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- PDB-8b10: Crystal Structure of Shank2-SAM mutant domain - L1800W -

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Basic information

Entry
Database: PDB / ID: 8b10
TitleCrystal Structure of Shank2-SAM mutant domain - L1800W
ComponentsSH3 and multiple ankyrin repeat domains protein 2
KeywordsMETAL BINDING PROTEIN / synaptic scaffold protein / Zn2+ binding / Zn-dependent polymerization
Function / homology
Function and homology information


synaptic receptor adaptor activity / : / structural constituent of postsynaptic density / vocalization behavior / Neurexins and neuroligins / anchoring junction / long-term synaptic depression / ciliary membrane / adult behavior / regulation of synapse organization ...synaptic receptor adaptor activity / : / structural constituent of postsynaptic density / vocalization behavior / Neurexins and neuroligins / anchoring junction / long-term synaptic depression / ciliary membrane / adult behavior / regulation of synapse organization / negative regulation of hippo signaling / presynaptic active zone / social behavior / associative learning / photoreceptor outer segment / synapse assembly / ionotropic glutamate receptor binding / photoreceptor inner segment / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / response to nutrient / learning / long-term synaptic potentiation / brush border membrane / brain development / SH3 domain binding / growth cone / dendritic spine / postsynaptic density / neuron projection / response to xenobiotic stimulus / apical plasma membrane / neuronal cell body / glutamatergic synapse / positive regulation of cell population proliferation / 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
DI(HYDROXYETHYL)ETHER / SH3 and multiple ankyrin repeat domains protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBento, I. / Gracia Alai, M. / Kreienkamp, J.-H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Kr1321/9-1 Germany
CitationJournal: Mol Psychiatry / Year: 2022
Title: Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans.
Authors: Hassani Nia, F. / Woike, D. / Bento, I. / Niebling, S. / Tibbe, D. / Schulz, K. / Hirnet, D. / Skiba, M. / Honck, H.H. / Veith, K. / Gunther, C. / Scholz, T. / Bierhals, T. / Driemeyer, J. / ...Authors: Hassani Nia, F. / Woike, D. / Bento, I. / Niebling, S. / Tibbe, D. / Schulz, K. / Hirnet, D. / Skiba, M. / Honck, H.H. / Veith, K. / Gunther, C. / Scholz, T. / Bierhals, T. / Driemeyer, J. / Bend, R. / Failla, A.V. / Lohr, C. / Alai, M.G. / Kreienkamp, H.J.
History
DepositionSep 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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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 2
B: SH3 and multiple ankyrin repeat domains protein 2
C: SH3 and multiple ankyrin repeat domains protein 2
D: SH3 and multiple ankyrin repeat domains protein 2
E: SH3 and multiple ankyrin repeat domains protein 2
F: SH3 and multiple ankyrin repeat domains protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,49210
Polymers49,1066
Non-polymers3864
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.940, 135.282, 131.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1954-

HOH

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Components

#1: Protein
SH3 and multiple ankyrin repeat domains protein 2 / Shank2 / Cortactin-binding protein 1 / CortBP1 / Proline-rich synapse-associated protein 1


Mass: 8184.262 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 193T / Gene: SHANK2, CORTBP1, KIAA1022, PROSAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPX8
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis Tris buffer, Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→65 Å / Num. obs: 38500 / % possible obs: 99.06 % / Redundancy: 13.5 % / Biso Wilson estimate: 40.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 20.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3620 / CC1/2: 0.774 / CC star: 0.934 / Rpim(I) all: 0.3855 / Rrim(I) all: 1.379 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ATJ

