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- PDB-6yx0: Crystal structure of SHANK1 PDZ in complex with a peptide-small m... -

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Basic information

Entry
Database: PDB / ID: 6yx0
TitleCrystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
Components
  • PWQ-THR-ARG-LEU
  • SH3 and multiple ankyrin repeat domains protein 1
KeywordsPEPTIDE BINDING PROTEIN / protein protein interactions PDZ domain hybrid structures / fragment-based drug discovery / beta-sheets / acylhydrazone
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 / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / SH3 domain binding / scaffold protein binding / postsynaptic membrane / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / dendrite / protein-containing complex binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
PDZ domain 6 / PDZ 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 6 / PDZ 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. / 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
Chem-PWQ / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsHegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N035267/1 United Kingdom
European CommissionMSCA-IF-2016-749012 United Kingdom
Royal SocietySRF/R1/191087 United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Identification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.
Authors: Hegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.Y. / Trinh, C.H. / Sessions, R.B. / Edwards, T.A. / Wilson, A.J.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 1
B: SH3 and multiple ankyrin repeat domains protein 1
C: PWQ-THR-ARG-LEU
D: PWQ-THR-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9586
Polymers25,4624
Non-polymers4962
Water3,225179
1
A: SH3 and multiple ankyrin repeat domains protein 1
C: PWQ-THR-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9793
Polymers12,7312
Non-polymers2481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 1
D: PWQ-THR-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9793
Polymers12,7312
Non-polymers2481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.305, 64.947, 88.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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.: 2
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 PWQ-THR-ARG-LEU


Mass: 389.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PWQ / 4-[[2-(4-oxidanylidenebutanoyl)hydrazinyl]methyl]benzoic acid


Mass: 248.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7 PEG 400 35%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.57→88.28 Å / Num. obs: 36380 / % possible obs: 99.61 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Net I/σ(I): 15.1
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.291 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1782 / CC1/2: 0.777 / Rpim(I) all: 0.55 / Rrim(I) all: 1.406 / % possible all: 98.91

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Processing

Software
NameVersionClassification
REFMAC5.5.0026refinement
PHENIX1.17.1_3660refinement
DIALSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3O

