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- PDB-7a00: Crystal structure of Shank1 PDZ in complex with L6F mutant of the... -

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Basic information

Entry
Database: PDB / ID: 7a00
TitleCrystal structure of Shank1 PDZ in complex with L6F mutant of the C-terminal hexapeptide from GKAP
Components
  • L6F mutant of C-terminal hexapeptide from Guanylate kinase-associated protein
  • SH3 and multiple ankyrin repeat domains protein 1
KeywordsPEPTIDE BINDING PROTEIN / Shank1 PDZ / GKAP
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
SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZsofia, H. / Hetherington, K. / Fruzsina, H. / Edwards, T.A. / Wilson, A.J.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N035267/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/KO39292/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Royal SocietySRF/R1/191087 United Kingdom
Engineering and Physical Sciences Research CouncilEP/N025652/1 United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Query-guided protein-protein interaction inhibitor discovery.
Authors: Celis, S. / Hobor, F. / James, T. / Bartlett, G.J. / Ibarra, A.A. / Shoemark, D.K. / Hegedus, Z. / Hetherington, K. / Woolfson, D.N. / Sessions, R.B. / Edwards, T.A. / Andrews, D.M. / Nelson, A. / Wilson, A.J.
History
DepositionAug 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: L6F mutant of C-terminal hexapeptide from Guanylate kinase-associated protein
D: L6F mutant of C-terminal hexapeptide from Guanylate kinase-associated protein


Theoretical massNumber of molelcules
Total (without water)26,2384
Polymers26,2384
Non-polymers00
Water3,045169
1
A: SH3 and multiple ankyrin repeat domains protein 1
C: L6F mutant of C-terminal hexapeptide from Guanylate kinase-associated protein


Theoretical massNumber of molelcules
Total (without water)13,1192
Polymers13,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-3 kcal/mol
Surface area6970 Å2
2
B: SH3 and multiple ankyrin repeat domains protein 1
D: L6F mutant of C-terminal hexapeptide from Guanylate kinase-associated protein


Theoretical massNumber of molelcules
Total (without water)13,1192
Polymers13,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area6560 Å2
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-13 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.180, 66.470, 88.580
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 L6F mutant of C-terminal hexapeptide from Guanylate kinase-associated protein


Mass: 777.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 7 PEG 400 40%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→53.17 Å / Num. obs: 25591 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Net I/σ(I): 16.6
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.993 / Num. unique obs: 1253 / CC1/2: 0.595 / Rpim(I) all: 0.559 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHASERphasing
xia2data processing
XDSdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3O

