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- PDB-4amh: Influence of circular permutation on the folding pathway of a PDZ... -

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Basic information

Entry
Database: PDB / ID: 4amh
TitleInfluence of circular permutation on the folding pathway of a PDZ domain
ComponentsDISKS LARGE HOMOLOG 1
KeywordsSTRUCTURAL PROTEIN / PERMUTATION / PROTEIN FOLDING
Function / homology
Function and homology information


regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / reproductive structure development / hard palate development / establishment of centrosome localization / guanylate kinase activity ...regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / reproductive structure development / hard palate development / establishment of centrosome localization / guanylate kinase activity / negative regulation of p38MAPK cascade / membrane repolarization during ventricular cardiac muscle cell action potential / embryonic skeletal system morphogenesis / structural constituent of postsynaptic density / astral microtubule organization / NrCAM interactions / immunological synapse formation / myelin sheath abaxonal region / lateral loop / receptor localization to synapse / peristalsis / cell projection membrane / cortical microtubule organization / regulation of sodium ion transmembrane transport / smooth muscle tissue development / bicellular tight junction assembly / Synaptic adhesion-like molecules / positive regulation of potassium ion transport / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / Trafficking of AMPA receptors / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / amyloid precursor protein metabolic process / endothelial cell proliferation / lens development in camera-type eye / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of myelination / cortical actin cytoskeleton organization / receptor clustering / positive regulation of actin filament polymerization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / establishment or maintenance of cell polarity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphoprotein phosphatase activity / Long-term potentiation / intercalated disc / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / bicellular tight junction / phosphatase binding / potassium channel regulator activity / negative regulation of T cell proliferation / T cell proliferation / ionotropic glutamate receptor binding / cytoskeletal protein binding / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of membrane potential / actin filament organization / protein localization to plasma membrane / synaptic membrane / positive regulation of protein localization to plasma membrane / adherens junction / postsynaptic density membrane / neuromuscular junction / sarcolemma / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / cytoplasmic side of plasma membrane / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / regulation of cell shape / RAF/MAP kinase cascade / basolateral plasma membrane / chemical synaptic transmission / transmembrane transporter binding / microtubule / molecular adaptor activity / neuron projection / cadherin binding / membrane raft / apical plasma membrane / glutamatergic synapse / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum
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
Disks large homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHultqvist, G. / Punekar, A.S. / Chi, C.N. / Selmer, M. / Gianni, S. / Jemth, P.
CitationJournal: Plos One / Year: 2012
Title: Tolerance of Protein Folding to a Circular Permutation in a Pdz Domain
Authors: Hultqvist, G. / Punekar, A.S. / Morrone, A. / Chi, C.N. / Engstrom, A. / Selmer, M. / Gianni, S. / Jemth, P.
History
DepositionMar 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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

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Assembly

Deposited unit
A: DISKS LARGE HOMOLOG 1
B: DISKS LARGE HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9604
Polymers22,7462
Non-polymers2142
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.900, 43.600, 51.700
Angle α, β, γ (deg.)90.00, 103.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0782, 0.4286, 0.9001), (-0.3532, -0.8324, 0.4271), (0.9323, -0.3513, 0.0863)
Vector: 2.6566, 32.3349, 16.5132)

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Components

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


Mass: 11373.049 Da / Num. of mol.: 2 / Fragment: PDZ2 DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-CPSAP97-PDZ2-I342W-C378A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q12959
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 342 TO TRP ENGINEERED RESIDUE IN CHAIN A, CYS 378 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ILE 342 TO TRP ENGINEERED RESIDUE IN CHAIN A, CYS 378 TO ALA ENGINEERED RESIDUE IN CHAIN B, ILE 342 TO TRP ENGINEERED RESIDUE IN CHAIN B, CYS 378 TO ALA
Sequence detailsTHIS IS A ENGINEERED CHIMERIC PROTEIN. THE AUTHORS HAVE USED RECOMBINANT TECHNIQUE (CIRCULAR ...THIS IS A ENGINEERED CHIMERIC PROTEIN. THE AUTHORS HAVE USED RECOMBINANT TECHNIQUE (CIRCULAR PERMUTATION) TO INTRODUCED NEW N AND C TERMINI IN THE PDZ2 DOMAIN OF SAP97 PROTEIN. THE EXPRESSION TAG INCLUDES A THROMBIN CLEAVAGE SITE.

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROP VAPOR DIFFUSION, 0.1 M MES PH 6.0, 2.4 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 3, 2011 / Details: PT COATED MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→41.3 Å / Num. obs: 10415 / % possible obs: 99.4 % / Observed criterion σ(I): 2.1 / Redundancy: 3.71 % / Biso Wilson estimate: 32.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X7Z

2x7z


Resolution: 2.3→41.324 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 521 5 %
Rwork0.2196 --
obs0.222 10415 99.46 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.817 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 40.37 Å2
Baniso -1Baniso -2Baniso -3
1--10.1541 Å20 Å2-6.0282 Å2
2--23.746 Å20 Å2
3----13.592 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 14 53 1453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081418
X-RAY DIFFRACTIONf_angle_d1.2641905
X-RAY DIFFRACTIONf_dihedral_angle_d15.658519
X-RAY DIFFRACTIONf_chiral_restr0.076217
X-RAY DIFFRACTIONf_plane_restr0.004240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.53160.41511270.28982436X-RAY DIFFRACTION99
2.5316-2.89780.30481300.26412461X-RAY DIFFRACTION100
2.8978-3.65060.31061290.22942465X-RAY DIFFRACTION100
3.6506-41.33070.19261330.18252529X-RAY DIFFRACTION99

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