[English] 日本語
Yorodumi
- PDB-8buy: Rac-binding domain of human MiniBAR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8buy
TitleRac-binding domain of human MiniBAR
ComponentsGranule associated Rac and RHOG effector protein 1
KeywordsPROTEIN TRANSPORT / Rac effector / Rab effector
Function / homology
Function and homology information


CCR4-NOT complex binding / Rac protein signal transduction / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / P-body / small GTPase binding / cytosol
Similarity search - Function
Domain of unknown function DUF4745 / Granule associated Rac and RHOG effector protein 1 / Domain of unknown function (DUF4745)
Similarity search - Domain/homology
Granule associated Rac and RHOG effector protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPylypenko, O. / Hammich, H. / Houdusse, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE13-0024-02 France
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0016-02 France
CitationJournal: To Be Published
Title: MiniBAR/KIAA0355 is a dual Rac and Rab effector that controls actin contractility and trafficking for successful ciliogenesis
Authors: Shaughnessy, R. / Serres, M. / Escot, S. / Hammich, H. / Cuvelier, F. / Rocancourt, M. / Verdon, Q. / Gaffuri, A. / Sourigues, Y. / Malherbe, G. / Velikovsky, L. / Chardon, F. / Thinevez, J. ...Authors: Shaughnessy, R. / Serres, M. / Escot, S. / Hammich, H. / Cuvelier, F. / Rocancourt, M. / Verdon, Q. / Gaffuri, A. / Sourigues, Y. / Malherbe, G. / Velikovsky, L. / Chardon, F. / Thinevez, J. / Callebaut, I. / Formstecher, E. / Houdusse, A. / David, N. / Pylypenko, O. / Echard, A.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Granule associated Rac and RHOG effector protein 1
B: Granule associated Rac and RHOG effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0475
Polymers31,8262
Non-polymers2203
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-65 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.714, 65.945, 90.438
Angle α, β, γ (deg.)90.000, 91.516, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Granule associated Rac and RHOG effector protein 1 / GARRE1


Mass: 15913.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GARRE1, KIAA0355 / Production host: Escherichia coli (E. coli) / References: UniProt: O15063
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98008 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 1.597→28.944 Å / Num. obs: 34818 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.8
Reflection shellResolution: 1.597→1.625 Å / Num. unique obs: 1681 / CC1/2: 0.796

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.33 Å / SU ML: 0.2176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1749 5.03 %
Rwork0.1806 33053 -
obs0.1825 34802 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 13 212 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632108
X-RAY DIFFRACTIONf_angle_d0.72552872
X-RAY DIFFRACTIONf_chiral_restr0.0414348
X-RAY DIFFRACTIONf_plane_restr0.0053364
X-RAY DIFFRACTIONf_dihedral_angle_d12.0701760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.32181310.28432738X-RAY DIFFRACTION99.83
1.64-1.70.31261370.26782734X-RAY DIFFRACTION99.9
1.7-1.760.32871380.2512755X-RAY DIFFRACTION99.97
1.76-1.830.2871880.21742699X-RAY DIFFRACTION99.9
1.83-1.910.25181540.212765X-RAY DIFFRACTION99.97
1.91-2.010.23641360.20672745X-RAY DIFFRACTION99.93
2.01-2.140.25941440.19382751X-RAY DIFFRACTION99.79
2.14-2.30.24191130.18332763X-RAY DIFFRACTION99.76
2.3-2.530.22841340.18392804X-RAY DIFFRACTION99.9
2.53-2.90.20391620.17582731X-RAY DIFFRACTION99.69
2.9-3.650.19481530.16542771X-RAY DIFFRACTION99.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.882471676593-0.156976540186-0.1941765846730.4052358293860.4613709071370.5388075957580.406817778952-0.303795107169-0.4908179526380.388029754282-0.0663858325598-0.3576185394310.397221104181-0.00629766723913-0.06989640493510.358705527727-0.0968612501417-0.108090000310.2271787378390.06158572162770.2885516645527.22623223950.202247929424.5038647622
20.271255539284-0.234430143197-0.2070260570611.040081938230.0833317223560.1963685391450.0732422095638-0.0649234859003-0.2286561404720.234438116604-0.1764068945940.3479793968210.09706219490320.262059287164-0.2965171297990.300824290196-0.2191051776280.006391479274660.3803408255270.1842360392640.005678422591417.755871848649.303044436229.556796376
30.4747537483140.0730219028943-0.3199783214610.129587751458-0.04425117477680.2313312501270.0737281744789-0.0631005223780.004868071918310.15027990629-0.1973754692770.09658795963460.1511169031610.0238012459746-0.007181001102520.204605089664-0.02845799330650.004743902974070.199949282737-0.002493697820590.1970064330118.3482530225247.306204237712.3756561995
40.1598612180610.078589679294-0.008618301172370.0472161580985-0.005990762397210.0002913934285270.132574021376-0.003403765688880.07553950875040.0214536656251-0.0278179554939-0.0157354590279-0.2308375945220.01092597160290.05892364235621.026135864290.2889239107020.0905614267470.642896977651-0.08083394593430.37842827301430.516993458569.693068088935.0394544152
50.5484921516460.40029866509-0.5414998721640.742476594533-0.1220087247370.557038942267-0.144102498870.536354639282-0.09588237512210.007426603726310.20819780234-0.187143603617-0.04798593074210.2399007251930.09477149538760.207508820919-0.0297129861932-0.008541472080520.188608402708-0.02724233314220.2358357050325.220414724652.377178129215.2738348933
60.2952990580650.18479446576-0.3650535624550.169189054718-0.09531845386930.509237961609-0.04328912368150.1016948623970.0550722318258-0.02541378242270.137922645355-0.08427230968820.007035405530360.005465215876640.04255743314490.194477890819-0.02915675583840.008276366784490.2148692074250.004909706258240.24355615911829.290076144661.947601279414.4299400922
70.154726866885-0.0398284782253-0.3258296968670.4952845928270.2381204315220.7225315089610.22919412774-0.1890603586490.3248844400970.126980127903-0.1877522478790.1195024315330.06891380256270.03901746406360.07552420147840.203322455464-0.0738769186760.01042103369390.230106044969-0.02323673120080.21838422580825.978412058762.752325354624.7702242276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 187 )
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 202 )
5X-RAY DIFFRACTION5chain 'B' and (resid 70 through 110 )
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 145 )
7X-RAY DIFFRACTION7chain 'B' and (resid 146 through 204 )

+
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://pdbjlvh1.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