8atj


Resolution: 1.95→65 Å / SU ML: 0.2615 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 1940 5.05 %
Rwork0.2071 36440 -
obs0.2098 38380 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 23 268 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00483550
X-RAY DIFFRACTIONf_angle_d0.74644817
X-RAY DIFFRACTIONf_chiral_restr0.0399516
X-RAY DIFFRACTIONf_plane_restr0.0125625
X-RAY DIFFRACTIONf_dihedral_angle_d6.379460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.3671270.3392432X-RAY DIFFRACTION94.12
2-2.050.35131220.28892601X-RAY DIFFRACTION99.63
2.05-2.110.32131440.25922588X-RAY DIFFRACTION99.93
2.11-2.180.30521290.24322609X-RAY DIFFRACTION99.71
2.18-2.260.34421310.30222486X-RAY DIFFRACTION96.39
2.26-2.350.22931360.22592599X-RAY DIFFRACTION99.78
2.35-2.460.29381380.23772632X-RAY DIFFRACTION99.82
2.46-2.590.28131140.22252601X-RAY DIFFRACTION99.71
2.59-2.750.2581430.2252611X-RAY DIFFRACTION99.6
2.75-2.960.30361410.23392631X-RAY DIFFRACTION99.78
2.96-3.260.33351510.23372613X-RAY DIFFRACTION99.75
3.26-3.730.25251340.19312635X-RAY DIFFRACTION99.39
3.73-4.70.20861760.16622628X-RAY DIFFRACTION99.89
4.7-650.22791540.18292774X-RAY DIFFRACTION99.25
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)
15.55156313779-0.429962520822-1.10144613575.64896040504-0.4635445748964.79099013437-0.0878298274149-0.166018806482-0.216357878220.3419950262850.0244512561782-0.278999407290.0756997554590.2444098192020.05824907198840.297549667239-0.03984880111460.007371374470720.2399342602240.005821524930280.233815624851-27.468914535113.84975919875.14613153336
26.98024296278-3.09501914565-5.647036744467.35970693245.343178325289.112909874720.2392291556930.6248132841740.128470909438-0.8135828676330.0603624288796-0.190996605858-0.722722229354-0.131720520056-0.3803391529590.457783719145-0.1311761093170.01844676430760.4012193622110.01171102480580.328451200675-25.79179377619.0806594018-4.60330854275
39.0693466433-3.81392534464-5.702450731063.463752887633.970003821087.945098107080.06096671520020.515182865556-0.610894528851-0.72036070106-0.391124419780.543366793685-0.292518699215-0.4387555919140.4822879128520.586912664685-0.06677099557520.05482548561970.425602359733-0.06959214665580.453389417077-29.877477528710.2133726173-7.55231108899
42.564925659022.194984628740.6998262146867.7579992966-2.446174568416.58399550467-0.0137789041211-0.1589791721130.02231403406760.8387835533040.3803302025620.653545610666-0.000369666183929-0.450213755522-0.3042521582080.490338292343-0.07978536599590.03607966759090.385300137880.09168708798170.394821502485-30.1282029208-6.41572442208-17.4908872398
53.265519784190.548430185886-1.250482985385.71178777143-0.3205595653599.02973975342-0.000744703580128-0.154913582695-0.226649991387-0.446186178199-0.0589238912708-0.6014581720552.231492430091.510718946290.08741593317520.6376955221310.1040005296010.05289062045140.400922657723-0.003995185291110.345272707198-19.9861824133-5.7754936842-19.6959257519
65.76705013264-1.12777881382-4.63706530837.198874050960.4373119750268.106133030110.102510515851-0.424347302994-0.565088396176-0.0773934993126-0.541931566902-0.8051439692011.406327806171.563524664910.5333113924620.4928433741420.1137068948580.01232493633660.4963920395160.05724632391410.4635785332-14.2197161467-0.745655031167-20.6699593849
76.156846241772.55766178426-2.473095541198.2698307991-4.364283830424.872904391720.2181683847570.03488842377980.5664161086890.4221560717590.05742508409180.364099922704-0.509246645985-0.0579819436089-0.2321307599050.432387949394-0.04280403822980.02228519214850.367457912847-0.01068130901240.383844517117-20.76631464757.27517002147-19.5075506509
84.633220141211.40106324918-1.386395462523.51859192801-1.997863066747.894542084740.8956429375930.2383539464160.440630196001-0.161644538269-0.2392397233760.3821514690090.000363943545416-0.196840354538-0.4862545499940.6130422763210.01375444668550.05977827998210.367256514451-0.02970116570610.425851413291-23.8033157463.94902412527-29.3298983655
97.65378669745-0.83781033003-1.294068119966.72016824198-2.576068183039.311047022650.04229140434680.07731709274720.6293154305780.9346485016170.03916508707310.536138511819-1.12932973274-0.565980039175-0.08562948378350.4699353338230.07641781892370.0605232973540.413086155197-0.01051451636760.468620423145-30.156993402847.16015693443.23917607683
104.75813796657-0.216467762665-2.839745013828.45383713208-2.041006010473.076062265360.203751602257-0.06606282120760.170947363320.252811192171-0.105598964511-0.000616194500318-0.620439612228-0.00114679328111-0.1043367227680.367869219724-0.0498464282819-0.03081062589850.340167051891-0.005833052929260.385813262535-23.438790850842.9979209833-1.22544487247
115.80213777851.45942144184-2.459177728345.15455256713-1.13746101245.79638960593-0.1654918948120.3423066039480.19898540217-0.6219561634070.4227699032870.6239337782670.395767466495-0.6253840743-0.2412707620760.443349335138-0.140066661561-0.06912953269980.4021860005140.05069153132920.438738767824-28.01599978133.5076227991-3.58759559347
