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- PDB-8s1r: Crystal structure of SHANK1 PDZ in complex with a SLiM internal ligand -

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Basic information

Entry
Database: PDB / ID: 8s1r
TitleCrystal structure of SHANK1 PDZ in complex with a SLiM internal ligand
Components
  • F-box only protein 41
  • SH3 and multiple ankyrin repeat domains protein 1
KeywordsPEPTIDE BINDING PROTEIN / Complex / Inhibitor / SHANK1 PDZ / Internal ligand
Function / homology
Function and homology information


somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / Neurexins and neuroligins / adult behavior / positive regulation of dendritic spine development / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / SH3 domain binding / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / scaffold protein binding / protein-containing complex assembly / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
F-box-like domain superfamily / F-box-like / PDZ domain 6 / PDZ domain / F-box domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...F-box-like domain superfamily / F-box-like / PDZ domain 6 / PDZ domain / F-box domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Leucine-rich repeat domain superfamily / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
ACETYL GROUP / F-box only protein 41 / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsLi, Y. / Trinh, C.H. / Wilson, A.J.
Funding support China, United Kingdom, 3items
OrganizationGrant numberCountry
Chinese Scholarship Council202008210289 China
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/N013573/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2024
Title: Biophysical and Structural Analyses of the Interaction between the SHANK1 PDZ Domain and an Internal SLiM.
Authors: Li, Y. / Trinh, C.H. / Acevedo-Jake, A. / Gimenez, D. / Warriner, S.L. / Wilson, A.J.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: SH3 and multiple ankyrin repeat domains protein 1
BBB: SH3 and multiple ankyrin repeat domains protein 1
CCC: SH3 and multiple ankyrin repeat domains protein 1
DDD: SH3 and multiple ankyrin repeat domains protein 1
EaE: F-box only protein 41
FaF: F-box only protein 41
GaG: F-box only protein 41
HaH: F-box only protein 41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,46512
Polymers53,2898
Non-polymers1764
Water2,072115
1
AAA: SH3 and multiple ankyrin repeat domains protein 1
EaE: F-box only protein 41
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 13.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)13,3663
Polymers13,3222
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area6750 Å2
MethodPISA
2
BBB: SH3 and multiple ankyrin repeat domains protein 1
FaF: F-box only protein 41
hetero molecules


  • defined by author&software
  • 13.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)13,3663
Polymers13,3222
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-3 kcal/mol
Surface area6470 Å2
MethodPISA
3
CCC: SH3 and multiple ankyrin repeat domains protein 1
GaG: F-box only protein 41
hetero molecules


  • defined by author&software
  • 13.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)13,3663
Polymers13,3222
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4 kcal/mol
Surface area6800 Å2
MethodPISA
4
DDD: SH3 and multiple ankyrin repeat domains protein 1
HaH: F-box only protein 41
hetero molecules


  • defined by author&software
  • 13.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)13,3663
Polymers13,3222
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-5 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.101, 149.101, 64.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11EaE-201-

HOH

21EaE-207-

HOH

31EaE-209-

HOH

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Components

#1: Protein
SH3 and multiple ankyrin repeat domains protein 1 / Shank1 / Somatostatin receptor-interacting protein / SSTRIP


Mass: 12341.283 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHANK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y566
#2: Protein/peptide
F-box only protein 41


Mass: 980.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TF61
#3: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % v/v ethylene glycol, 10 % w/v PEG 8000, 0.018 M magnesium chloride, 0.018 M calcium chloride, 0.1 M tris pH 7.5, 0.1 M bicine pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Jul 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.979→129.125 Å / Num. obs: 57199 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.039 / Net I/σ(I): 14.7
Reflection shellResolution: 1.979→2.01 Å / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2827 / CC1/2: 0.837 / Rpim(I) all: 0.56

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Processing

Software
NameVersionClassification
DIALS3.11data reduction
PHASER2.8.3phasing
Coot0.8.9.2model building
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.979→129.125 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.431 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.134 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2358 3012 5.268 %
Rwork0.2158 54166 -
all0.217 --
obs-57178 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.681 Å2
Baniso -1Baniso -2Baniso -3
1-0.787 Å20.393 Å20 Å2
2--0.787 Å20 Å2
3----2.553 Å2
Refinement stepCycle: LAST / Resolution: 1.979→129.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 12 115 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133674
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173502
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.6524957
X-RAY DIFFRACTIONr_angle_other_deg1.2361.5788131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74522.246187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31315642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0861523
X-RAY DIFFRACTIONr_chiral_restr0.0590.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02743
X-RAY DIFFRACTIONr_nbd_refined0.1840.2523
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.23131
X-RAY DIFFRACTIONr_nbtor_refined0.1530.21721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1050.210
X-RAY DIFFRACTIONr_nbd_other0.1640.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.214
X-RAY DIFFRACTIONr_mcbond_it3.4264.7591869
X-RAY DIFFRACTIONr_mcbond_other3.4264.7581868
X-RAY DIFFRACTIONr_mcangle_it5.1797.112319
X-RAY DIFFRACTIONr_mcangle_other5.1787.1112320
X-RAY DIFFRACTIONr_scbond_it3.9495.2991805
X-RAY DIFFRACTIONr_scbond_other3.9495.2991805
X-RAY DIFFRACTIONr_scangle_it6.2737.7782639
X-RAY DIFFRACTIONr_scangle_other6.2737.7782639
X-RAY DIFFRACTIONr_lrange_it8.82254.5613686
X-RAY DIFFRACTIONr_lrange_other8.82654.553675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.979-2.0310.3352130.31239950.31342080.7210.7150.299
2.031-2.0870.2832120.338400.29940520.7570.7490.288
2.087-2.1470.2962070.28737860.28739930.7810.7820.268
2.147-2.2130.2582150.26236560.26238710.8540.8430.239
2.213-2.2860.2832100.24735520.24937620.8720.8730.219
2.286-2.3660.2922290.2533970.25336260.8560.8720.221
2.366-2.4550.3041710.2433320.24435030.8760.8880.21
2.455-2.5550.2461790.23731810.23733600.9010.9070.207
2.555-2.6690.2871720.22430760.22732480.8910.9110.193
2.669-2.7990.231640.22229510.22231150.9290.930.195
2.799-2.950.2821560.2327480.23329040.8920.9180.202
2.95-3.1290.2531360.23926830.23928190.910.9180.216
3.129-3.3450.241380.23424910.23426290.9370.9250.216
3.345-3.6130.231230.21223270.21324500.9350.9490.201
3.613-3.9580.2061210.19521580.19522790.9480.950.187
3.958-4.4240.178950.16719590.16720540.9640.9660.167
4.424-5.1080.172740.15817450.15918190.970.9710.163
5.108-6.2530.222890.19514690.19615580.9610.9650.192
6.253-8.8330.215560.20911550.20912110.9350.9440.215
8.833-129.1250.21520.2116640.2117160.9580.9540.251

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