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- PDB-8i3e: Crystal structure of ELKS1 in complex with Piccolo -

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Basic information

Entry
Database: PDB / ID: 8i3e
TitleCrystal structure of ELKS1 in complex with Piccolo
Components
  • ELKS/Rab6-interacting/CAST family member 1
  • MKIAA0559 protein
KeywordsPROTEIN BINDING / ELKS / Piccolo / Scaffold protein / Presynapse / Synaptic vesicle
Function / homology
Function and homology information


cellular anatomical entity / presynapse / cytoplasm
Similarity search - Function
Active zone protein ELKS / RIM-binding protein of the cytomatrix active zone / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Active zone protein ELKS / RIM-binding protein of the cytomatrix active zone / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
ELKS/RAB6-interacting/CAST family member 1 / MKIAA0559 protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.7 Å
AuthorsCai, Q. / Zhang, M.
Funding support China, Hong Kong, France, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
Ministry of Science and Technology (MoST, China)2019YFA0508402 China
The University Grants Committee, Research Grants Council (RGC)AoE-M09-12 Hong Kong
The University Grants Committee, Research Grants Council (RGC)16104518 Hong Kong
The University Grants Committee, Research Grants Council (RGC)16101419 Hong Kong
Human Frontier Science Program (HFSP)RGP0020/2019 France
CitationJournal: Cell / Year: 2024
Title: Short-distance vesicle transport via phase separation.
Authors: Qiu, H. / Wu, X. / Ma, X. / Li, S. / Cai, Q. / Ganzella, M. / Ge, L. / Zhang, H. / Zhang, M.
History
DepositionJan 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELKS/Rab6-interacting/CAST family member 1
B: ELKS/Rab6-interacting/CAST family member 1
C: MKIAA0559 protein


Theoretical massNumber of molelcules
Total (without water)44,3763
Polymers44,3763
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS result proved the complex was composed of two ELKS1 molecules and one Piccolo molecule.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-76 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.379, 46.111, 84.359
Angle α, β, γ (deg.)90.000, 110.438, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 471 through 604)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLEUA1 - 134
d_21ens_1SERLEUB2 - 135

NCS oper: (Code: givenMatrix: (-0.139593553565, 0.0237646178674, -0.98992367521), (0.687837408593, 0.721478773606, -0.0796748302536), (0.712315477259, -0.692028628146, -0.117059979)Vector: 18. ...NCS oper: (Code: given
Matrix: (-0.139593553565, 0.0237646178674, -0.98992367521), (0.687837408593, 0.721478773606, -0.0796748302536), (0.712315477259, -0.692028628146, -0.117059979)
Vector: 18.0076630292, -0.23394186356, 18.2876487045)

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Components

#1: Protein ELKS/Rab6-interacting/CAST family member 1


Mass: 16857.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erc1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: A0A8I6AIL7
#2: Protein MKIAA0559 protein


Mass: 10661.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pclo, mKIAA0559 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8CHE8

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Sodium Formate pH 7.0, 12 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11119 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 59.05 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.074 / Rrim(I) all: 0.256 / Net I/σ(I): 16
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.65 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 538 / CC1/2: 0.614 / CC star: 0.872 / Rpim(I) all: 0.489 / Rrim(I) all: 1.723 / Χ2: 0.447 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.7→31.11 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.2781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2979 560 5.05 %
Rwork0.2453 20114 -
obs0.2479 11093 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.59 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 0 0 2647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252649
X-RAY DIFFRACTIONf_angle_d1.64373527
X-RAY DIFFRACTIONf_chiral_restr0.0695418
X-RAY DIFFRACTIONf_plane_restr0.008457
X-RAY DIFFRACTIONf_dihedral_angle_d19.8706346
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 8.54947122975 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.35781330.3252476X-RAY DIFFRACTION98.08
2.83-2.970.33631310.27832532X-RAY DIFFRACTION99.89
2.97-3.160.33511350.29312524X-RAY DIFFRACTION99.81
3.16-3.40.37591220.26252515X-RAY DIFFRACTION99.89
3.4-3.750.34631260.24652553X-RAY DIFFRACTION99.78
3.75-4.290.29011340.21462545X-RAY DIFFRACTION99.81
4.29-5.40.28681570.24082491X-RAY DIFFRACTION99.03
5.4-31.110.22921310.22842478X-RAY DIFFRACTION98.12
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)
10.483235656080.657026871219-0.2303735431450.470702426692-0.3928098774950.407324267867-0.1855793414540.02822195477220.02951048072910.3008684339960.19965404133-0.118277398075-0.0729656596724-0.1247756174210.0006921891609770.212449031321-0.0206390230148-0.01731481272450.363289478134-0.02806084325310.36229432650916.518997259237.77898057062.08714812211
20.03935226260.0470277686730.128007415510.0297483876815-0.1254772217970.1014362158480.3591991246220.377507246851-0.0339374114889-0.152362592454-0.0624966310355-0.125398498057-0.136319155506-0.6139901995210.002287328138271.0348022222-0.1384677509060.454623488060.7208869937120.137783370571.07381921893-25.3102610979-47.994109277135.1517239526
30.1482684588060.130032785972-0.003840105658060.7526969715590.231206103134-0.3205256083960.01791505720190.04877455236080.005669162352820.4648156005970.03620386387630.00290784887997-0.279999755168-0.003564774341270.0002722971654810.488887146497-0.0108075185509-0.07367891296910.396260461744-0.01500784838810.34637215364616.181969737639.78405147821.68149614532
40.03758742461380.05248811350610.0248749664858-0.01820479171140.1017963670180.0286502740588-0.143073313540.433073158912-0.224181811139-0.171958085551-0.1101675099180.1531948178990.589229087532-0.4274827778980.0007337250867251.09268941729-0.1835954502810.3898514957280.7986234254780.1030069188171.07070492364-17.7044150634-52.796692741834.1342527919
50.460732506264-0.1096488037750.171105192410.4687063544920.2328468972410.241619569317-0.3634866425420.00788680215704-0.249864384971-0.307617476140.170838511007-0.2235694534020.449318832062-0.21879351156-0.001733352229460.393144182329-0.01586054171230.02233600369820.4114829830980.04490623732640.388138486173-0.4488828727456.9794033576712.7416761768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 471 through 576 )AA471 - 5761 - 106
22chain 'A' and (resid 577 through 604 )AA577 - 604107 - 134
33chain 'B' and (resid 470 through 574 )BB470 - 5741 - 105
44chain 'B' and (resid 575 through 604 )BB575 - 604106 - 135
55chain 'C' and (resid 3690 through 3745 )CC3690 - 37451 - 56

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