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- PDB-7d2h: Tetrameric coiled-coil structure of liprin-alpha2_H2 -

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Basic information

Entry
Database: PDB / ID: 7d2h
TitleTetrameric coiled-coil structure of liprin-alpha2_H2
ComponentsLiprin-alpha-2
KeywordsPROTEIN BINDING / Coiled-coil
Function / homology
Function and homology information


structural constituent of presynapse / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / 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 / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,4955
Polymers30,4034
Non-polymers921
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-78 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.879, 101.907, 37.445
Angle α, β, γ (deg.)90.000, 96.410, 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: 7600.626 Da / Num. of mol.: 4 / Fragment: UNP residues 102-163 / Mutation: C143A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 40.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v Polyethylene glycol 8,000

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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: Jul 4, 2017
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: 11895 / % possible obs: 93.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.35 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Rrim(I) all: 0.092 / Χ2: 1.845 / Net I/σ(I): 9.5 / Num. measured all: 43572
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.60.8475990.7530.4830.981.40994.3
2.24-2.283.70.7695920.6670.4340.8861.51294.7
2.28-2.323.60.7875840.780.4450.9081.35293.1
2.32-2.373.60.4656180.9170.2660.5381.36694.9
2.37-2.423.70.5095860.8820.290.5881.47594.2
2.42-2.483.70.3685960.9220.2050.4231.44594.3
2.48-2.543.50.3486160.9520.1990.4031.47793.5
2.54-2.613.70.3675930.9550.2050.4221.50894.4
2.61-2.693.70.3265910.9340.1820.3751.43692.1
2.69-2.773.70.2286110.9720.1280.2631.63395
2.77-2.873.70.1945670.9780.1080.2231.81792.3
2.87-2.993.60.1546120.9880.0850.1771.99695
2.99-3.123.60.1326000.9890.0730.1511.89793
3.12-3.293.70.1085940.9920.0590.1241.98694.6
3.29-3.493.60.0865940.9940.0470.0992.10392.7
3.49-3.763.50.0676010.9960.0370.0772.39992.7
3.76-4.143.60.0495950.9970.0270.0562.49292
4.14-4.743.80.0425840.9970.0240.0492.50191.2
4.74-5.973.90.0445820.9980.0240.052.3891.9
5.97-503.70.0425800.9980.0230.0482.69887.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D2G

7d2g


Resolution: 2.2→30.051 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 532 4.61 %
Rwork0.2288 11007 -
obs0.2313 11539 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.11 Å2 / Biso mean: 73.6322 Å2 / Biso min: 31.55 Å2
Refinement stepCycle: final / Resolution: 2.2→30.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 6 10 1853
Biso mean--70.17 69.41 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011857
X-RAY DIFFRACTIONf_angle_d0.3422479
X-RAY DIFFRACTIONf_chiral_restr0.015292
X-RAY DIFFRACTIONf_plane_restr0.001322
X-RAY DIFFRACTIONf_dihedral_angle_d11.729739
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.42130.40831230.343274894
2.4213-2.77150.3681450.2903278593
2.7715-3.4910.2811380.2615273893
3.491-30.0510.24091260.1806273691
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)
17.14653.22667.02342.99033.69467.905-0.00870.1482-0.0571-0.54510.07510.1216-0.13740.298-0.16730.4513-0.02960.08810.43630.05720.39481.528728.5509-0.2885
23.69442.22754.44132.66012.54733.95720.67070.028-0.62950.1641-0.0631-0.1931.0045-0.0968-0.54050.65670.0432-0.17560.4441-0.03870.64452.390221.77314.0047
34.12512.19394.34523.62092.90345.2642-0.31380.10280.34450.4608-0.1541-0.3809-0.3065-0.07170.18870.45590.0137-0.06830.39430.00940.590426.357338.549334.217
46.28472.20576.31152.43822.29467.3416-0.6774-0.17670.74470.1599-0.218-0.1144-0.9485-0.26640.54720.76570.0707-0.23830.4459-0.120.723218.894943.198632.1341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A99 - 155
2X-RAY DIFFRACTION2chain 'B'B101 - 155
3X-RAY DIFFRACTION3chain 'C'C100 - 155
4X-RAY DIFFRACTION4chain 'D'D101 - 160

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