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- PDB-7d2g: Coiled-coil structure of liprin-alpha2_H2delC -

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Basic information

Entry
Database: PDB / ID: 7d2g
TitleCoiled-coil structure of liprin-alpha2_H2delC
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 / Serotonin Neurotransmitter Release Cycle / postsynaptic specialization / 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 / Serotonin Neurotransmitter Release Cycle / postsynaptic specialization / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9045
Polymers25,8124
Non-polymers921
Water2,018112
1
A: Liprin-alpha-2
B: Liprin-alpha-2


Theoretical massNumber of molelcules
Total (without water)12,9062
Polymers12,9062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-26 kcal/mol
Surface area8000 Å2
MethodPISA
2
C: Liprin-alpha-2
D: Liprin-alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9983
Polymers12,9062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-25 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.057, 33.410, 73.631
Angle α, β, γ (deg.)90.000, 111.250, 90.000
Int Tables number5
Space group name H-MC121

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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: 6453.071 Da / Num. of mol.: 4 / Fragment: UNP residues 102-150 / Mutation: L106M, 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350

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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: Jan 16, 2017
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: 31730 / % possible obs: 98 % / Redundancy: 12.5 % / Biso Wilson estimate: 27.62 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.041 / Rrim(I) all: 0.138 / Χ2: 3.72 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.769.61.31230060.9020.4051.3761.25192.4
1.76-1.8311.21.11930500.9520.3311.171.33696.7
1.83-1.9112.40.94831780.9690.2730.9881.39699.6
1.91-2.0213.50.62932280.9820.1770.6531.612100
2.02-2.14140.37832030.990.1060.3931.875100
2.14-2.31140.23832330.9940.0680.2482.412100
2.31-2.5413.80.17532400.9940.0510.1823.214100
2.54-2.9113.10.13532190.9940.0420.1424.55499.8
2.91-3.6612.10.09432570.9920.030.0996.8499.1
3.66-5010.70.09431160.9910.0310.09914.15692.4

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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: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 3005 5 %
Rwork0.2362 57057 -
obs0.2375 31588 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.01 Å2 / Biso mean: 50.1042 Å2 / Biso min: 26.83 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 6 112 1723
Biso mean--59.6 53.02 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021646
X-RAY DIFFRACTIONf_angle_d0.3692198
X-RAY DIFFRACTIONf_chiral_restr0.015250
X-RAY DIFFRACTIONf_plane_restr0.001290
X-RAY DIFFRACTIONf_dihedral_angle_d11.662657
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71960.43031260.3838233982
1.7196-1.74930.37621260.3703244886
1.7493-1.78110.39431350.3621251791
1.7811-1.81530.40271430.3507264093
1.8153-1.85240.38581450.3706274396
1.8524-1.89270.37151450.3444277699
1.8927-1.93670.31461470.3314284499
1.9367-1.98510.41261480.3021279299
1.9851-2.03880.30221490.2902282899
2.0388-2.09880.28921460.2672281499
2.0988-2.16650.28651460.27292776100
2.1665-2.24390.30291530.24992838100
2.2439-2.33370.26761480.23542790100
2.3337-2.43990.24791500.2347281599
2.4399-2.56850.29871450.2343282899
2.5685-2.72940.2721480.241279299
2.7294-2.940.18341450.2356277798
2.94-3.23570.24211450.231276698
3.2357-3.70340.23041490.2019280198
3.7034-4.6640.2061360.187260593
4.664-500.29331300.225252889
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)
14.6079-4.12564.59112.6595-4.47035.59950.17430.38270.0199-0.1069-0.15890.0234-0.05410.2311-0.19210.34210.02870.00830.29290.03120.291546.796726.9024-6.1059
25.0639-1.95314.53792.5336-3.23689.13430.24250.3769-0.2183-0.0609-0.04770.06510.18010.0635-0.20410.2728-0.01170.05060.26580.00430.323850.724922.7633-8.5874
37.6763-4.0956.68162.4188-3.27126.27420.0164-0.31490.00060.1654-0.0012-0.0651-0.09690.02380.00240.3996-0.0190.02740.37310.09190.362251.513225.308713.8701
47.4407-1.45346.56990.5277-1.25495.9538-0.3895-0.83570.21840.21180.0645-0.0531-0.5085-0.54870.22990.3796-0.02220.02570.34550.06370.37946.944324.776417.7067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A98 - 148
2X-RAY DIFFRACTION2chain 'B'B97 - 146
3X-RAY DIFFRACTION3chain 'C'C99 - 145
4X-RAY DIFFRACTION4chain 'D'D97 - 146

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