[English] 日本語
Yorodumi
- PDB-6fne: Structure of human Brag2 (Sec7-PH domains) with the inhibitor Bra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fne
TitleStructure of human Brag2 (Sec7-PH domains) with the inhibitor Bragsin bound to the PH domain
ComponentsIQ motif and SEC7 domain-containing protein 1
KeywordsHYDROLASE / ARF GEF
Function / homology
Function and homology information


positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding ...positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding / nucleolus / membrane
Similarity search - Function
IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / IQ motif, EF-hand binding site ...IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / IQ motif, EF-hand binding site / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Chem-DY5 / IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsNawrotek, A. / Zeghouf, M. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
INCA France
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling.
Authors: Nawrotek, A. / Benabdi, S. / Niyomchon, S. / Kryszke, M.H. / Ginestier, C. / Caneque, T. / Tepshi, L. / Mariani, A. / St Onge, R.P. / Giaever, G. / Nislow, C. / Charafe-Jauffret, E. / ...Authors: Nawrotek, A. / Benabdi, S. / Niyomchon, S. / Kryszke, M.H. / Ginestier, C. / Caneque, T. / Tepshi, L. / Mariani, A. / St Onge, R.P. / Giaever, G. / Nislow, C. / Charafe-Jauffret, E. / Rodriguez, R. / Zeghouf, M. / Cherfils, J.
History
DepositionFeb 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 25, 2020Group: Refinement description / Structure summary / Category: software / struct / Item: _software.name / _struct.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IQ motif and SEC7 domain-containing protein 1
B: IQ motif and SEC7 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4754
Polymers94,7852
Non-polymers6902
Water32418
1
A: IQ motif and SEC7 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0823
Polymers47,3931
Non-polymers6902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IQ motif and SEC7 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)47,3931
Polymers47,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.912, 66.161, 218.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein IQ motif and SEC7 domain-containing protein 1 / ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine ...ADP-ribosylation factors guanine nucleotide-exchange protein 100 / ADP-ribosylation factors guanine nucleotide-exchange protein 2 / Brefeldin-resistant Arf-GEF 2 protein / BRAG2


Mass: 47392.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC1, ARFGEP100, BRAG2, KIAA0763 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DN90
#2: Chemical ChemComp-DY5 / (2~{S})-6-methyl-5-nitro-2-(trifluoromethyl)-2,3-dihydrochromen-4-one


Mass: 275.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8F3NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 18% PEG 20000, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→65.9 Å / Num. all: 286171 / Num. obs: 21954 / % possible obs: 93.9 % / Redundancy: 13 % / Biso Wilson estimate: 70.64 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.18 / Net I/σ(I): 9.9
Reflection shellResolution: 2.5→2.78 Å / Num. measured obs: 11487 / Num. unique all: 1099 / Num. unique obs: 11487 / Rpim(I) all: 0.46 / % possible all: 70

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPROCdata collection
STARANISOdata scaling
Cootmodel building
BUSTERrefinement
PHENIXmodel building
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NLY

5nly


Resolution: 2.501→63.33 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.53
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 1093 4.98 %RANDOM
Rwork0.2176 ---
obs0.2209 21952 64.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→63.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 47 18 5700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095788
X-RAY DIFFRACTIONf_angle_d1.1367769
X-RAY DIFFRACTIONf_dihedral_angle_d22.7063583
X-RAY DIFFRACTIONf_chiral_restr0.055841
X-RAY DIFFRACTIONf_plane_restr0.0061013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5015-2.61530.3747150.3022209X-RAY DIFFRACTION5
2.6153-2.75320.3332360.3283661X-RAY DIFFRACTION17
2.7532-2.92570.2966660.29211213X-RAY DIFFRACTION31
2.9257-3.15160.3441150.29682448X-RAY DIFFRACTION61
3.1516-3.46880.36142020.26453981X-RAY DIFFRACTION99
3.4688-3.97060.29121940.22764019X-RAY DIFFRACTION100
3.9706-5.00230.24592070.18154083X-RAY DIFFRACTION100
5.0023-63.34990.25762580.19994245X-RAY DIFFRACTION100

+
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