1q3o


Resolution: 1.78→44.29 Å / SU ML: 0.281 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.8298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 1234 4.83 %
Rwork0.2134 24300 -
obs0.2153 25534 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.44 Å2
Refinement stepCycle: LAST / Resolution: 1.78→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 169 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561806
X-RAY DIFFRACTIONf_angle_d0.71952441
X-RAY DIFFRACTIONf_chiral_restr0.0522274
X-RAY DIFFRACTIONf_plane_restr0.0052322
X-RAY DIFFRACTIONf_dihedral_angle_d10.06191077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.850.41121310.35782667X-RAY DIFFRACTION99.75
1.85-1.940.29831240.28112647X-RAY DIFFRACTION99.53
1.94-2.040.25381330.23942669X-RAY DIFFRACTION99.57
2.04-2.170.28231220.23372683X-RAY DIFFRACTION99.36
2.17-2.330.26461360.2242688X-RAY DIFFRACTION99.44
2.33-2.570.27781290.2262696X-RAY DIFFRACTION99.47
2.57-2.940.29881370.23552704X-RAY DIFFRACTION99.41
2.94-3.70.25161530.20672738X-RAY DIFFRACTION99.48
3.7-44.290.21071690.18622808X-RAY DIFFRACTION98.48
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)
10.351204383520.191355266854-0.1366728524820.09729753669790.2932854786760.4436594417310.1102265302260.0844474084019-0.01759020411960.0232036513968-0.0334421706416-0.048068932822-0.2054704903790.21016219625-0.000109255456680.3278280301620.02083089396460.02841877799910.350034060197-0.001062514525170.28941603064-12.90459104015.929216778561.22862150351
20.27563073728-0.3799760168240.8260436550850.477706077649-0.9873598774443.18279749499-0.250803298989-0.639709293988-0.3002012437760.981750409644-0.183366068082-0.1154949310230.1051095461440.7370491180140.08924583749190.6057856519420.1354866987520.03701571966450.4084574609070.1164101552310.517666927038-7.41134246463-8.128647705419.1163243706
30.779265905007-1.12541108935-0.1734772951511.259148187590.02542888903040.8445819607770.490239212999-0.898601894976-0.5185238035520.990420346898-0.534182877166-0.0609038570887-0.1560087731311.18900235661-0.002178985619860.55074020196-0.0441019192460.003025978028390.346941364460.02785868129070.382760740334-12.3793337139-2.2932393390911.5786357528
41.20796891703-0.649885492255-0.8243339438361.32560891942-0.2080578558831.635719546830.03506289824110.00390200598299-0.130357712979-0.07845875769740.0715080335566-0.128596285237-0.02262027999010.213082514887-5.57951840249E-50.350109352799-0.0508841241946-0.01547598814420.2748761976180.006056275858980.315842694377-10.75361810782.072504871750.75815269671
52.153556260170.750087031461-0.7455995242580.841335515375-0.1077846153391.52266375048-0.05203656046980.229087471597-0.2815393084380.1741243899190.0131015710681-0.2248140740810.3881778234-0.05038675641020.0001371971779590.3396992047720.0379532007658-0.02043386653550.315434548773-0.04888418321130.364161478015-10.7780448457-4.26278762304-1.99742232105
61.687696039980.7514580896341.162127359910.3031580764650.5336736709230.8138202495681.25800435546-0.6815357290671.09872659870.761362475946-0.103147010830.02946981675970.0228116356684-0.01522389000490.4539529198050.871239578072-0.3008348831090.2695125315260.617374004651-0.2795316741950.652785122893-15.512669272914.939722449920.0550990461
7-0.00782513578549-0.0336874710277-0.01201483912380.0474011828118-0.0117966378506-0.002545208228180.1193858223130.2506904887810.5970914415320.4562286003670.1356322797960.391570325924-1.05602342618-0.8684170818480.0003034152431590.5889654984450.1086087143460.1041202843320.3858478071080.06151084841120.432460337385-21.370608586711.31497336760.629064250676
80.268688989250.3923209073710.1854527857331.318833386270.2572200497650.2716843743990.111876944282-0.179564911074-0.177747535423-0.22647651239-0.328456940583-0.244056466591-0.1837801455620.2647579078980.0004277273123880.359486072013-0.009847898687630.02317733251760.3649629421210.02043010358150.311001056886-28.22686635947.0818871642224.9150627851
91.823812164380.3857028338660.1485035017312.39753888885-0.9473511485620.3683641455130.06959554025270.163954234125-0.249535296214-0.459118558069-0.19129689346-0.105035532647-0.198692035656-0.343253169405-0.001039021525910.302766534470.0255783403288-0.003082446026110.36360848748-0.01355347440690.355432845307-35.8583048207-1.674100259721.5212375405
101.430085427351.64779934681-1.225485917132.01020958153-0.524537505181.916225755120.1859007411890.1528146197690.0948694638005-0.0260407507117-0.03032047687120.110130656896-0.234684296687-0.2484307188889.48467490285E-50.311326096420.0953813577936-0.01374227273690.3417249896770.01073069853590.30133450657-36.49556583045.6354474546723.7431588901
110.270105458501-0.3473202230780.160996060391.1127129203-0.159528199530.5454991523320.126137904675-0.386079602866-0.876750110820.0414493940019-0.062207648438-0.1094301366270.8391290163970.388289606724-5.68247769162E-50.432132097665-0.035494299603-0.01041334115990.4227327536960.05174590795460.505047369004-32.4311169007-8.338679155325.5422648898
121.29653177038-0.2755461672690.2115035201741.523934723570.7476734830150.4094291796680.2781617068130.05993747391840.0409528221507-0.256155474503-0.330454586229-0.0886513722025-0.7815431809020.3608638917680.0002176249610760.4232850087820.05318428852670.006334137530220.3670601464080.06386772283490.342873061229-29.91022101966.6187515120518.5771804331
130.05870639356410.1547770834930.1188865001710.8478994492340.6233051759630.4490232413910.508839931403-0.546050864543-0.1332637923090.2398093394680.59740565696-0.886593076920.09184218715480.5712544021040.1803557409780.5571687843860.179644198457-0.07794053652910.6720744308130.06679210060020.607817017834-0.706786072965-4.049357076722.48946280933
140.256827499924-0.1019848862990.01604224891740.510970683382-0.2392526184750.102862159338-0.1883361171080.1927505658880.187206016114-0.446437990196-0.05619076545220.305893050880.368816199151-0.885104183269-0.0010856175910.432668678459-0.129279021707-0.04155329606170.490550763725-0.07628419973240.471602601201-43.152851747-3.3772841310821.8598175148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 651 through 675 )
2X-RAY DIFFRACTION2chain 'A' and (resid 676 through 687 )
3X-RAY DIFFRACTION3chain 'A' and (resid 688 through 705 )
4X-RAY DIFFRACTION4chain 'A' and (resid 706 through 734 )
5X-RAY DIFFRACTION5chain 'A' and (resid 735 through 756 )
6X-RAY DIFFRACTION6chain 'A' and (resid 757 through 762 )
7X-RAY DIFFRACTION7chain 'B' and (resid 651 through 656 )
8X-RAY DIFFRACTION8chain 'B' and (resid 657 through 667 )
9X-RAY DIFFRACTION9chain 'B' and (resid 668 through 699 )
10X-RAY DIFFRACTION10chain 'B' and (resid 700 through 725 )
11X-RAY DIFFRACTION11chain 'B' and (resid 726 through 745 )
12X-RAY DIFFRACTION12chain 'B' and (resid 746 through 762 )
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 7 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 7 )

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