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- PDB-6kyk: Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 -

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Basic information

Entry
Database: PDB / ID: 6kyk
TitleCrystal structure of Shank3 NTD-ANK mutant in complex with Rap1
Components
  • Ras-related protein Rap-1b
  • 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


response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / Rap protein signal transduction / postsynaptic density assembly / embryonic epithelial tube formation / positive regulation of synapse structural plasticity ...response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / Rap protein signal transduction / postsynaptic density assembly / embryonic epithelial tube formation / positive regulation of synapse structural plasticity / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / regulation of cell junction assembly / regulation of grooming behavior / positive regulation of long-term neuronal synaptic plasticity / modification of postsynaptic structure / NMDA glutamate receptor clustering / vocalization behavior / negative regulation of calcium ion-dependent exocytosis / negative regulation of cell volume / positive regulation of integrin activation / calcium-ion regulated exocytosis / negative regulation of synaptic vesicle exocytosis / RET signaling / positive regulation of glutamate receptor signaling pathway / regulation of behavioral fear response / neuron spine / AMPA glutamate receptor clustering / regulation of dendritic spine morphogenesis / dendritic spine morphogenesis / Rap1 signalling / locomotion / brain morphogenesis / establishment of endothelial barrier / regulation of long-term synaptic potentiation / MET activates RAP1 and RAC1 / neural precursor cell proliferation / long-term synaptic depression / exploration behavior / regulation of establishment of cell polarity / azurophil granule membrane / ciliary membrane / positive regulation of dendritic spine development / regulation of long-term synaptic depression / p130Cas linkage to MAPK signaling for integrins / social behavior / locomotory exploration behavior / associative learning / GRB2:SOS provides linkage to MAPK signaling for Integrins / neuromuscular process controlling balance / positive regulation of excitatory postsynaptic potential / excitatory synapse / glial cell proliferation / synapse assembly / ionotropic glutamate receptor binding / cellular response to cAMP / lipid droplet / Integrin signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of synaptic transmission, glutamatergic / small monomeric GTPase / learning / positive regulation of long-term synaptic potentiation / establishment of localization in cell / locomotory behavior / long-term synaptic potentiation / modulation of chemical synaptic transmission / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of synaptic plasticity / SH3 domain binding / memory / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / GDP binding / Signaling by BRAF and RAF1 fusions / cell-cell junction / G protein activity / actin binding / scaffold protein binding / gene expression / dendritic spine / positive regulation of ERK1 and ERK2 cascade / cell population proliferation / learning or memory / postsynaptic density / neuron projection / GTPase activity / Neutrophil degranulation / protein-containing complex binding / GTP binding / glutamatergic synapse / 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 / SAM domain profile. / small GTPase Ras family profile. / Sterile alpha motif. ...Ras-related protein Rap1 / : / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Small GTPase, Ras-type / SAM domain profile. / small GTPase Ras family profile. / Sterile alpha motif. / Sterile alpha motif domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Domain present in PSD-95, Dlg, and ZO-1/2. / Ras subfamily of RAS small GTPases / PDZ domain / Small GTPase / Ras family / PDZ superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Rab subfamily of small GTPases / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rap-1b / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 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 19, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Ras-related protein Rap-1b
D: Ras-related protein Rap-1b
E: Ras-related protein Rap-1b
F: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,22714
Polymers160,0416
Non-polymers2,1868
Water1,31573
1
A: SH3 and multiple ankyrin repeat domains protein 3
C: Ras-related protein Rap-1b
D: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1137
Polymers80,0203
Non-polymers1,0934
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 3
E: Ras-related protein Rap-1b
F: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1137
Polymers80,0203
Non-polymers1,0934
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.032, 54.107, 203.110
Angle α, β, γ (deg.)90.000, 109.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23E
14C
24F
15D
25E
16D
26F
17E
27F

