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- PDB-3tac: Crystal Structure of the Liprin-alpha/CASK complex -

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Basic information

Entry
Database: PDB / ID: 3tac
TitleCrystal Structure of the Liprin-alpha/CASK complex
Components
  • Liprin-alpha-2
  • Peripheral plasma membrane protein CASK
KeywordsTRANSFERASE/PROTEIN BINDING / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


structural constituent of presynapse / negative regulation of cellular response to growth factor stimulus / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / postsynaptic specialization / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / guanylate kinase activity / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle ...structural constituent of presynapse / negative regulation of cellular response to growth factor stimulus / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / postsynaptic specialization / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / guanylate kinase activity / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / Glutamate Neurotransmitter Release Cycle / regulation of dendritic spine morphogenesis / 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 / presynaptic active zone / basement membrane / negative regulation of keratinocyte proliferation / cell-matrix adhesion / establishment of localization in cell / synapse organization / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / synaptic vesicle / presynaptic membrane / basolateral plasma membrane / vesicle / dendritic spine / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / phosphorylation / axon / protein serine kinase activity / focal adhesion / signaling receptor binding / protein serine/threonine kinase activity / glutamatergic synapse / nucleolus / cell surface / positive regulation of transcription by RNA polymerase II / extracellular exosome / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / CASK, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. ...Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / 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 / Transcription Factor, Ets-1 / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / DNA polymerase; domain 1 / 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
Peripheral plasma membrane protein CASK / Liprin-alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWei, Z. / Zheng, S. / Yu, C. / Zhang, M.
CitationJournal: Mol.Cell / Year: 2011
Title: Liprin-mediated large signaling complex organization revealed by the liprin-alpha/CASK and liprin-alpha/liprin-beta complex structures
Authors: Wei, Z. / Zheng, S. / Spangler, S.A. / Yu, C. / Hoogenraad, C.C. / Zhang, M.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: Liprin-alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,90810
Polymers79,2002
Non-polymers7088
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-126 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.592, 78.592, 227.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 40732.848 Da / Num. of mol.: 1 / Fragment: UNP residues 1-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK / Plasmid: pET32m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Protein Liprin-alpha-2 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF- ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF-interacting protein alpha-2


Mass: 38466.797 Da / Num. of mol.: 1 / Fragment: UNP residues 866-1193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPFIA2 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75334
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.22 Å3/Da / Density % sol: 44.52 % / Mosaicity: 0.586 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M ammonium sulfate, 0.2M NaCl, MES buffer, pH 6.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36535 / % possible obs: 98.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.078 / Χ2: 1.191 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.244.10.55417800.949196.6
2.24-2.284.60.48117591.001198.8
2.28-2.325.40.40118061.018199.8
2.32-2.376.20.37418271.026199.9
2.37-2.426.40.31118001.0291100
2.42-2.486.30.27518101.0951100
2.48-2.546.30.25218311.1051100
2.54-2.616.30.22518291.152199.8
2.61-2.696.30.19418211.265199.9
2.69-2.776.30.16218111.246199.9
2.77-2.876.30.1418341.3521100
2.87-2.996.20.1118241.299199.9
2.99-3.126.20.09618571.447199.6
3.12-3.296.10.08118261.381199.5
3.29-3.4960.06818271.503199.1
3.49-3.7660.06218401.35198.2
3.76-4.145.90.05918481.202198
4.14-4.745.70.05918371.07197.1
4.74-5.9760.0618671.182196.8
5.97-505.70.05219010.95190.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.06 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.708 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1818 5 %RANDOM
Rwork0.1947 ---
obs0.1968 36437 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 145.11 Å2 / Biso mean: 53.5429 Å2 / Biso min: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4889 0 36 110 5035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225023
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9656798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3075612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36823.217230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92315878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8231542
X-RAY DIFFRACTIONr_chiral_restr0.0820.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213764
X-RAY DIFFRACTIONr_mcbond_it1.3621.53065
X-RAY DIFFRACTIONr_mcangle_it2.39624920
X-RAY DIFFRACTIONr_scbond_it4.03831958
X-RAY DIFFRACTIONr_scangle_it6.2114.51878
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 136 -
Rwork0.243 2174 -
all-2310 -
obs--85.68 %
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)
13.1077-1.4085-0.77462.26850.2091.90780.33510.6502-0.4451-0.3476-0.35420.18920.3662-0.22420.01910.32170.0078-0.14160.2917-0.03680.1835-7.846-0.059-29.839
21.1923-0.37190.46431.8591-0.65962.23690.08190.0439-0.0851-0.1454-0.0848-0.11080.14730.21180.00290.0987-0.0192-0.01570.15530.03260.0256-3.524.095-18.076
33.2006-1.28361.51533.4711-1.75244.4257-0.2504-0.01790.30820.18040.21750.1585-0.5452-0.41290.03290.1891-0.0292-0.03240.19690.03050.0588-7.60836.8068.666
48.7028-6.7921-1.36289.94821.34694.7789-0.1469-0.52170.16460.07060.18020.4245-0.2077-0.4766-0.03330.23680.0121-0.06320.38560.01940.1885-21.48641.158-27.035
53.12811.93560.12723.07790.19231.24830.0082-0.0565-0.30770.0053-0.0240.00560.1089-0.08030.01580.0776-0.0332-0.01810.1730.05390.0668-17.7325.3719.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 92
2X-RAY DIFFRACTION2A93 - 316
3X-RAY DIFFRACTION3B871 - 977
4X-RAY DIFFRACTION4B978 - 997
5X-RAY DIFFRACTION5B1018 - 1182

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