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- PDB-6kyh: Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas -

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Basic information

Entry
Database: PDB / ID: 6kyh
TitleCrystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas
Components
  • GTPase HRas
  • SH3 and multiple ankyrin repeat domains protein 3
KeywordsSTRUCTURAL PROTEIN/SIGNALING PROTEIN / Shank3 / GTPase / synaptic scaffold protein / STRUCTURAL PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Activation of RAS in B cells / Estrogen-stimulated signaling through PRKCZ / GTPase complex / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 ...Activation of RAS in B cells / Estrogen-stimulated signaling through PRKCZ / GTPase complex / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / response to interleukin-17 / regulation of AMPA glutamate receptor clustering / Tie2 Signaling / embryonic epithelial tube formation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / VEGFR2 mediated cell proliferation / MET activates RAS signaling / FLT3 Signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / NCAM signaling for neurite out-growth / Neurexins and neuroligins / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / positive regulation of synapse structural plasticity / Downstream signal transduction / synaptic receptor adaptor activity / FCERI mediated MAPK activation / fibroblast proliferation / Signaling by SCF-KIT / postsynaptic density assembly / sensory perception of touch / RAF activation / Negative regulation of MAPK pathway / EPHB-mediated forward signaling / oncogene-induced cell senescence / Regulation of RAS by GAPs / MAP2K and MAPK activation / vocal learning / regulation of grooming behavior / RAS processing / structural constituent of postsynaptic density / glial cell proliferation / negative regulation of actin filament bundle assembly / RAF/MAP kinase cascade / p38MAPK events / brain morphogenesis / NMDA glutamate receptor clustering / positive regulation of long-term neuronal synaptic plasticity / CD209 (DC-SIGN) signaling / RET signaling / negative regulation of cell volume / T-helper 1 type immune response / regulation of long-term synaptic potentiation / dendritic spine morphogenesis / defense response to protozoan / neuron spine / neuromuscular process controlling balance / regulation of dendritic spine morphogenesis / vocalization behavior / long-term synaptic depression / locomotion / adult behavior / regulation of behavioral fear response / neural precursor cell proliferation / DAP12 signaling / exploration behavior / positive regulation of miRNA metabolic process / regulation of postsynapse organization / positive regulation of ruffle assembly / ciliary membrane / positive regulation of wound healing / positive regulation of dendritic spine development / ERBB2-ERBB3 signaling pathway / adipose tissue development / small GTPase-mediated signal transduction / locomotory exploration behavior / positive regulation of glutamate receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / AMPA glutamate receptor clustering / social behavior / associative learning / positive regulation of protein targeting to membrane / neuron apoptotic process / Schwann cell development / regulation of long-term neuronal synaptic plasticity / postsynaptic density, intracellular component / positive regulation of Ras protein signal transduction / myelination / insulin-like growth factor receptor signaling pathway / intrinsic apoptotic signaling pathway / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / protein-membrane adaptor activity / positive regulation of epithelial cell proliferation / synapse assembly
Similarity search - Function
: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Small GTPase, Ras-type / Sterile alpha motif domain / Small GTPase Ras domain profile. ...: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Small GTPase, Ras-type / Sterile alpha motif domain / Small GTPase Ras domain profile. / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Rab subfamily of small GTPases / Src homology 3 domains / Ankyrin repeat-containing domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / SH3 and multiple ankyrin repeat domains protein 3 / GTPase HRas
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsCai, Q. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)AoE-M09-12 Hong Kong
CitationJournal: Structure / Year: 2020
Title: Shank3 Binds to and Stabilizes the Active Form of Rap1 and HRas GTPases via Its NTD-ANK Tandem with Distinct Mechanisms.
Authors: Cai, Q. / Hosokawa, T. / Zeng, M. / Hayashi, Y. / Zhang, M.
History
DepositionSep 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 3
B: SH3 and multiple ankyrin repeat domains protein 3
C: SH3 and multiple ankyrin repeat domains protein 3
D: SH3 and multiple ankyrin repeat domains protein 3
F: GTPase HRas
G: GTPase HRas
H: GTPase HRas
E: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,41516
Polymers238,2298
Non-polymers2,1868
Water00
1
A: SH3 and multiple ankyrin repeat domains protein 3
E: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1044
Polymers59,5572
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 3
F: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1044
Polymers59,5572
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SH3 and multiple ankyrin repeat domains protein 3
G: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1044
Polymers59,5572
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SH3 and multiple ankyrin repeat domains protein 3
H: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1044
Polymers59,5572
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.569, 154.464, 116.949
Angle α, β, γ (deg.)90.000, 108.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17F
27G
18F
28H
19F
29E
110G
210H
111G
211E
112H
212E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEARGARGAA7 - 3556 - 354
21PHEPHEARGARGBB7 - 3556 - 354
12PHEPHEARGARGAA7 - 3556 - 354
22PHEPHEARGARGCC7 - 3556 - 354
13PHEPHEARGARGAA7 - 3556 - 354
23PHEPHEARGARGDD7 - 3556 - 354
14PHEPHEARGARGBB7 - 3556 - 354
24PHEPHEARGARGCC7 - 3556 - 354
15PHEPHEARGARGBB7 - 3556 - 354
25PHEPHEARGARGDD7 - 3556 - 354
16PHEPHEARGARGCC7 - 3556 - 354
26PHEPHEARGARGDD7 - 3556 - 354
17METMETGLNGLNFE1 - 1655 - 169
27METMETGLNGLNGF1 - 1655 - 169
18METMETGLNGLNFE1 - 1655 - 169
28METMETGLNGLNHG1 - 1655 - 169
19METMETGLNGLNFE1 - 1655 - 169
29METMETGLNGLNEH1 - 1655 - 169
110METMETHISHISGF1 - 1665 - 170
210METMETHISHISHG1 - 1665 - 170
111METMETHISHISGF1 - 1665 - 170
211METMETHISHISEH1 - 1665 - 170
112METMETHISHISHG1 - 1665 - 170
212METMETHISHISEH1 - 1665 - 170

