[English] 日本語
Yorodumi
- PDB-2w83: Crystal structure of the ARF6 GTPase in complex with a specific e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w83
TitleCrystal structure of the ARF6 GTPase in complex with a specific effector, JIP4
Components
  • ADP-RIBOSYLATION FACTOR 6
  • C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4
KeywordsPROTEIN TRANSPORT / GOLGI APPARATUS / ER-GOLGI TRANSPORT / ARF / GTPASE / EFFECTOR / MYRISTATE / CYTOPLASM / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / GTP-BINDING / PHOSPHOPROTEIN / HETEROTETRAMER / TRANSPORT / COILED-COIL / LIPOPROTEIN / COILED COIL
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / negative regulation of dendrite extension / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / negative regulation of dendrite extension / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / MAP-kinase scaffold activity / lysosome localization / JUN kinase binding / endocytic recycling / MET receptor recycling / thioesterase binding / Flemming body / retrograde transport, endosome to Golgi / filopodium membrane / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / Myogenesis / hepatocyte apoptotic process / cleavage furrow / kinesin binding / synaptic vesicle endocytosis / endocytic vesicle / regulation of presynapse assembly / negative regulation of neuron differentiation / vesicle-mediated transport / ruffle / signaling adaptor activity / striated muscle cell differentiation / positive regulation of neuron differentiation / acrosomal vesicle / liver development / small monomeric GTPase / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / cellular response to nerve growth factor stimulus / positive regulation of neuron projection development / centriolar satellite / recycling endosome membrane / GDP binding / nervous system development / signaling receptor complex adaptor activity / presynapse / Clathrin-mediated endocytosis / G protein activity / midbody / cell cortex / early endosome membrane / cell differentiation / postsynapse / positive regulation of MAPK cascade / endosome / cell adhesion / positive regulation of cell migration / lysosomal membrane / cell division / focal adhesion / GTPase activity / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
arf6 gtpase in complex with a specific effector, jip4 / JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / WD40 repeated domain / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. ...arf6 gtpase in complex with a specific effector, jip4 / JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / WD40 repeated domain / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / ADP-ribosylation factor 6 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / GUANOSINE-5'-TRIPHOSPHATE / C-Jun-amino-terminal kinase-interacting protein 4 / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsIsabet, T. / Montagnac, G. / Regazzoni, K. / Raynal, B. / El Khadali, F. / Franco, M. / England, P. / Chavrier, P. / Houdusse, A. / Menetrey, J.
CitationJournal: Embo J. / Year: 2009
Title: The Structural Basis of Arf Effector Specificity: The Crystal Structure of Arf6 in a Complex with Jip4.
Authors: Isabet, T. / Montagnac, G. / Regazzoni, K. / Raynal, B. / El Khadali, F. / England, P. / Franco, M. / Chavrier, P. / Houdusse, A. / Menetrey, J.
History
DepositionJan 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ADP-RIBOSYLATION FACTOR 6
B: ADP-RIBOSYLATION FACTOR 6
C: C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4
D: C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4
E: ADP-RIBOSYLATION FACTOR 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,99218
Polymers74,7295
Non-polymers2,26313
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-58.8 kcal/mol
Surface area35270 Å2
MethodPQS
Unit cell
Length a, b, c (Å)137.270, 137.270, 165.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

21B-2028-

HOH

31C-2003-

HOH

-
Components

-
Protein , 2 types, 5 molecules ABECD

#1: Protein ADP-RIBOSYLATION FACTOR 6 / ARF6


Mass: 18990.822 Da / Num. of mol.: 3 / Fragment: G DOMAIN, RESIDUES 13-175 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 12 RESIDUES N-TERMINAL DELETION / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62330
#2: Protein C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4 / JIP4 / JNK-INTERACTING PROTEIN 4 / JIP-4 / JLP / HLC-6 / PHET / CT89 / JNK-ASSOCIATED LEUCINE- ...JIP4 / JNK-INTERACTING PROTEIN 4 / JIP-4 / JLP / HLC-6 / PHET / CT89 / JNK-ASSOCIATED LEUCINE-ZIPPER PROTEIN / SPERM-ASSOCIATED ANTIGEN 9 / MITOGEN-ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 4 / HUMAN LUNG CANCER ONCOGENE 6 PROTEIN / PROLIFERATION-INDUCING PROTEIN 6 / SPERM-SPECIFIC PROTEIN / SPERM SURFACE PROTEIN / PROTEIN HIGHLY EXPRESSED IN TESTIS / SUNDAY DRIVER 1 / CANCER/TESTIS ANTIGEN 89


Mass: 8878.157 Da / Num. of mol.: 2 / Fragment: LEUCINE ZIPPER II, RESIDUES 392-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60271

-
Non-polymers , 5 types, 287 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 67 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLN 67 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, GLN 67 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLN 67 TO LEU ENGINEERED RESIDUE IN CHAIN E, GLN 67 TO LEU
Sequence detailsRTEV PROTEASE SITE REMAINING LINKER: RESIDUES 11-12 IN CHAINS A, B & E, AND RESIDUES 386-391 IN CHAINS C & D.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.56 % / Description: NONE
Crystal growDetails: 2.0 M AMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.2 M NACL, 2 MM MGCL2, 6 % MPD

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1271
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.93→35 Å / Num. obs: 62165 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5X

2j5x


Resolution: 1.93→118.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.811 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN B, RESIDUES 91-97 AND 129-137 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 6987 10.1 %RANDOM
Rwork0.214 ---
obs0.217 62165 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.93→118.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 141 274 5346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9976888
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73124.933225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53915898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1561531
X-RAY DIFFRACTIONr_chiral_restr0.080.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.22292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.53168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10424920
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54132234
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4624.51965
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: 1.93→1.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 497
Rwork0.26 4521

+
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