1q3o


Resolution: 1.57→52.31 Å / SU ML: 0.1963 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2313 1833 5.07 %
Rwork0.2056 34352 -
obs0.2069 36185 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.65 Å2
Refinement stepCycle: LAST / Resolution: 1.57→52.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 90 179 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551776
X-RAY DIFFRACTIONf_angle_d0.74482393
X-RAY DIFFRACTIONf_chiral_restr0.0533267
X-RAY DIFFRACTIONf_plane_restr0.005313
X-RAY DIFFRACTIONf_dihedral_angle_d19.5004665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.39871520.37192547X-RAY DIFFRACTION98.86
1.61-1.660.3581360.33382591X-RAY DIFFRACTION99.06
1.66-1.710.27561550.29042603X-RAY DIFFRACTION99.32
1.71-1.770.32681490.28382574X-RAY DIFFRACTION99.52
1.77-1.850.28591320.25712630X-RAY DIFFRACTION99.68
1.85-1.930.24831370.23262619X-RAY DIFFRACTION99.64
1.93-2.030.2521210.20522636X-RAY DIFFRACTION99.71
2.03-2.160.23881440.21212609X-RAY DIFFRACTION99.71
2.16-2.330.22121370.21272670X-RAY DIFFRACTION99.82
2.33-2.560.2591350.21222642X-RAY DIFFRACTION99.93
2.56-2.930.24971350.21772687X-RAY DIFFRACTION99.82
2.93-3.690.21211450.19812719X-RAY DIFFRACTION99.93
3.69-52.310.20991550.17842825X-RAY DIFFRACTION99.97
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)
14.7919592561-2.28666154237-3.018264634681.791563868582.524731547653.808100066290.3316312141081.162219015740.360548397961-0.694213159818-0.387493517541-0.506897410865-0.900653578409-0.573636936057-0.2776087869790.7737667544350.2148407636340.1762580624550.6679287531310.1563059336250.5801058435970.32562485889111.56845869693.82486101595
24.40860078417-0.327070211626-1.083586884241.64158460819-0.2110244293732.808908735920.314418280076-0.5366820832630.2936054802840.0162966933090.004919865640570.145475250605-0.2582560615620.0340960220842-0.1633516589070.31338762007-0.001486839066850.005028666468560.290417546985-0.05985304989740.307769710839-12.09235731324.0968157957631.9173648152
35.79084729251-1.03891273844-1.825801170110.783265401026-0.3545252328531.190714818210.2447489248692.07299565402-1.0620628929-0.651643842836-0.4822595692010.1385860165810.104434003529-1.025826082750.04517881232640.4648833415730.0879650699944-0.0739565497020.598657918703-0.2327433321380.471074203632-10.3896498435-2.9042158713415.296572052
45.88165546342-0.490168719836-1.516780033622.931256394110.271051366083.904305362320.2061121289430.49105676208-0.0789564961504-0.218588590093-0.1205707241230.336665103198-0.305745412202-0.469999493296-0.1114184646950.3314347844680.0434082442239-0.0305516175360.336047474227-0.03833598698030.302221556678-14.54267179084.9755858210424.8050687358
53.511207881740.620567265529-1.839577353881.73695191807-0.03917794882513.86125980803-0.6854620385930.250964961562-1.61355998978-0.0874243019441-0.07370941155330.2442943036051.191167402-0.1365056420510.1110725136520.386401191285-0.07165244776070.03098239474770.212902387096-0.1487518152210.609799686143-11.0728308366-9.2124515963726.2077053457
66.305922976520.499589115042-3.509252760742.94749976748-1.302705758415.396955869470.4205859508030.002325857418230.398977915255-0.225375409744-0.07236925652230.102012950822-0.1224743654080.343448282169-0.09886219168210.3135898257820.0209440944803-0.003441074122210.248939675772-0.04367611185450.316092539248-8.181767904254.1198794290924.3597411853
76.27294445623.285931710753.619829262422.233781900661.518985742612.369157699730.1047821549790.2365928047110.07999476133880.1177829374690.333024318463-0.06076735968880.394643363387-0.832450546132-0.7425721097280.388858150516-0.03942746441160.02295836217850.543630359219-0.1144848799690.602575958164-21.9445428323-2.3999915766927.1928234747
82.39440991494-0.0322288288737-1.840012800520.599985811497-0.1520381286041.129355792230.2848810842890.2911863462620.3250384728480.0018031456022-0.0560126128891-0.0434340592653-0.330622774481-0.0461593895715-0.1458344740720.3151783546-0.008231263375620.01243910632180.3789278882950.01185653842020.3287444842669.149669138556.558502517713.12237704301
92.888587330480.580410973552-1.701207496212.37304832058-1.682866506023.66187008999-0.050505111407-0.295016542096-0.6739181413350.28331032523-0.143940112104-0.265478810211-0.08231692608320.3757403233330.237062157120.40453570557-0.007687355537630.0001487083204080.5273518984840.08513549287680.42664385756715.6480086215-5.480944496429.21754933152
102.45977411162-2.474787944130.9124084448583.73444606899-2.358731509722.00568239312-0.10112735942-0.2994369139250.45158385938-0.06797240651990.3731704388261.070750721980.872014672283-0.00935069648779-0.2066982266910.5389396190780.07137369455480.1345996300920.308979235370.03340141913470.6154675604385.78827497494-13.654515399515.2520155952
112.88380795949-0.282112459902-1.417014304454.2899518528-0.5719682734715.081247507960.0642409987247-0.07376647388220.1044572527390.274147658308-0.141615819628-0.0670164013498-0.417341055760.5996163906580.02583282864930.332715652919-0.0460942024856-0.01402612458680.3366930060970.02788195831510.32502898981612.51494741964.053314882995.35436029943
122.594466359010.443191323385-1.469376205613.9513408154-1.082952387245.93943018919-0.5288930157310.160982258752-0.938846060125-0.2297674575650.0196745116794-0.2453403444831.234864057090.1021464713370.3368458037240.4082208206820.02950355056310.07380416332240.313767723108-0.0008997896655780.43382515501510.9647034939-8.354703372240.692353472201
133.37014646418-0.136773096035-1.09725034522.533771005551.222205244683.665073654290.244152433562-0.0928091868970.3464802907770.241709671436-0.1643718153460.197339900027-0.352191192699-0.4569510559760.04332954112240.375803605073-0.0339138747230.03793499409690.343327108411-0.0003135803786810.4014446993367.286837007857.063455671396.54057675652
147.59381276248-3.304780368363.465831241862.27544615006-0.7401858363162.283974341480.1618624198610.06389442884480.604553547414-0.126212591090.17229362624-0.5266224231460.2028122828670.917540027068-0.5235224820260.4334565862680.03995238499470.003952710977580.7636000430540.07201890153840.46042413435221.9291222908-1.67942831879-0.142042485822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 651 through 657 )
2X-RAY DIFFRACTION2chain 'A' and (resid 658 through 675 )
3X-RAY DIFFRACTION3chain 'A' and (resid 676 through 699 )
4X-RAY DIFFRACTION4chain 'A' and (resid 700 through 725 )
5X-RAY DIFFRACTION5chain 'A' and (resid 726 through 745 )
6X-RAY DIFFRACTION6chain 'A' and (resid 746 through 758 )
7X-RAY DIFFRACTION7chain 'A' and (resid 802 through 804 )
8X-RAY DIFFRACTION8chain 'B' and (resid 651 through 675 )
9X-RAY DIFFRACTION9chain 'B' and (resid 676 through 685 )
10X-RAY DIFFRACTION10chain 'B' and (resid 686 through 690 )
11X-RAY DIFFRACTION11chain 'B' and (resid 691 through 725 )
12X-RAY DIFFRACTION12chain 'B' and (resid 726 through 745 )
13X-RAY DIFFRACTION13chain 'B' and (resid 746 through 762 )
14X-RAY DIFFRACTION14chain 'B' and (resid 802 through 804 )

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