[English] 日本語
Yorodumi
- PDB-2p4r: Structural basis for a novel interaction between AIP4 and beta-PIX -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of microtubule nucleation / regulation of protein deubiquitination / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle ...negative regulation of microtubule nucleation / regulation of protein deubiquitination / presynaptic actin cytoskeleton organization / Ephrin signaling / NRAGE signals death through JNK / EGFR downregulation / RHOU GTPase cycle / RHOV GTPase cycle / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / postsynaptic actin cytoskeleton organization / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / RHOA GTPase cycle / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of growth hormone secretion / storage vacuole / protein K29-linked ubiquitination / astrocyte cell migration / T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process / positive regulation of T cell anergy / protein branched polyubiquitination / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / HECT-type E3 ubiquitin transferase / negative regulation of JNK cascade / arrestin family protein binding / gamma-tubulin binding / regulation of hematopoietic stem cell differentiation / lamellipodium assembly / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / positive regulation of receptor catabolic process / small GTPase-mediated signal transduction / mitotic spindle pole / ligase activity / Golgi organization / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / protein monoubiquitination / Rho protein signal transduction / hematopoietic progenitor cell differentiation / ribonucleoprotein complex binding / protein K48-linked ubiquitination / protein autoubiquitination / ruffle / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / guanyl-nucleotide exchange factor activity / GABA-ergic synapse / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / receptor internalization / Regulation of necroptotic cell death / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / 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 / growth cone / cell cortex / ubiquitin-dependent protein catabolic process / early endosome membrane / cytoplasmic vesicle / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / neuron projection / protein ubiquitination / positive regulation of apoptotic process / inflammatory response / symbiont entry into host cell / innate immune response / focal adhesion / neuronal cell body / intracellular membrane-bounded organelle / apoptotic process / centrosome / 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 ...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. / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more