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- PDB-6kmh: The crystal structure of CASK/Mint1 complex -

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Basic information

Entry
Database: PDB / ID: 6kmh
TitleThe crystal structure of CASK/Mint1 complex
Components
  • Amyloid-beta A4 precursor protein-binding family A member 1
  • Peripheral plasma membrane protein CASK
KeywordsSTRUCTURAL PROTEIN / CASK-CaMK domain / Mint1 / CASK-Mint1 complex / hydrophobic interactions
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / glutamate secretion ...negative regulation of cellular response to growth factor stimulus / gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / glutamate secretion / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / synaptic vesicle exocytosis / basement membrane / negative regulation of keratinocyte proliferation / presynaptic active zone membrane / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / locomotory behavior / PDZ domain binding / establishment of localization in cell / intracellular protein transport / multicellular organism growth / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / regulation of gene expression / basolateral plasma membrane / in utero embryonic development / vesicle / dendritic spine / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / phosphorylation / signaling receptor binding / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / 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
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 ...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 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / Peripheral plasma membrane protein CASK / Amyloid-beta A4 precursor protein-binding family A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, W. / Feng, W.
CitationJournal: Cell Discov / Year: 2020
Title: CASK modulates the assembly and function of the Mint1/Munc18-1 complex to regulate insulin secretion.
Authors: Zhang, Z. / Li, W. / Yang, G. / Lu, X. / Qi, X. / Wang, S. / Cao, C. / Zhang, P. / Ren, J. / Zhao, J. / Zhang, J. / Hong, S. / Tan, Y. / Burchfield, J. / Yu, Y. / Xu, T. / Yao, X. / James, D. ...Authors: Zhang, Z. / Li, W. / Yang, G. / Lu, X. / Qi, X. / Wang, S. / Cao, C. / Zhang, P. / Ren, J. / Zhao, J. / Zhang, J. / Hong, S. / Tan, Y. / Burchfield, J. / Yu, Y. / Xu, T. / Yao, X. / James, D. / Feng, W. / Chen, Z.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: Peripheral plasma membrane protein CASK
C: Amyloid-beta A4 precursor protein-binding family A member 1
D: Amyloid-beta A4 precursor protein-binding family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,42818
Polymers88,8344
Non-polymers1,59414
Water2,270126
1
A: Peripheral plasma membrane protein CASK
C: Amyloid-beta A4 precursor protein-binding family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,34110
Polymers44,4172
Non-polymers9248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area16600 Å2
MethodPISA
2
B: Peripheral plasma membrane protein CASK
D: Amyloid-beta A4 precursor protein-binding family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0878
Polymers44,4172
Non-polymers6706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-32 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.978, 96.321, 97.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASNASNchain AAA5 - 31811 - 324
21ASPASPSERSERchain BBB5 - 31911 - 325
12PHEPHEGLNGLNchain CCC0 - 3856 - 54
22SERSERILEILEchain DDD-2 - 3874 - 56

NCS ensembles :
ID
1
2

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Components

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


Mass: 36682.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Production host: Escherichia coli (E. coli)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Protein 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: 7734.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Apba1, Mint1, X11 / Production host: Escherichia coli (E. coli) / References: UniProt: O35430
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M KI, 20% PEG 3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 37889 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.04 / Rrim(I) all: 0.127 / Χ2: 1.157 / Net I/σ(I): 12.1 / Num. measured all: 381609
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.4310.20.51837250.9720.1690.5451.245100
2.43-2.5310.20.39837370.9810.1290.4181.222100
2.53-2.6510.20.34637480.9840.1130.3651.202100
2.65-2.7910.20.25437320.9890.0830.2671.149100
2.79-2.9610.20.19137470.9910.0630.2011.108100
2.96-3.1910.20.15837630.9910.0520.1661.328100
3.19-3.5110.10.13637820.9890.0450.1441.274100
3.51-4.02100.11438090.9920.0380.1211.148100
4.02-5.069.70.08238560.9960.0280.0870.942100
5.06-509.60.07139900.9970.0240.0750.94699.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TAC

3tac


Resolution: 2.4→42.232 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1737 4.93 %
Rwork0.1882 33502 -
obs0.19 35239 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.99 Å2 / Biso mean: 46.9959 Å2 / Biso min: 18.21 Å2
Refinement stepCycle: final / Resolution: 2.4→42.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 14 126 6001
Biso mean--50.87 42.09 -
Num. residues----731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095993
X-RAY DIFFRACTIONf_angle_d1.2318080
X-RAY DIFFRACTIONf_chiral_restr0.052878
X-RAY DIFFRACTIONf_plane_restr0.0071033
X-RAY DIFFRACTIONf_dihedral_angle_d14.3472276
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3029X-RAY DIFFRACTION5.433TORSIONAL
12B3029X-RAY DIFFRACTION5.433TORSIONAL
21C498X-RAY DIFFRACTION5.433TORSIONAL
22D498X-RAY DIFFRACTION5.433TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.47060.25871390.20432749100
2.4706-2.55030.2581320.20462744100
2.5503-2.64150.24791370.21042773100
2.6415-2.74720.25461150.20582783100
2.7472-2.87220.24461540.21812768100
2.8722-3.02360.23891190.21722789100
3.0236-3.2130.24141580.2152749100
3.213-3.4610.26791720.20492773100
3.461-3.80910.21071900.18542736100
3.8091-4.35980.21051380.16152830100
4.3598-5.49090.18151390.17112854100
5.4909-42.230.20481440.1702295499

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