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- PDB-3qjn: Structural flexibility of Shank PDZ domain is important for its b... -

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Basic information

Entry
Database: PDB / ID: 3qjn
TitleStructural flexibility of Shank PDZ domain is important for its binding to different ligands
Components
  • Beta-PIX
  • SH3 and multiple ankyrin repeat domains protein 1
KeywordsPROTEIN BINDING / PDZ domain / Protein-protein interaction / Beta-PIX
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / somatostatin receptor binding / determination of affect / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events ...presynaptic actin cytoskeleton organization / somatostatin receptor binding / determination of affect / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / synaptic receptor adaptor activity / RHOA GTPase cycle / olfactory behavior / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / structural constituent of postsynaptic density / righting reflex / postsynaptic actin cytoskeleton organization / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / gamma-tubulin binding / positive regulation of dendritic spine development / lamellipodium assembly / adult behavior / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / social behavior / positive regulation of excitatory postsynaptic potential / associative learning / neuromuscular process controlling balance / Rho protein signal transduction / excitatory synapse / GABA-ergic synapse / long-term memory / hematopoietic progenitor cell differentiation / ruffle / ionotropic glutamate receptor binding / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / SH3 domain binding / signaling receptor complex adaptor activity / lamellipodium / cell cortex / growth cone / postsynaptic membrane / postsynapse / scaffold protein binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / protein-containing complex / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PDZ domain 6 / PDZ domain / Variant SH3 domain ...Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7 / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsLee, J.H. / Park, H. / Park, S.J. / Kim, H.J. / Eom, S.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands
Authors: Lee, J.H. / Park, H. / Park, S.J. / Kim, H.J. / Eom, S.H.
History
DepositionJan 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Derived calculations
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 1
B: SH3 and multiple ankyrin repeat domains protein 1
C: SH3 and multiple ankyrin repeat domains protein 1
D: SH3 and multiple ankyrin repeat domains protein 1
E: SH3 and multiple ankyrin repeat domains protein 1
F: SH3 and multiple ankyrin repeat domains protein 1
G: SH3 and multiple ankyrin repeat domains protein 1
H: SH3 and multiple ankyrin repeat domains protein 1
I: Beta-PIX
J: Beta-PIX
K: Beta-PIX
L: Beta-PIX
M: Beta-PIX
N: Beta-PIX
O: Beta-PIX
P: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)108,82916
Polymers108,82916
Non-polymers00
Water2,324129
1
A: SH3 and multiple ankyrin repeat domains protein 1
I: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3 and multiple ankyrin repeat domains protein 1
J: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SH3 and multiple ankyrin repeat domains protein 1
K: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SH3 and multiple ankyrin repeat domains protein 1
L: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: SH3 and multiple ankyrin repeat domains protein 1
M: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: SH3 and multiple ankyrin repeat domains protein 1
N: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: SH3 and multiple ankyrin repeat domains protein 1
O: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: SH3 and multiple ankyrin repeat domains protein 1
P: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,6042
Polymers13,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.373, 95.155, 108.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SH3 and multiple ankyrin repeat domains protein 1 / Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Somatostatin receptor-interacting protein / ...Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Somatostatin receptor-interacting protein / SSTR-interacting protein / SSTRIP / Synamon


Mass: 12755.696 Da / Num. of mol.: 8 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WV48
#2: Protein/peptide
Beta-PIX


Mass: 847.869 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: O55043*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 12% ethanol, 10% ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 24385 / Num. obs: 24385 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 71.03 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
BUSTER2.9.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→21.3 Å / Cor.coef. Fo:Fc: 0.8992 / Cor.coef. Fo:Fc free: 0.8467 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 1230 5.06 %RANDOM
Rwork0.214 ---
obs0.2169 24304 --
Displacement parametersBiso max: 158.44 Å2 / Biso mean: 69.24 Å2 / Biso min: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1-18.3554 Å20 Å20 Å2
2---18.6936 Å20 Å2
3---0.3383 Å2
Refine analyzeLuzzati coordinate error obs: 0.379 Å
Refinement stepCycle: LAST / Resolution: 2.71→21.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 0 129 6545
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2320SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes920HARMONIC5
X-RAY DIFFRACTIONt_it6496HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion824SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7024SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6496HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8736HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion22.04
LS refinement shellResolution: 2.71→2.83 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3306 149 5.34 %
Rwork0.2282 2642 -
all0.2337 2791 -
Refinement TLS params.Method: refined / Origin x: 35.8438 Å / Origin y: 94.4871 Å / Origin z: 93.7995 Å
111213212223313233
T0.1062 Å2-0.0136 Å2-0.0026 Å2--0.027 Å20.0083 Å2---0.0801 Å2
L4.762 °2-0.7575 °20.081 °2-2.845 °20.5484 °2--0.6084 °2
S0.0152 Å °0.0524 Å °0.2022 Å °-0.2265 Å °0.0073 Å °-0.0199 Å °0.0108 Å °-0.0047 Å °-0.0226 Å °
Refinement TLS groupSelection details: { A|656 - A|757 }

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