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- PDB-7d2e: Tetrameric coiled-coil structure of liprin-alpha2_H3 -

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Basic information

Entry
Database: PDB / ID: 7d2e
TitleTetrameric coiled-coil structure of liprin-alpha2_H3
ComponentsLiprin-alpha-2
KeywordsPROTEIN BINDING / Coiled-coil
Function / homology
Function and homology information


structural constituent of presynapse / dense core granule cytoskeletal transport / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / postsynaptic specialization / Serotonin Neurotransmitter Release Cycle / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle ...structural constituent of presynapse / dense core granule cytoskeletal transport / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / postsynaptic specialization / Serotonin Neurotransmitter Release Cycle / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / regulation of dendritic spine morphogenesis / regulation of synaptic vesicle exocytosis / presynaptic active zone / cell-matrix adhesion / synapse organization / synaptic vesicle / presynaptic membrane / dendritic spine / axon / glutamatergic synapse / cell surface / extracellular exosome / cytosol / cytoplasm
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 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLiang, M. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)31770791 China
CitationJournal: Cell Rep / Year: 2021
Title: Oligomerized liprin-alpha promotes phase separation of ELKS for compartmentalization of presynaptic active zone proteins.
Authors: Liang, M. / Jin, G. / Xie, X. / Zhang, W. / Li, K. / Niu, F. / Yu, C. / Wei, Z.
History
DepositionSep 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Liprin-alpha-2
B: Liprin-alpha-2
C: Liprin-alpha-2
D: Liprin-alpha-2


Theoretical massNumber of molelcules
Total (without water)34,6634
Polymers34,6634
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-65 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.307, 71.293, 53.473
Angle α, β, γ (deg.)90.000, 103.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: 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: 8665.760 Da / Num. of mol.: 4 / Fragment: UNP residues 164-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPFIA2 / Plasmid: pET32m / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75334
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30192 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.34 Å2 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.903 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.733.70.75715280.7440.4570.8860.9499.5
1.73-1.763.70.69915080.7990.4220.8180.95399.5
1.76-1.793.70.52715150.880.3170.6160.98899.6
1.79-1.833.70.41215360.9130.2470.4820.96199.5
1.83-1.873.70.36615080.9270.220.4280.95899.7
1.87-1.913.70.27315400.9490.1650.320.99799.8
1.91-1.963.70.1814900.9790.1080.210.93199.7
1.96-2.023.70.14715710.9750.0880.1710.93499.8
2.02-2.073.70.10215030.9870.0610.1190.89899.8
2.07-2.143.70.07715350.9910.0460.090.8199.9
2.14-2.223.80.06215180.9930.0370.0730.78799.8
2.22-2.313.80.0515200.9940.030.0580.76399.8
2.31-2.413.70.04315530.9950.0260.050.792100
2.41-2.543.70.04415330.9940.0260.0521.004100
2.54-2.73.70.04715240.9920.0280.0551.311100
2.7-2.913.70.04415240.9930.0270.0511.37799.9
2.91-3.23.70.03815450.9940.0230.0451.23699.9
3.2-3.663.70.02315290.9980.0140.0270.51299.5
3.66-4.613.60.01914530.9970.0120.0220.35894.2
4.61-503.60.02212590.9970.0130.0260.36679

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1514 5 %
Rwork0.2394 28739 -
obs0.2409 30192 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.47 Å2 / Biso mean: 46.1563 Å2 / Biso min: 16.58 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 0 123 2085
Biso mean---45.42 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062011
X-RAY DIFFRACTIONf_angle_d0.7582700
X-RAY DIFFRACTIONf_chiral_restr0.031319
X-RAY DIFFRACTIONf_plane_restr0.003352
X-RAY DIFFRACTIONf_dihedral_angle_d13.767802
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.75340.33361380.3322261098
1.7534-1.81610.34441380.3109263799
1.8161-1.88880.36361390.30712634100
1.8888-1.97470.29551400.27412655100
1.9747-2.07880.30031380.2649263199
2.0788-2.2090.24481390.24792638100
2.209-2.37940.27121410.24082671100
2.3794-2.61860.26941400.23142655100
2.6186-2.9970.28711400.25132648100
2.997-3.7740.25681390.2167264199
3.774-500.24381220.2227231985
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)
11.13531.58622.36770.90833.25845.90840.2073-0.0615-0.1833-0.1294-0.0947-0.04140.52070.2105-0.02760.44430.1661-0.03030.3202-0.07770.35211.062717.51928.9209
23.82032.74235.63862.39433.97387.9135-0.12-0.4654-0.2347-0.1410.1307-0.1025-1.0578-0.71090.16660.43560.03060.03320.3019-0.03730.3891-15.6995-0.3217-54.124
31.16341.06543.30771.27322.88976.80520.23790.0267-0.13540.1850.0356-0.01520.37050.1261-0.29170.2110.00450.05410.2894-0.0360.2904-13.6952-6.4491-52.9055
43.95392.39185.18371.09383.19236.8546-0.3344-0.1713-0.0428-0.55610.01860.1412-0.8865-0.26340.36570.35080.0556-0.0490.2658-0.01530.277910.939123.6467.8561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A168 - 229
2X-RAY DIFFRACTION2chain 'B'B169 - 226
3X-RAY DIFFRACTION3chain 'C'C169 - 227
4X-RAY DIFFRACTION4chain 'D'D169 - 231

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