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- PDB-2x7z: Crystal Structure of the SAP97 PDZ2 I342W C378A mutant protein domain -

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Basic information

Entry
Database: PDB / ID: 2x7z
TitleCrystal Structure of the SAP97 PDZ2 I342W C378A mutant protein domain
ComponentsDISKS LARGE HOMOLOG 1
KeywordsSTRUCTURAL PROTEIN / SH3 DOMAIN / PHOSPHOPROTEIN / SYNAPTIC PROTEIN / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / myelin sheath abaxonal region / GMP kinase activity / structural constituent of postsynaptic density ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / membrane raft organization / establishment of centrosome localization / myelin sheath abaxonal region / GMP kinase activity / structural constituent of postsynaptic density / NrCAM interactions / embryonic skeletal system morphogenesis / astral microtubule organization / reproductive structure development / immunological synapse formation / membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of p38MAPK cascade / peristalsis / receptor localization to synapse / lateral loop / smooth muscle tissue development / cell projection membrane / bicellular tight junction assembly / cortical microtubule organization / regulation of sodium ion transmembrane transport / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of potassium ion transport / regulation of ventricular cardiac muscle cell action potential / Trafficking of AMPA receptors / hard palate development / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / lens development in camera-type eye / cortical actin cytoskeleton organization / regulation of myelination / Activation of Ca-permeable Kainate Receptor / branching involved in ureteric bud morphogenesis / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / basement membrane / Long-term potentiation / intercalated disc / lateral plasma membrane / immunological synapse / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / regulation of postsynaptic membrane neurotransmitter receptor levels / cytoskeletal protein binding / negative regulation of T cell proliferation / actin filament polymerization / ionotropic glutamate receptor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / actin filament organization / synaptic membrane / protein localization to plasma membrane / regulation of membrane potential / positive regulation of protein localization to plasma membrane / adherens junction / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell-cell adhesion / sarcolemma / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / kinase binding / cytoplasmic side of plasma membrane / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / nervous system development / regulation of cell shape / RAF/MAP kinase cascade / basolateral plasma membrane / molecular adaptor activity / chemical synaptic transmission / microtubule / transmembrane transporter binding / neuron projection / apical plasma membrane / cadherin binding / membrane raft / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / AMMONIUM ION / Disks large homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHaq, S.R. / Jurgens, M.C. / Chi, C.N. / Elfstrom, L. / Koh, C.S. / Selmer, M. / Gianni, S. / Jemth, P.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Plastic Energy Landscape of Protein Folding: A Triangular Folding Mechanism with an Equilibrium Intermediate for a Small Protein Domain.
Authors: Haq, S.R. / Jurgens, M.C. / Chi, C.N. / Elfstrom, L. / Koh, C.S. / Selmer, M. / Gianni, S. / Jemth, P.
History
DepositionMar 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DISKS LARGE HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5713
Polymers10,4841
Non-polymers872
Water1,47782
1
A: DISKS LARGE HOMOLOG 1
hetero molecules

A: DISKS LARGE HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1426
Polymers20,9682
Non-polymers1744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2180 Å2
ΔGint2 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.905, 47.905, 123.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein DISKS LARGE HOMOLOG 1 / SYNAPSE-ASSOCIATED PROTEIN 97 / SAP97 / SAP-97 / HDLG


Mass: 10484.023 Da / Num. of mol.: 1 / Fragment: PDZ2 DOMAIN, RESIDUES 260-356 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-SAP97-PDZ2-I342W-C378A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q12959
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.37 Å3/Da / Density % sol: 63.5 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 8.4
Details: VAPOR DIFFUSION, 100MM TRIS-HCL PH 8.4, 2.4M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jan 21, 2009 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2→29.9 Å / Num. obs: 10153 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 15.4 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AWU

2awu


Resolution: 2→29.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.174 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23236 516 5 %RANDOM
Rwork0.19381 ---
obs0.19576 9801 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 6 82 826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9821017
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.556598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52826.92326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15415138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1320.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021547
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0441.5487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7642781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9993268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0564.5236
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 36 -
Rwork0.212 686 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 10.8916 Å / Origin y: -4.2617 Å / Origin z: 10.8723 Å
111213212223313233
T0.0267 Å20.0149 Å2-0.003 Å2-0.0782 Å20.0209 Å2--0.0717 Å2
L4.3035 °2-0.5061 °2-0.8472 °2-1.3123 °20.6062 °2--4.6422 °2
S-0.0756 Å °-0.0212 Å °-0.0649 Å °0.0685 Å °0.0399 Å °-0.2384 Å °0.2071 Å °0.534 Å °0.0357 Å °

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