 3883 - 44
263GLYGLYGLNGLNDD347 - 3883 - 44
174GLYGLYARGARGBB347 - 3873 - 43
284GLYGLYARGARGFF347 - 3873 - 43
195VALVALPROPROCC6 - 33512 - 341
2105VALVALPROPROEE6 - 33512 - 341
1116GLYGLYARGARGDD347 - 3873 - 43
2126GLYGLYARGARGFF347 - 3873 - 43

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 39505.418 Da / Num. of mol.: 3 / Fragment: CaMK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cask / Plasmid: pETM3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q62915, non-specific serine/threonine protein kinase
#2: Protein/peptide Amyloid-beta A4 precursor protein-binding family A member 1 / Adapter protein X11alpha / Neuron-specific X11 protein / Neuronal Munc18-1-interacting protein 1 / Mint-1


Mass: 5734.535 Da / Num. of mol.: 3 / Fragment: CID
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apba1, Mint1, X11 / Plasmid: pET32M3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: B2RUJ5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.41 Å3/Da / Density % sol: 49 % / Mosaicity: 0.59 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 6 / Details: 0.1M BisTris (pH 6.0), 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2019
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.57
11-K, -H, -L20.43
ReflectionResolution: 2.4→50 Å / Num. obs: 49568 / % possible obs: 99.5 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.058 / Rrim(I) all: 0.178 / Χ2: 0.532 / Net I/σ(I): 3.4 / Num. measured all: 454664
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.448.60.99224680.5460.3581.0570.4299.3
2.44-2.498.70.86625050.6140.310.9210.4399.1
2.49-2.538.80.81824270.6590.2930.8710.42499.8
2.53-2.598.70.73724910.660.2640.7840.42399.3
2.59-2.648.70.65924660.7390.2370.7020.43799.6
2.64-2.78.50.56725010.7490.2070.6050.49399.4
2.7-2.777.70.47624440.8130.1810.510.44498.4
2.77-2.8580.38424520.8840.1430.410.45998.6
2.85-2.9390.3524970.9070.1230.3720.46699.5
2.93-3.029.50.32424580.9350.1110.3430.4799.5
3.02-3.139.40.26924900.9430.0920.2850.47299.7
3.13-3.269.40.21724730.9630.0740.230.50599.6
3.26-3.419.30.18624790.9740.0640.1970.52299.6
3.41-3.589.60.15624780.9820.0530.1650.57399.8
3.58-3.819.50.12525210.9880.0430.1320.60199.9
3.81-4.18.50.09524910.9870.0340.1010.68499.6
4.1-4.5210.30.08224750.9940.0270.0860.67999.9
4.52-5.1710.80.07524730.9960.0240.0790.64100
5.17-6.5110.50.0824840.9960.0260.0840.607100
6.51-50100.05624950.9980.0180.0590.76299.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TAC

3tac


Resolution: 2.4→41.4 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.82 / SU ML: 0.121 / SU R Cruickshank DPI: 0.0792 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2383 4.8 %RANDOM
Rwork0.1713 ---
obs0.1734 47166 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.32 Å2 / Biso mean: 30.74 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2--1.63 Å20 Å2
3----3.25 Å2
Refinement stepCycle: final / Resolution: 2.4→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8795 0 0 167 8962
Biso mean---27.89 -
Num. residues----1096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139036
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178554
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.64712200
X-RAY DIFFRACTIONr_angle_other_deg1.3061.57719852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99251093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04221.219484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.159151612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5031570
X-RAY DIFFRACTIONr_chiral_restr0.0850.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021960
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A105820.09
12C105820.09
21A104920.1
22E104920.1
31B10760.19
32D10760.19
41B10600.16
42F10600.16
51C105160.1
52E105160.1
61D10280.2
62F10280.2
LS refinement shellResolution: 2.4→2.459 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.448 156 -
Rwork0.312 3511 -
obs--99.05 %

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