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- PDB-32cr: SHANK3 PDZ (570-664) in complex with an internal PDZ binding moti... -

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Basic information

Entry
Database: PDB / ID: 32cr
TitleSHANK3 PDZ (570-664) in complex with an internal PDZ binding motif (843-864) in Densin-180
Components
  • Leucine-rich repeat-containing protein 7
  • SH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / Postsynaptic density PDZ domain
Function / homology
Function and homology information


response to toluene / response to interleukin-17 / regulation of AMPA glutamate receptor clustering / Neurexins and neuroligins / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / positive regulation of synapse structural plasticity / synaptic receptor adaptor activity / sensory perception of touch / postsynaptic density assembly ...response to toluene / response to interleukin-17 / regulation of AMPA glutamate receptor clustering / Neurexins and neuroligins / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / positive regulation of synapse structural plasticity / synaptic receptor adaptor activity / sensory perception of touch / postsynaptic density assembly / embryonic epithelial tube formation / vocal learning / regulation of grooming behavior / structural constituent of postsynaptic density / negative regulation of actin filament bundle assembly / neurotransmitter receptor transport, endosome to postsynaptic membrane / NMDA glutamate receptor clustering / positive regulation of long-term neuronal synaptic plasticity / RET signaling / negative regulation of cell volume / establishment or maintenance of epithelial cell apical/basal polarity / brain morphogenesis / dendritic spine morphogenesis / neuron spine / regulation of dendritic spine morphogenesis / vocalization behavior / axon initial segment / regulation of behavioral fear response / regulation of long-term synaptic potentiation / neural precursor cell proliferation / neuromuscular process controlling balance / long-term synaptic depression / locomotion / exploration behavior / RAF/MAP kinase cascade / regulation of postsynapse organization / Neutrophil degranulation / ciliary membrane / adult behavior / positive regulation of dendritic spine development / positive regulation of glutamate receptor signaling pathway / receptor clustering / AMPA glutamate receptor clustering / associative learning / locomotory exploration behavior / social behavior / Unblocking of NMDA receptors, glutamate binding and activation / glial cell proliferation / postsynaptic density, intracellular component / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / synapse assembly / ionotropic glutamate receptor binding / learning / excitatory synapse / positive regulation of excitatory postsynaptic potential / positive regulation of long-term synaptic potentiation / locomotory behavior / filopodium / adherens junction / positive regulation of neuron projection development / cell-cell adhesion / regulation of synaptic plasticity / memory / SH3 domain binding / synapse organization / postsynaptic density membrane / G protein-coupled receptor binding / modulation of chemical synaptic transmission / long-term synaptic potentiation / gene expression / MAPK cascade / actin cytoskeleton / actin binding / scaffold protein binding / dendritic spine / basolateral plasma membrane / learning or memory / neuron projection / postsynaptic density / protein kinase binding / protein-containing complex binding / glutamatergic synapse / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / PDZ domain 6 / : / PDZ domain / : / Leucine-rich repeat region / Variant SH3 domain / SAM domain (Sterile alpha motif) / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily ...: / PDZ domain 6 / : / PDZ domain / : / Leucine-rich repeat region / Variant SH3 domain / SAM domain (Sterile alpha motif) / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Sterile alpha motif/pointed domain superfamily / Leucine-rich repeat profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Leucine-rich repeat / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Leucine-rich repeat domain superfamily / Ankyrin repeat / Src homology 3 domains / Ankyrin repeat-containing domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Leucine-rich repeat-containing protein 7 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKallem, T. / Goult, B.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationSP/F/23/150045 United Kingdom
CitationJournal: Biorxiv / Year: 2026
Title: An internal PDZ-binding motif in Densin-180 promotes activity-dependent SHANK scaffold remodelling
Authors: Otani, Y. / Srinivasan, V. / Toller, J. / Kallem, T. / Ball, N. / Barsukov, I. / Saarikangas, J. / Kreienkamp, H.J. / Goult, B.T.
History
DepositionJul 5, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3
B: Leucine-rich repeat-containing protein 7
C: SH3 and multiple ankyrin repeat domains protein 3
D: Leucine-rich repeat-containing protein 7
E: SH3 and multiple ankyrin repeat domains protein 3
F: Leucine-rich repeat-containing protein 7
G: SH3 and multiple ankyrin repeat domains protein 3
H: Leucine-rich repeat-containing protein 7


