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- PDB-6yx2: Crystal structure of SHANK1 PDZ in complex with a peptide-small m... -

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Basic information

Entry
Database: PDB / ID: 6yx2
TitleCrystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
Components
  • PWW-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 / olfactory behavior / synapse maturation / 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 / olfactory behavior / synapse maturation / 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 / positive regulation of dendritic spine development / adult behavior / social behavior / positive regulation of excitatory postsynaptic potential / associative learning / 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 / dendrite / glutamatergic synapse / 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-PWW / 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: 1.62 Å
AuthorsHegedus, Z. / Hobor, F. / Shoemark, D.K. / Celis, S. / Lian, L.J. / 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: PWW-THR-ARG-LEU
D: PWW-THR-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9866
Polymers25,4624
Non-polymers5252
Water4,324240
1
A: SH3 and multiple ankyrin repeat domains protein 1
C: PWW-THR-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9933
Polymers12,7312
Non-polymers2621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 1
D: PWW-THR-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9933
Polymers12,7312
Non-polymers2621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.435, 65.642, 86.346
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 PWW-THR-ARG-LEU


Mass: 389.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PWW / 4-[[(~{E})-5-oxidanylidenepentanoyldiazenyl]methyl]benzoic acid


Mass: 262.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75 / Details: 0.1 M HEPES 7.75 PEG 400 40%

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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 S 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: 1.618→65.64 Å / Num. obs: 33616 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 8.1
Reflection shellResolution: 1.618→1.65 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1 / Num. unique obs: 8301 / CC1/2: 0.863 / Rpim(I) all: 0.522 / Rrim(I) all: 1.24 / % possible all: 90.8

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Processing

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

1q3o


Resolution: 1.62→52.26 Å / SU ML: 0.2582 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7788
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 1693 5.05 %
Rwork0.2097 31811 -
obs0.2116 33504 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.75 Å2
Refinement stepCycle: LAST / Resolution: 1.62→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 92 240 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571774
X-RAY DIFFRACTIONf_angle_d0.73362386
X-RAY DIFFRACTIONf_chiral_restr0.0526265
X-RAY DIFFRACTIONf_plane_restr0.0057311
X-RAY DIFFRACTIONf_dihedral_angle_d16.6419666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.670.48291190.44492499X-RAY DIFFRACTION94.17
1.67-1.720.41461410.38142597X-RAY DIFFRACTION99.78
1.72-1.780.37061340.31722634X-RAY DIFFRACTION99.6
1.78-1.850.33071410.26932600X-RAY DIFFRACTION99.64
1.85-1.940.28511610.24512622X-RAY DIFFRACTION99.93
1.94-2.040.29521340.2322650X-RAY DIFFRACTION100
2.04-2.170.2611280.2092664X-RAY DIFFRACTION99.89
2.17-2.330.23671520.19972630X-RAY DIFFRACTION100
2.33-2.570.23961370.21062682X-RAY DIFFRACTION99.86
2.57-2.940.21351260.21092695X-RAY DIFFRACTION99.89
2.94-3.70.23971650.18932693X-RAY DIFFRACTION99.93
3.7-52.260.21371550.18132845X-RAY DIFFRACTION99.9
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)
11.689561130450.5145318453380.4265182359940.6166165283790.3478737420910.3842490614310.1520339010210.004769560877220.1217779583480.0783503499933-0.100674205496-0.0358967484085-0.09404589758280.143568129305-0.002279223992330.244645600306-0.004362338840190.02223401432550.2957591213310.05296100269470.212187195118-34.52749239684.8235679322-23.2727565055
20.02227237311250.06994863121460.0168383138360.8450631660120.496494088140.3895913772670.216682907954-1.09530239914-0.4464307680910.613916743096-0.4058239532940.434104003081-0.6563331346560.211251571508-0.09415552869230.445958783832-0.1155847568140.07229103021160.350223410560.128366330170.297454516738-38.7799126074-4.02845776621-11.1494599472
32.473700797320.0459253622536-0.643049573850.767864783534-0.5363672085951.500399026620.03854746046280.164168806702-0.05361389680680.105008751773-0.0256297928676-0.1519929243710.009084755573130.139301648253-6.4403629408E-50.215941310619-0.0209017083696-0.01605412150180.1920553202340.04280078360030.214418743132-33.24310408040.228106335307-24.0510006381
40.01031448451780.0327319140405-0.009120996328890.0504463096287-0.006501691965770.00540387571204-0.3010169345510.42814687860.07285694679190.1906241732340.132807460991-0.3203593515090.08871655883770.4053666840010.001469003712390.3034868378150.0362223793985-0.0642974485480.5372196368150.002311260135640.464653712822-23.1613982089-2.02622967381-25.6537412108
51.63172573329-0.0143709724802-0.40978381954-0.135903681087-0.2497710343780.1596601413790.162045476533-0.2832380987890.182208994684-0.0508067746909-0.102847190670.0127921426036-0.05415879756240.06413234147350.0002113737231110.234715558807-0.03517548220250.03517335588540.276524894162-0.05293533608230.21027512647-56.70800757823.27781693106-4.67389026017
60.0944932474915-0.018311575279-0.08482677522270.009136474824960.02835910547810.05920929004650.09383128392340.236383447002-0.16141781669-0.2816256029520.014012063633-0.01500553733150.199523449201-0.2109504688890.004201087365240.36870109937-0.003954905663040.0951718406450.198481702781-0.08835527376810.453107720686-51.3657415858-13.6634657721-14.9254447117
72.798525038370.153070017806-1.173225715772.10850765394-0.05204836559931.729940814030.0722495667009-0.2823601670410.0316661247867-0.0804521550951-0.0191089059759-0.0756030604677-0.02163291074320.0569433717990.01333204564650.192128520807-0.00109336653192-0.009029749642490.176018030704-0.03279286929840.195587759972-56.66159832521.26101642777-4.05777327449
80.02256262803330.0270394851111-0.0293581650490.0383450260179-0.03986786625450.03580513312710.336256492205-0.04467228633410.4327952277670.3215469456420.08109460537820.152933673108-0.260021126774-0.3000677721760.001203647145080.287382292678-0.007697417965470.001439689771760.492394447601-0.07848907847440.332415801766-67.8321732376-1.36227133845-0.143140430435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 651 through 680 )
2X-RAY DIFFRACTION2chain 'A' and (resid 681 through 699 )
3X-RAY DIFFRACTION3chain 'A' and (resid 700 through 759 )
4X-RAY DIFFRACTION4chain 'C' and (resid 802 through 804 )
5X-RAY DIFFRACTION5chain 'B' and (resid 651 through 685 )
6X-RAY DIFFRACTION6chain 'B' and (resid 686 through 690 )
7X-RAY DIFFRACTION7chain 'B' and (resid 691 through 761 )
8X-RAY DIFFRACTION8chain 'D' and (resid 802 through 804 )

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