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- PDB-7c7j: Crystal structure of SHANK3 SPN domain in complex with GTP-bound ... -

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Basic information

Entry
Database: PDB / ID: 7c7j
TitleCrystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)
Components
  • Ras-related protein Rap-1b
  • SH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / SHANK3 / Rap1b / SPN / Ras
Function / homology
Function and homology information


guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / positive regulation of glutamate receptor signaling pathway / negative regulation of synaptic vesicle exocytosis / Rap protein signal transduction / negative regulation of cell volume / negative regulation of actin filament bundle assembly / positive regulation of synapse structural plasticity ...guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / positive regulation of glutamate receptor signaling pathway / negative regulation of synaptic vesicle exocytosis / Rap protein signal transduction / negative regulation of cell volume / negative regulation of actin filament bundle assembly / positive regulation of synapse structural plasticity / positive regulation of long-term neuronal synaptic plasticity / vocal learning / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / regulation of dendritic spine morphogenesis / vocalization behavior / NMDA glutamate receptor clustering / positive regulation of AMPA receptor activity / neuron spine / Rap1 signalling / AMPA glutamate receptor clustering / brain morphogenesis / dendritic spine morphogenesis / regulation of long-term synaptic depression / establishment of endothelial barrier / Neurexins and neuroligins / regulation of long-term synaptic potentiation / regulation of establishment of cell polarity / ciliary membrane / MET activates RAP1 and RAC1 / azurophil granule membrane / positive regulation of dendritic spine development / adult behavior / p130Cas linkage to MAPK signaling for integrins / ionotropic glutamate receptor binding / social behavior / GRB2:SOS provides linkage to MAPK signaling for Integrins / RET signaling / positive regulation of synaptic transmission, glutamatergic / positive regulation of excitatory postsynaptic potential / synapse assembly / lipid droplet / G protein activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / Integrin signaling / cellular response to cAMP / learning / positive regulation of long-term synaptic potentiation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / memory / extrinsic component of cytoplasmic side of plasma membrane / GDP binding / SH3 domain binding / protein self-association / Signaling by RAF1 mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling by moderate kinase activity BRAF mutants / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin binding / scaffold protein binding / cell population proliferation / protein C-terminus binding / dendritic spine / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / neuron projection / GTPase activity / protein-containing complex binding / GTP binding / Neutrophil degranulation / extracellular exosome / zinc ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rap1 / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / small GTPase Ras family profile. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Ras-related protein Rap1 / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / small GTPase Ras family profile. / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / PDZ domain profile. / ankyrin repeats / Domain present in PSD-95, Dlg, and ZO-1/2. / Ankyrin repeat / PDZ domain / PDZ superfamily / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rap-1b / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsXiao, L.X. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
Citation
Journal: Chin.J.Chem. / Year: 2020
Title: Mechanistic Insights into the Interactions of Ras Subfamily GTPases with the SPN Domain of Autism-associated SHANK3.
Authors: Xu, X.L. / Liu, J.P. / Wang, Y.L. / Wang, Y. / Gong, X. / Pan, L.F.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L.W. / Kapral, G.J. / Grosse-Kunstleve, R.W. / McCoy, A.J. / Moriarty, N.W. / ...Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Hung, L.W. / Kapral, G.J. / Grosse-Kunstleve, R.W. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R. / Read, R.J. / Richardson, D.C. / Richardson, J.S. / Terwilliger, T.C. / Zwart, P.H.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rap-1b
B: Ras-related protein Rap-1b
C: SH3 and multiple ankyrin repeat domains protein 3
D: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6509
Polymers60,5154
Non-polymers1,1355
Water1,63991
1
A: Ras-related protein Rap-1b
C: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8455
Polymers30,2572
Non-polymers5883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rap-1b
D: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8054
Polymers30,2572
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.215, 191.926, 48.876
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

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19063.572 Da / Num. of mol.: 2 / Mutation: G12V,Q63E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P61224
#2: Protein SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2


Mass: 11193.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHANK3, KIAA1650, PROSAP2, PSAP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYB0

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Non-polymers , 4 types, 96 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 8000, 100 mM Imidazole/Hydrochloric acid (pH 8.0), 200 mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.39→191.93 Å / Num. obs: 20943 / % possible obs: 92.4 % / Redundancy: 12.7 % / Biso Wilson estimate: 37.29 Å2 / Rmerge(I) obs: 0.264 / Net I/σ(I): 8.6
Reflection shellResolution: 2.39→2.52 Å / Rmerge(I) obs: 1.346 / Num. unique obs: 1118