Theoretical massNumber of molelcules
Total (without water)54,7468
Polymers54,7468
Non-polymers00
Water6,612367
1
A: SH3 and multiple ankyrin repeat domains protein 3
B: Leucine-rich repeat-containing protein 7
G: SH3 and multiple ankyrin repeat domains protein 3
H: Leucine-rich repeat-containing protein 7


Theoretical massNumber of molelcules
Total (without water)27,3734
Polymers27,3734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-17 kcal/mol
Surface area12220 Å2
MethodPISA
2
C: SH3 and multiple ankyrin repeat domains protein 3
D: Leucine-rich repeat-containing protein 7

E: SH3 and multiple ankyrin repeat domains protein 3
F: Leucine-rich repeat-containing protein 7


Theoretical massNumber of molelcules
Total (without water)27,3734
Polymers27,3734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3810 Å2
ΔGint-20 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.89, 71.34, 114.92
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: 10971.632 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3, Kiaa1650, Prosap2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4ACU6
#2: Protein/peptide
Leucine-rich repeat-containing protein 7 / Densin-180 / Densin / Protein LAP1


Mass: 2714.980 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P70587
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 60 mM magnesium chloride hexahydrate, 60 mM calcium chloride dihydrate, 100 mM Tris/Bicine pH 8.5, 12% v/v PEG 500 MME, 6% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.62 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 25, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 1.98→47.64 Å / Num. obs: 37309 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.201 / Net I/σ(I): 7.6
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1820 / CC1/2: 0.4 / Rrim(I) all: 1.804 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia23diidata reduction
xia23diidata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→47.639 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.239 / SU ML: 0.161 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2566 1727 4.635 %
Rwork0.201 35533 -
all0.204 --
obs-37260 99.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.889 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å20 Å2
2--1.401 Å20 Å2
3---0.149 Å2
Refinement stepCycle: LAST / Resolution: 1.98→47.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 0 367 3891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123640
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163568
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.834951
X-RAY DIFFRACTIONr_angle_other_deg0.5811.758186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.428528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62210592
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.49910155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02847
X-RAY DIFFRACTIONr_nbd_refined0.2060.2645
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23280
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21707
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.221
X-RAY DIFFRACTIONr_nbd_other0.2080.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.210
X-RAY DIFFRACTIONr_mcbond_it4.0113.8241839
X-RAY DIFFRACTIONr_mcbond_other4.013.8241840
X-RAY DIFFRACTIONr_mcangle_it5.9136.8092285
X-RAY DIFFRACTIONr_mcangle_other5.9126.812286
X-RAY DIFFRACTIONr_scbond_it4.3224.251801
X-RAY DIFFRACTIONr_scbond_other4.324.251802
X-RAY DIFFRACTIONr_scangle_it6.5437.7142655
X-RAY DIFFRACTIONr_scangle_other6.5427.7142656
X-RAY DIFFRACTIONr_lrange_it9.29139.4523952
X-RAY DIFFRACTIONr_lrange_other9.27238.5483870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.0310.3671170.3372580X-RAY DIFFRACTION99.778
2.031-2.0870.3331160.32522X-RAY DIFFRACTION99.7731
2.087-2.1470.3361080.2922461X-RAY DIFFRACTION99.8057
2.147-2.2130.3161240.2722387X-RAY DIFFRACTION99.8807
2.213-2.2860.277910.2322334X-RAY DIFFRACTION99.9588
2.286-2.3660.2931200.2342229X-RAY DIFFRACTION99.9575
2.366-2.4550.3061030.222191X-RAY DIFFRACTION99.9129
2.455-2.5550.261110.2122065X-RAY DIFFRACTION99.9541
2.555-2.6680.2651050.192004X-RAY DIFFRACTION99.9526
2.668-2.7980.2471030.1911894X-RAY DIFFRACTION99.95
2.798-2.9490.227910.1791833X-RAY DIFFRACTION100
2.949-3.1270.245850.1891739X-RAY DIFFRACTION99.9452
3.127-3.3420.267890.1981623X-RAY DIFFRACTION100
3.342-3.6080.243710.1891546X-RAY DIFFRACTION99.9382
3.608-3.950.225780.1711409X-RAY DIFFRACTION100
3.95-4.4120.206570.1591298X-RAY DIFFRACTION99.9263
4.412-5.0880.214590.1431154X-RAY DIFFRACTION100
5.088-6.2130.194360.172997X-RAY DIFFRACTION99.8068
6.213-8.7130.247400.195787X-RAY DIFFRACTION99.5187
8.713-47.6390.384230.225480X-RAY DIFFRACTION99.604

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