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- PDB-8whm: Crystal structure of the ELKS2/LL5beta complex -

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Basic information

Entry
Database: PDB / ID: 8whm
TitleCrystal structure of the ELKS2/LL5beta complex
Components
  • ERC protein 2
  • Pleckstrin homology-like domain family B member 2
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / maintenance of presynaptic active zone structure / cytoskeleton of presynaptic active zone / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / regulation of gastrulation / basal cortex / neuromuscular synaptic transmission / regulation of epithelial to mesenchymal transition ...regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / maintenance of presynaptic active zone structure / cytoskeleton of presynaptic active zone / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / regulation of gastrulation / basal cortex / neuromuscular synaptic transmission / regulation of epithelial to mesenchymal transition / regulation of presynaptic cytosolic calcium ion concentration / negative regulation of focal adhesion assembly / presynaptic active zone cytoplasmic component / podosome / intermediate filament cytoskeleton / negative regulation of stress fiber assembly / synaptic vesicle priming / Golgi-associated vesicle / establishment of cell polarity / cell leading edge / presynaptic active zone / regulation of microtubule cytoskeleton organization / GABA-ergic synapse / synapse assembly / PDZ domain binding / synapse organization / establishment of protein localization / regulation of synaptic plasticity / terminal bouton / microtubule cytoskeleton organization / cell migration / presynaptic membrane / cell cortex / growth cone / cadherin binding / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
PHLDB1/2/3, PH domain / : / Active zone protein ELKS / RIM-binding protein of the cytomatrix active zone / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Pleckstrin homology-like domain family B member 2 / ERC protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJia, X. / Wei, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
National Natural Science Foundation of China (NSFC)32370743 China
National Natural Science Foundation of China (NSFC)32371009 China
CitationJournal: Nat Commun / Year: 2024
Title: CLASP-mediated competitive binding in protein condensates directs microtubule growth.
Authors: Jia, X. / Lin, L. / Guo, S. / Zhou, L. / Jin, G. / Dong, J. / Xiao, J. / Xie, X. / Li, Y. / He, S. / Wei, Z. / Yu, C.
History
DepositionSep 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERC protein 2
B: Pleckstrin homology-like domain family B member 2


Theoretical massNumber of molelcules
Total (without water)17,4132
Polymers17,4132
Non-polymers00
Water37821
1
A: ERC protein 2
B: Pleckstrin homology-like domain family B member 2

A: ERC protein 2
B: Pleckstrin homology-like domain family B member 2


Theoretical massNumber of molelcules
Total (without water)34,8254
Polymers34,8254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area9730 Å2
ΔGint-72 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.743, 90.716, 59.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ERC protein 2 / CAZ-associated structural protein 1 / CAST1 / Cast / Cytomatrix protein p110


Mass: 7828.954 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erc2, Cast1, Cmbp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8K3M6
#2: Protein Pleckstrin homology-like domain family B member 2 / Protein LL5-beta


Mass: 9583.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHLDB2, LL5B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86SQ0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium formate pH 6.6 and 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→37.58 Å / Num. obs: 7147 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.085 / Rrim(I) all: 0.185 / Χ2: 0.91 / Net I/σ(I): 9.1 / Num. measured all: 32594
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.415 / Num. measured all: 3955 / Num. unique obs: 678 / CC1/2: 0.834 / Rpim(I) all: 0.188 / Rrim(I) all: 0.457 / Χ2: 0.6 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.58 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 346 4.87 %
Rwork0.2573 --
obs0.2586 7108 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 0 21 1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011063
X-RAY DIFFRACTIONf_angle_d0.291417
X-RAY DIFFRACTIONf_dihedral_angle_d18.752437
X-RAY DIFFRACTIONf_chiral_restr0.028162
X-RAY DIFFRACTIONf_plane_restr0.001185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.90.32561540.30223359X-RAY DIFFRACTION100
2.9-37.580.2641920.23463403X-RAY DIFFRACTION98
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)
10.7003-0.78170.34487.2459-0.06181.28260.0229-0.1309-0.3578-0.7163-0.2605-0.34580.34850.03120.15250.1850.02920.08250.1989-0.01530.366326.14193.8343-15.9764
20.81732.012-1.55695.0481-3.40744.8673-0.10490.0705-0.42621.1133-0.6638-0.1680.26360.28010.70311.1093-0.0654-0.18950.42560.03981.514632.5549-5.7935-4.402
32.455-0.55680.20913.1185-3.56184.14370.1670.07720.00890.2009-0.00520.628-0.0092-0.2271-0.12430.1589-0.01670.0020.223-0.08810.163420.144214.5098-11.8649
44.9695-0.5382-0.21585.3469-1.71465.58750.2288-0.26140.58120.08780.0488-0.24370.36220.038-0.30650.1949-0.0247-0.03030.32460.04290.462817.34832.0092-12.2624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 261 through 314 )
2X-RAY DIFFRACTION2chain 'B' and (resid 415 through 421 )
3X-RAY DIFFRACTION3chain 'B' and (resid 422 through 461 )
4X-RAY DIFFRACTION4chain 'B' and (resid 462 through 488 )

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