128.4331619549-1.218412762274.793357227463.47438769156-0.2461966169143.09040889809-0.06416699963221.148339962-0.443686245436-0.1395322839940.09341957962380.04934214074930.04545027079810.3965928966420.1072255072160.415141064821-0.06375011293720.007641246854470.485389183913-0.0638117525110.376933099492-19.801414625927.133794019414.9602834632
133.34850874877-2.916157934080.2074535877749.05654040311-4.078981754949.58609328632-0.168287202146-0.301645392446-0.3157775918470.5426438504640.04816600538480.149479075253-0.09916858332690.2725075875340.1129014737970.370392648266-0.03367074408480.01333702416020.4011572590360.002148264553510.3237633985-19.805365002231.209748440525.4354362683
144.25583883534-2.269344616613.807950993553.70863108329-2.653799244284.05722181664-0.1140108362160.08786076750630.2652555574040.342161133672-0.0475310279891-0.455779971339-0.7012085374940.2664452398720.09318325137040.51020237949-0.05184254145230.03376221343420.435580993040.006377972281920.372188120766-14.438920001124.137349048728.2430143486
156.30902873275-1.83395649986-0.09444247129857.52202985943-0.1445119786043.96442867936-0.110314041208-0.798438324965-0.5003699855590.6750432416140.1630390793560.08465289252360.0904869378888-0.210511624650.1171673592020.5456719832540.05251988346020.192612825330.424980345650.0323707581070.40903597871-45.08405761747.44952725845-17.8168421256
164.1134036844-2.929117577761.596572170234.065764311472.640726355048.02130030795-0.1591541054880.1635431979170.209080551594-0.0604484609634-0.2081637852680.26449423406-0.243774874485-0.7794794944990.380308443150.3846897906250.01826385218650.08270099112210.4155911446230.008194626111710.409639743062-47.582440434514.4383607282-27.2684946268
178.1057947801-2.664452575550.1598879928495.723112737440.1603315950822.81960318688-0.433777310412-0.4751755266710.307610033681.058000912440.259008098404-0.564204034567-0.8922711293390.1145446450860.05640639182450.6201175876780.1109536778080.07701170152970.440415479638-0.03468611499420.494548608295-42.958187734722.101926826-20.8977863107
188.21038104378-4.58471629682.270480947688.35518919073-3.039220715891.172271277330.500943070889-3.18255523971-0.7475615305552.085696172550.2058493012280.5102696354550.484433130063-1.049226601630.1039922606360.880343187818-0.440579731393-0.0009838149509070.846281795040.4264248746880.510116950975-52.00441855277.0167071317330.9794961823
195.424890852991.545868295392.153881019066.416046666211.368631163029.399589558630.0710861959623-0.109475537288-0.5387544325740.4057002942260.140551673479-0.6641935503490.5684289724180.00491183551545-0.2645782688480.3670018494570.04749901182650.02004473314390.2841237598620.03934124009920.386381068335-44.00151255210.536170428520.16034304
207.141094668440.8844874160332.51144105956.14904599621-0.9928907900068.2661152883-0.0601271587182-0.7995386994750.3874553317710.556533944140.06152989302730.315011048593-0.811951744754-0.7769728870630.01996822909910.3393387703650.03483305701190.03867914910040.421613210184-0.03336546437320.347297422565-47.657208735920.607112874523.4094753958
216.52769337051.872047108090.34476315762.87751282162-3.356476913327.45111147747-0.0464263121609-0.3579808748790.06206111778930.4051102987270.1947232724370.546390159351-0.317122415133-1.32863482266-0.202009309320.3373821037120.07295084807490.05034369033380.5612529760470.07686346748850.351620707935-54.894979836817.750355393516.506370409
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1780 through 1809 )AA1780 - 18091 - 30
22chain 'A' and (resid 1810 through 1832 )AA1810 - 183231 - 53
33chain 'A' and (resid 1833 through 1848 )AA1833 - 184854 - 69
44chain 'B' and (resid 1780 through 1787 )BB1780 - 17871 - 8
55chain 'B' and (resid 1788 through 1797 )BB1788 - 17979 - 18
66chain 'B' and (resid 1798 through 1809 )BB1798 - 180919 - 30
77chain 'B' and (resid 1810 through 1832 )BB1810 - 183231 - 53
88chain 'B' and (resid 1833 through 1849 )BB1833 - 184954 - 70
99chain 'C' and (resid 1780 through 1798 )CC1780 - 17981 - 19
1010chain 'C' and (resid 1799 through 1819 )CC1799 - 181920 - 40
1111chain 'C' and (resid 1820 through 1849 )CC1820 - 184841 - 69
1212chain 'D' and (resid 1780 through 1798 )DD1780 - 17981 - 19
1313chain 'D' and (resid 1799 through 1827 )DD1799 - 182720 - 48
1414chain 'D' and (resid 1828 through 1848 )DD - E1828 - 190149
1515chain 'E' and (resid 1780 through 1798 )EF1780 - 17981 - 19
1616chain 'E' and (resid 1799 through 1832 )EF1799 - 183220 - 53
1717chain 'E' and (resid 1833 through 1847 )EF1833 - 184754 - 68
1818chain 'F' and (resid 1781 through 1787 )FH1781 - 17871 - 7
1919chain 'F' and (resid 1788 through 1809 )FH1788 - 18098 - 29
2020chain 'F' and (resid 1810 through 1832 )FH1810 - 183230 - 52
2121chain 'F' and (resid 1833 through 1847 )FH1833 - 184753 - 67

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