[English] 日本語
Yorodumi
- PDB-3lvq: The crystal structure of ASAP3 in complex with Arf6 in transition... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lvq
TitleThe crystal structure of ASAP3 in complex with Arf6 in transition state
ComponentsArf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6
KeywordsPROTEIN TRANSPORT / Arf / GAP / GDP / ASAP3 / UPLC1 / Arf6 / ArfGAP / Linkers / Alternative splicing / ANK repeat / Coiled coil / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Zinc / Zinc-finger / Cell membrane / Endosome / ER-Golgi transport / Golgi apparatus / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Transport
Function / homology
Function and homology information


erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of protein localization to cell surface / protein localization to endosome / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of protein localization to cell surface / protein localization to endosome / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / MET receptor recycling / endocytic recycling / regulation of stress fiber assembly / thioesterase binding / Flemming body / TBC/RABGAPs / filopodium membrane / protein localization to cell surface / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / endocytic vesicle / synaptic vesicle endocytosis / regulation of presynapse assembly / signaling adaptor activity / vesicle-mediated transport / ruffle / GTPase activator activity / liver development / positive regulation of GTPase activity / cellular response to nerve growth factor stimulus / small monomeric GTPase / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / G protein activity / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / cell migration / Clathrin-mediated endocytosis / presynapse / nervous system development / cell cortex / early endosome membrane / midbody / postsynapse / cell differentiation / cell adhesion / endosome / cell division / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #950 / Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / ADP-ribosylation factor 6 / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #950 / Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / ADP-ribosylation factor 6 / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / BAR domain / Small GTPase superfamily, ARF type / Annexin V; domain 1 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / AH/BAR domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Ankyrin repeat-containing domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Rab subfamily of small GTPases / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 6 / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsIsmail, S.A. / Vetter, I.R. / Sot, B. / Wittinghofer, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism
Authors: Ismail, S.A. / Vetter, I.R. / Sot, B. / Wittinghofer, A.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 5, 2018Group: Advisory / Data collection / Structure summary
Category: pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id
Revision 1.5Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4676
Polymers54,8261
Non-polymers6415
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.290, 146.290, 49.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

-
Protein , 1 types, 1 molecules E

#1: Protein Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6 / ASAP3 / Development and differentiation-enhancing factor-like 1 / Protein up-regulated in liver ...ASAP3 / Development and differentiation-enhancing factor-like 1 / Protein up-regulated in liver cancer 1 / Arf6 / UPLC1


Mass: 54825.930 Da / Num. of mol.: 1
Fragment: GAP and Ankyrin domain, residues 416-697, residues 11-175
Source method: isolated from a genetically manipulated source
Details: Missing the N-terminus amphipathic helix for Arf6
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ASAP3, ARF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDY4, UniProt: P62330

-
Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsNLSSDSSLSSPSALNSLSSPSALNSTASNSPGIEGLS IS A FLEXIBLE LINKER REGION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.38→29.42 Å / Num. obs: 8700 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.25 % / Rmerge(I) obs: 0.066 / Rsym value: 0.079 / Net I/σ(I): 22.52 / Num. measured all: 80498
Reflection shellResolution: 3.38→3.5 Å / Redundancy: 9.45 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 4.94 / Num. unique all: 847 / Rsym value: 0.55 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2B0o and 2J5X

2b0o

2j5x


Resolution: 3.38→29.42 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 58.227 / SU ML: 0.482 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 435 5 %RANDOM
Rwork0.21881 ---
all0.2207 ---
obs0.2207 8263 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 136.436 Å2
Baniso -1Baniso -2Baniso -3
1--5.06 Å2-2.53 Å20 Å2
2---5.06 Å20 Å2
3---7.59 Å2
Refinement stepCycle: LAST / Resolution: 3.38→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 35 5 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223354
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9774550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68124.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64115575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4721525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022517
X-RAY DIFFRACTIONr_nbd_refined0.210.21552
X-RAY DIFFRACTIONr_nbtor_refined0.30.22254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2117
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.21
LS refinement shellResolution: 3.38→3.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 30 -
Rwork0.272 585 -
obs-585 100 %

+
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