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4X, 4DXA

5g4x

4dxa


Resolution: 2.39→47.98 Å / SU ML: 0.3642 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7631
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 1048 5.03 %
Rwork0.1854 19797 -
obs0.1889 20845 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.19 Å2
Refinement stepCycle: LAST / Resolution: 2.39→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 67 91 4235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00964213
X-RAY DIFFRACTIONf_angle_d1.13345715
X-RAY DIFFRACTIONf_chiral_restr0.0573635
X-RAY DIFFRACTIONf_plane_restr0.0066741
X-RAY DIFFRACTIONf_dihedral_angle_d12.06212571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.510.30581400.25093015X-RAY DIFFRACTION100
2.51-2.670.34011280.24592173X-RAY DIFFRACTION98.63
2.67-2.880.33791080.23622229X-RAY DIFFRACTION99.91
2.88-3.170.32561710.22523005X-RAY DIFFRACTION100
3.17-3.620.28011570.19323061X-RAY DIFFRACTION99.75
3.62-4.570.20721620.15093083X-RAY DIFFRACTION99.82
4.57-47.980.2141820.15863231X-RAY DIFFRACTION99.62
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)
13.033757722020.387760321332-0.3224635083912.777901439110.140342997964.13130176265-0.1044799794080.218226637338-0.161441521522-0.07718181646340.0234421836617-0.0717338703828-0.0543013873890.0640629637760.0526717987110.2424002826990.0379524562374-0.02245185520980.2670538478650.03123704961320.265638571489-9.06406110254-23.77443531980.61649921517
25.52008102468-0.2419460027520.5152437864462.170441625310.4793255287866.007944058670.1569249094480.518548644907-0.1150846457090.123026883325-0.06035441199430.2956975390580.000671493372733-0.502567107869-0.1361624637920.29273092478-0.0127605276741-0.002103237616730.272427068549-0.05858993888940.355711207569-17.0964482144-26.43314464962.87869980517
34.672362988482.05982163552-0.6039080679674.7740586467-1.680949272622.129080165250.2245833007230.5956794380710.5919932702820.07913080719180.1296130348580.827880372318-0.480664652829-0.59318601363-0.3771324314860.3551761391480.156318335871-0.02337635968150.458967850427-0.0008255434841290.304847531034-19.9146684132-12.53033749930.429232744827
43.3895283051-2.23945372351-3.37110867655.346851651541.719751482256.102322418030.787627158349-0.2692545059280.998064807603-0.33844457261-0.314967341122-0.302376793938-1.187774563730.247646383681-0.5230342923610.5191843719740.04238431052980.09010032968660.340865332750.03895769413750.446499105166-8.03550528022-3.517186133150.828814344138
55.60562457646-5.03316271376-2.100352530196.219208327251.633343716983.004740120150.595592489738-0.6443638498040.6805671864270.299848191766-0.10927843425-0.42253113121-0.4515737270040.0339898594456-0.4177761353690.3315939192410.03902590357150.006795823132640.2644473833210.005246646831650.231983919879-9.33073830693-10.98074273146.45891521738
66.376743435844.644190998821.225762784586.42595924717-3.349007869156.643905857480.280497755618-0.354504208-0.04472960183260.272877722064-0.1007720384380.244023864473-0.129674248082-0.263025128999-0.1727465965080.2276212639430.07074472682120.01194206901410.275214586709-0.08156929629420.221425921337-14.158452985-18.574633397513.6246904786
73.89928151637-0.4548657567830.9131376180012.15624375060.1115525863992.715049845130.0306406721064-0.201023133947-0.2244988777140.1835195188370.0334047442524-0.2146001409720.2057239634190.00749984732142-0.03786902031870.3621120188550.0691814681894-0.03158691520170.228965360643-0.02287409775730.2181863355655.84168888314-21.620813520924.3917229678
84.87286772071.17812922964-1.003050611825.97606889442-0.5130714946973.04023475250.202643248831-0.4319238709130.4455067882020.305950034032-0.0695690537974-0.249551577163-0.1062116265440.545509234667-0.1310310868790.3370268469590.0647610938203-0.05314129656060.460737970886-0.06846845294690.37673938364614.4471673954-21.890737711222.146270649
95.98223207497-0.894294581226-0.4124170190733.417269831891.92358460873.24067074426-0.251455801031-0.2873688415850.3262535639060.2190396137520.182206089553-0.587197491695-0.4810167600490.60208984220.003480546369580.330656937994-0.0975336673204-0.0800067722690.333725198072-0.0003073806904080.36122525794612.6244878839-7.5198707112524.6619526084
103.95987652889-0.157494270517-1.73231509552.394901511410.1044405745065.233922222670.1880156651610.1630733352690.413516180217-0.00720732069166-0.0256616175007-0.0398453403754-0.578092727386-0.0815540532859-0.1908859044410.317110874660.0107558161175-0.05107029858260.2915732652840.01686290949380.2843843866752.6815216785-8.4389843999218.7666866629