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
11ALAALAPROPROAA6 - 36112 - 367
21ALAALAPROPROBB6 - 36112 - 367
12HISHISASNASNCC0 - 1663 - 169
22HISHISASNASNDD0 - 1663 - 169
13PROPROARGARGCC-1 - 1672 - 170
23PROPROARGARGEE-1 - 1672 - 170
14HISHISASNASNCC0 - 1663 - 169
24HISHISASNASNFF0 - 1663 - 169
15HISHISASNASNDD0 - 1663 - 169
25HISHISASNASNEE0 - 1663 - 169
16HISHISARGARGDD0 - 1673 - 170
26HISHISARGARGFF0 - 1673 - 170
17HISHISASNASNEE0 - 1663 - 169
27HISHISASNASNFF0 - 1663 - 169

NCS ensembles :
ID
1
2
3
4
5
6
7

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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: 41394.734 Da / Num. of mol.: 2 / Fragment: NTD-ANK tandem / Mutation: L231R,F304Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3, Kiaa1650, Prosap2 / Plasmid: pETM3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4ACU6
#2: Protein
Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 19312.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Plasmid: pSKB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61224
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.56 % / Mosaicity: 0.711 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.1M bicine (pH8.5), 1% Dextran sulfate sodium salt, 5% PEG 20000, 10% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 40063 / % possible obs: 94 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.065 / Rrim(I) all: 0.164 / Χ2: 0.726 / Net I/σ(I): 4.2 / Num. measured all: 242504
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.81-2.865.60.94818120.7570.4211.0420.43585.4
2.86-2.9160.93719210.7470.4021.0230.4291.9
2.91-2.976.40.7820000.8670.3230.8460.44294.2
2.97-3.036.40.66520210.8830.2750.7210.46196.7
3.03-3.096.30.52320660.9290.2160.5670.48597.5
3.09-3.166.30.49720740.9310.2060.5390.48296.8
3.16-3.246.30.39820310.9510.1680.4330.54598.6
3.24-3.336.30.3320920.9680.1380.3580.55698.3
3.33-3.436.20.28720680.9760.1210.3120.59797.9
3.43-3.546.20.26820780.9740.1140.2920.59898
3.54-3.674.60.23315550.9380.1130.2611.46173.5
3.67-3.815.40.19718540.9820.0880.2160.787.2
3.81-3.995.20.15219750.9830.070.1680.84794.1
3.99-4.25.60.11918910.9910.0530.1310.96787.7
4.2-4.466.10.10620520.9930.0460.1160.99495.2
4.46-4.86.30.09720790.9950.0420.1061.00697.9
4.8-5.296.50.09621090.9950.0410.1040.96998.3
5.29-6.056.60.09421200.9950.040.1020.9398.7
6.05-7.626.20.0821220.9940.0350.0871.11197.4
7.62-5060.06521430.9950.0290.0710.81494.7

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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, 4DXA

5g4x

4dxa


Resolution: 2.82→49 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.2772 / WRfactor Rwork: 0.2142 / FOM work R set: 0.6654 / SU B: 27.926 / SU ML: 0.489 / SU Rfree: 0.4776 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 1976 4.9 %RANDOM
Rwork0.2403 ---
obs0.2433 38087 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 191.43 Å2 / Biso mean: 66.375 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å2-0 Å2-1.72 Å2
2--8.87 Å20 Å2
3----3.87 Å2
Refinement stepCycle: final / Resolution: 2.82→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10982 0 132 73 11187
Biso mean--67.09 42.95 -
Num. residues----1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311338
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710338
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.64715364
X-RAY DIFFRACTIONr_angle_other_deg1.2011.58223982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69851388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90922.598662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.416151958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2041586
X-RAY DIFFRACTIONr_chiral_restr0.0560.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022370
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109940.11
12B109940.11
21C50940.12
22D50940.12
31C52200.11
32E52200.11
41C50730.13
42F50730.13
51D49600.14
52E49600.14
61D51930.11
62F51930.11
71E49300.15
72F49300.15
LS refinement shellResolution: 2.821→2.895 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 128 -
Rwork0.392 2341 -
all-2469 -
obs--78.31 %

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