[English] 日本語
Yorodumi
- PDB-4dcn: Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dcn
TitleCrystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1
Components
  • ADP-ribosylation factor-like protein 1
  • Arfaptin-2
KeywordsPROTEIN BINDING/SIGNALING PROTEIN / Small GTPase Effector Complex / BAR domain / Membrane deformation / PROTEIN BINDING-SIGNALING PROTEIN complex
Function / homology
Function and homology information


phospholipase D activator activity / membrane curvature sensor activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to Golgi apparatus / protein localization to phagophore assembly site / GTP-dependent protein binding / ruffle organization / phosphatidylinositol-4-phosphate binding ...phospholipase D activator activity / membrane curvature sensor activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to Golgi apparatus / protein localization to phagophore assembly site / GTP-dependent protein binding / ruffle organization / phosphatidylinositol-4-phosphate binding / retrograde transport, endosome to Golgi / lamellipodium assembly / small GTPase-mediated signal transduction / Golgi organization / mitophagy / enzyme activator activity / vesicle-mediated transport / ruffle / trans-Golgi network membrane / phospholipid binding / intracellular protein transport / trans-Golgi network / small GTPase binding / cell cortex / actin cytoskeleton organization / cadherin binding / protein domain specific binding / Golgi membrane / GTPase activity / GTP binding / nucleolus / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Arfaptin homology (AH) domain/BAR domain / 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 ...Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Arfaptin homology (AH) domain/BAR domain / 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 / ARF-like small GTPases; ARF, ADP-ribosylation factor / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor-like protein 1 / Arfaptin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsNakamura, K. / Xie, Y. / Kawasaki, M. / Kato, R. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for membrane binding specificity of the Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin-2 determined by Arl1 GTPase
Authors: Nakamura, K. / Man, Z. / Xie, Y. / Hanai, A. / Makyio, H. / Kawasaki, M. / Kato, R. / Shin, H.-W. / Nakayama, K. / Wakatsuki, S.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribosylation factor-like protein 1
B: ADP-ribosylation factor-like protein 1
C: Arfaptin-2
D: Arfaptin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6498
Polymers82,5564
Non-polymers1,0934
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-82 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.764, 111.125, 119.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ADP-ribosylation factor-like protein 1 / Arl1


Mass: 18729.568 Da / Num. of mol.: 2 / Fragment: N-terminus truncated Arl1, residues 14-179 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL1 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40616
#2: Protein Arfaptin-2 / / ADP-ribosylation factor-interacting protein 2 / Partner of RAC1 / Protein POR1


Mass: 22548.592 Da / Num. of mol.: 2 / Fragment: C-terminal BAR domain, residues 118-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFIP2 / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53365
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES, 200mM Ammonium Sulfate, 25%(w/v) PEG3350, pH 7.5, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2009
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 17135 / Num. obs: 16567 / % possible obs: 96.68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.777 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.661 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.333 834 5 %RANDOM
Rwork0.2642 ---
all-17135 --
obs-16567 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.42 Å2 / Biso mean: 51.5695 Å2 / Biso min: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---4.41 Å20 Å2
3---4.18 Å2
Refinement stepCycle: LAST / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5735 0 66 4 5805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225887
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9877954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7625715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32524.382267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.424151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3091540
X-RAY DIFFRACTIONr_chiral_restr0.0640.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024284
X-RAY DIFFRACTIONr_mcbond_it0.3411.53559
X-RAY DIFFRACTIONr_mcangle_it0.64625720
X-RAY DIFFRACTIONr_scbond_it0.68132328
X-RAY DIFFRACTIONr_scangle_it1.2134.52234
LS refinement shellResolution: 3.015→3.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 53 -
Rwork0.322 1003 -
all-1056 -
obs--85.51 %

+
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