115.59004807869-0.3766926237971.902927668885.3403934689-2.457741932048.29909978533-0.05705663064460.208490873171-0.2929747684150.09837069101680.1356382969710.306568712518-0.676336015113-0.4762746896670.07044379122090.3613129487990.0341275130989-0.03560359652160.317790203049-0.100501339470.306231830333-12.5673475689-36.299656304-7.06302783835
124.282551884451.24548402109-2.349440263367.053786950791.703911318065.914911657240.1501630550530.344547030182-0.0384702455762-0.374173045962-0.339902423077-0.35196864674-0.306594305614-0.5309138114050.3124414933190.2397435128860.04364129787260.0349752747810.346258038842-0.0856002779520.368773024566-4.47666168784-40.4975821172-10.8264225027
132.198522085740.89741387725-1.688260427054.328164169750.2420270222313.78726109155-0.316556666318-0.735232893907-0.627032755955-0.291633374967-0.517786143202-0.4211945542640.17829964003-0.09220069024280.449570905260.249869875738-0.08109884002550.08369999398190.267452805579-0.03814482413640.388137730555-5.36568245871-46.8537025376-4.54124115153
145.432594804252.30756166161-4.499382029650.972545089152-1.909627211853.72177629929-0.1235084364080.8237774550241.71477445578-0.6420286110320.0409599910436-0.8511216113840.77936371184-0.4163502113230.2809354459640.2664872682410.006166481223560.03649194369110.412401219180.06976449576180.508067745381-22.6735828437-50.6125786712-5.26670396359
151.882312210792.33026658982-1.713141506175.18792802965-3.464899393472.91978091189-0.4957731520850.716569161709-0.903851843547-1.183069984990.301072952872-0.1521224484341.333688263260.004034391175930.234181239530.344574025727-0.07950976073580.05710839146410.725825650404-0.5110710467910.902753497768-12.249529975-50.664248184-15.3130853097
162.97307511011.736072295661.335515030723.007759174620.1258077910986.02977904875-0.3976911982860.319934116293-0.04091475685410.46035493768-0.002343999767430.9676900169460.648469716471-0.842069805707-0.2031618742930.221776927266-0.1049069954190.08882653111690.486044024693-0.1875832299510.700811937103-16.0159524344-44.6344594126-6.007141054
173.07651655549-0.321826782868-0.9075047812594.17205070562-0.8081871392290.4401987810190.205851865052-0.2492059114310.102770659652-0.0927482995723-0.06377071354220.00288669654727-0.210842283593-0.000842934931062-0.09616778756810.3327308235570.02784938315610.01426384878410.288986061162-0.01690652666110.31872626236110.6766634506-35.704054267134.9103557929
188.221212484217.885339353110.6286139167527.581150653740.344748075924.449530382510.789286291034-1.889718258711.233754843230.546646705766-0.1118278354441.144777887340.457270471575-1.626576956310.07055679071840.610436761446-0.0924710792779-0.2842343248461.35324511263-0.4830695259321.36422001306-0.256398696021-38.574839337426.6903180584
192.564797483752.15084409136-1.739976900788.521664509640.6507893069437.839401783270.435401311524-0.379991874375-0.4753002722030.151942031026-0.4333987580440.0324039556310.6472519505811.127850444420.06132828300730.3609542096290.1753522887240.02431154227350.3091886393-0.03895051767090.44028565391716.2548990634-46.045534635331.3701326978
203.37610177076-1.58130768786-0.5701601649376.880497940380.6222994477946.025535887390.1800954141830.0514393771606-0.681185265686-0.738973498225-0.318628188402-1.030588056790.1628610164950.566825853482-0.02843143525820.1186831816860.0223783375235-0.03563681838790.4724904373070.07749577685410.61602725556618.5500171587-40.781497110433.8999395468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 116 )
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 153 )
6X-RAY DIFFRACTION6chain 'A' and (resid 154 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 36 )
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 116 )
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 167 )
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 26 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 49 )
13X-RAY DIFFRACTION13chain 'C' and (resid 50 through 56 )
14X-RAY DIFFRACTION14chain 'C' and (resid 57 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 76 )
16X-RAY DIFFRACTION16chain 'C' and (resid 77 through 94 )
17X-RAY DIFFRACTION17chain 'D' and (resid 7 through 43 )
18X-RAY DIFFRACTION18chain 'D' and (resid 44 through 49 )
19X-RAY DIFFRACTION19chain 'D' and (resid 50 through 71 )
20X-RAY DIFFRACTION20chain 'D' and (resid 72 through 94 )

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