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2 / SPANK-2


Mass: 40254.496 Da / Num. of mol.: 4 / Fragment: NTD-ANK tandem / Mutation: A42K,L231R,F304Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3, Kiaa1650, Prosap2 / Plasmid: pET32M3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4ACU6
#2: Protein
GTPase HRas / H-Ras-1 / Transforming protein p21 / c-H-ras / p21ras


Mass: 19302.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hras, Hras1 / Plasmid: pETM3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q61411
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: 2.9 Å3/Da / Density % sol: 57.62 % / Mosaicity: 1.279 ° / Mosaicity esd: 0.026 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.1M bicine (pH8.5), 3% Dextran sulfate sodium salt, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.91904 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91904 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 40509 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.147 / Rrim(I) all: 0.276 / Χ2: 0.492 / Net I/σ(I): 2.2 / Num. measured all: 137645
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.363.20.73720060.5460.4830.8840.41798.9
3.36-3.4230.66920250.5070.4620.8160.42699.2
3.42-3.4830.5720200.6420.3850.6910.44898.6
3.48-3.553.40.56320000.6930.3560.6680.4499.9
3.55-3.633.60.50820280.7760.3110.5970.4399.5
3.63-3.723.60.39720170.8390.2440.4670.44899.7
3.72-3.813.60.38220150.8430.2340.4490.44699.7
3.81-3.913.60.32220190.8930.1970.3780.48399.3
3.91-4.033.60.2720480.9190.1660.3180.47899.8
4.03-4.163.50.23920220.9270.1480.2820.47399.6
4.16-4.313.50.2120110.9490.1310.2480.48399.2
4.31-4.483.50.17920320.9610.1110.2110.50499.5
4.48-4.683.40.16719920.9680.1050.1980.49699
4.68-4.933.20.16220210.9620.1060.1950.51498.7
4.93-5.2430.16520060.9590.1140.2020.50398.8
5.24-5.643.60.18520420.9610.1140.2180.47299.8
5.64-6.213.60.1720630.9710.1050.20.48599.8
6.21-7.13.50.14720250.970.0910.1730.49499.8
7.1-8.943.30.08720590.990.0550.1030.58899
8.94-503.20.06520580.9920.0430.0780.83598.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4X, 6AMB

5g4x

6amb


Resolution: 3.3→46.75 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.2323 / WRfactor Rwork: 0.2029 / FOM work R set: 0.7542 / SU B: 36.853 / SU ML: 0.562 / SU Rfree: 0.5648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1980 4.9 %RANDOM
Rwork0.2269 ---
obs0.2283 38498 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.19 Å2 / Biso mean: 53.413 Å2 / Biso min: 21.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-0 Å2-0.89 Å2
2---0.88 Å2-0 Å2
3---2.87 Å2
Refinement stepCycle: final / Resolution: 3.3→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16297 0 132 0 16429
Biso mean--67.87 --
Num. residues----2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316749
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715253
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.64922707
X-RAY DIFFRACTIONr_angle_other_deg1.5371.58235347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.92552053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35222.033984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.59152828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.81315136
X-RAY DIFFRACTIONr_chiral_restr0.0790.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218943
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023569
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A106300.13
12B106300.13
21A105450.14
22C105450.14
31A105210.14
32D105210.14
41B105350.14
42C105350.14
51B105120.14
52D105120.14
61C106730.13
62D106730.13
71F48070.17
72G48070.17
81F47400.18
82H47400.18
91F48780.15
92E48780.15
101G49030.17
102H49030.17
111G48610.17
112E48610.17
121H48120.18
122E48120.18
LS refinement shellResolution: 3.3→3.382 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.333 150 -
Rwork0.32 2604 -
obs--90.68 %

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