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- PDB-2p4r: Structural basis for a novel interaction between AIP4 and beta-PIX -

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Basic information

Entry
Database: PDB / ID: 2p4r
TitleStructural basis for a novel interaction between AIP4 and beta-PIX
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • Rho guanine nucleotide exchange factor 7
KeywordsLIGASE / SH3 domain peptide ligand complex
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / regulation of protein deubiquitination / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / regulation of protein deubiquitination / 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 / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / RHOA GTPase cycle / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / : / T cell anergy / positive regulation of T cell anergy / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / CXCR chemokine receptor binding / HECT-type E3 ubiquitin transferase / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / gamma-tubulin binding / arrestin family protein binding / regulation of hematopoietic stem cell differentiation / lamellipodium assembly / negative regulation of type I interferon production / small GTPase-mediated signal transduction / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / mitotic spindle pole / Golgi organization / protein monoubiquitination / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / ligase activity / Rho protein signal transduction / GABA-ergic synapse / protein K48-linked ubiquitination / protein autoubiquitination / ribonucleoprotein complex binding / hematopoietic progenitor cell differentiation / ruffle / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / guanyl-nucleotide exchange factor activity / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / receptor internalization / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cell cortex / growth cone / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / early endosome membrane / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / neuron projection / inflammatory response / symbiont entry into host cell / positive regulation of apoptotic process / focal adhesion / innate immune response / intracellular membrane-bounded organelle / centrosome / neuronal cell body / apoptotic process / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / 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 / E3 ubiquitin-protein ligase, SMURF1 type / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / HECT domain / HECT, E3 ligase catalytic 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 / E3 ubiquitin-protein ligase, SMURF1 type / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Variant SH3 domain / 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / C2 domain / WW/rsp5/WWP domain profile. / C2 domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / SH3 Domains / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3 type barrels. / 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 / E3 ubiquitin-protein ligase Itchy homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsMin, K.C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A novel interaction between atrophin-interacting protein 4 and beta-p21-activated kinase-interactive exchange factor is mediated by an SH3 domain.
Authors: Janz, J.M. / Sakmar, T.P. / Min, K.C.
History
DepositionMar 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Rho guanine nucleotide exchange factor 7
T: E3 ubiquitin-protein ligase Itchy homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6184
Polymers9,4292
Non-polymers1882
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-18 kcal/mol
Surface area4740 Å2
MethodPISA
2
A: Rho guanine nucleotide exchange factor 7
T: E3 ubiquitin-protein ligase Itchy homolog
hetero molecules

A: Rho guanine nucleotide exchange factor 7
T: E3 ubiquitin-protein ligase Itchy homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2358
Polymers18,8594
Non-polymers3764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4190 Å2
ΔGint-39 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.747, 41.747, 149.278
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-99-

HOH

21A-131-

HOH

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix


Mass: 6731.333 Da / Num. of mol.: 1 / Fragment: Beta-PIX SH3 (10-63)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef7 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O55043
#2: Protein/peptide E3 ubiquitin-protein ligase Itchy homolog / Itch / Atrophin-1-interacting protein 4 / AIP4 / NFE2-associated polypeptide 1 / NAPP1


Mass: 2698.135 Da / Num. of mol.: 1 / Fragment: AIP4 (209-224) / Source method: obtained synthetically
Details: Chemically synthesized. Occurs naturally in humans (homo sapien).
References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.99 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 11, 2006 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→36.15 Å / Num. all: 5612 / Num. obs: 5610 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.083 / Net I/σ(I): 36.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 17.2 / Num. unique all: 519 / Rsym value: 18.7 / % possible all: 94.2

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2AK5
Resolution: 2.001→20.87 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.217 / SU B: 4.08 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 254 4.5 %RANDOM
Rwork0.217 ---
all0.218 5610 --
obs-5603 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.481 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.001→20.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 0 11 69 654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022622
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.938849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.978573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9322.25831
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3911589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.761157
X-RAY DIFFRACTIONr_chiral_restr0.070.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02497
X-RAY DIFFRACTIONr_nbd_refined0.1730.2255
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2408
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.218
X-RAY DIFFRACTIONr_mcbond_it0.5051.5380
X-RAY DIFFRACTIONr_mcangle_it0.8532607
X-RAY DIFFRACTIONr_scbond_it1.0983281
X-RAY DIFFRACTIONr_scangle_it1.8974.5242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.001-2.0520.269120.22236039410394.416
2.052-2.1080.377150.22836740113595.262
2.108-2.1690.195240.21634138116695.801
2.169-2.2350.209110.20234437019195.946
2.235-2.3070.268170.21734537621096.277
2.307-2.3870.309160.22632034722496.83
2.387-2.4760.379120.22732835123996.866
2.476-2.5750.177130.22430332624696.933
2.575-2.6880.208110.2230232026397.812
2.688-2.8170.223110.22729431426897.134
2.817-2.9660.225210.20126829429498.299
2.966-3.1420.226190.21526328630298.601
3.142-3.3540.154130.19124626230398.855
3.354-3.6150.221120.18823925532898.431
3.615-3.9480.69290.176224233320100
3.948-4.3940.10680.19121021934599.543
4.394-5.0370.28880.2119120034499.5
5.037-6.0810.466100.23916617734199.435
6.081-8.2570.16470.25613514336799.301
8.257-20.8740.23750.46110311036098.182

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