[English] 日本語
Yorodumi
- PDB-8oum: Arf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oum
TitleArf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GTP
ComponentsGTP-binding protein
KeywordsSIGNALING PROTEIN / GTPASE / GTP / ARF FAMILY / ASGARD ARCHAEA / Gerdarchaea
Function / homology
Function and homology information


GTPase activity / GTP binding / metal ion binding
Similarity search - Function
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 / Small GTPase Rab domain profile. / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding protein
Similarity search - Component
Biological speciesAsgard group archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsMenetrey, J. / Jackson, C. / Dacks, J.B. / Elias, M. / Vargova, R.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE13-0007 France
CitationJournal: Nat Microbiol / Year: 2025
Title: The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics.
Authors: Vargova, R. / Chevreau, R. / Alves, M. / Courbin, C. / Terry, K. / Legrand, P. / Elias, M. / Menetrey, J. / Dacks, J.B. / Jackson, C.L.
History
DepositionApr 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding protein
B: GTP-binding protein
C: GTP-binding protein
D: GTP-binding protein
E: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,68915
Polymers100,9525
Non-polymers2,73710
Water2,198122
1
A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,1901
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.250, 54.880, 121.790
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
GTP-binding protein / Arf GTPase


Mass: 20190.365 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Arf GTPase / Source: (gene. exp.) Asgard group archaeon (archaea) / Gene: FK733_07565 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J7ZFD1
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 8.5% PEG 8000, 0.1M MgCl2 and 0.1M Tris pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.67→48 Å / Num. obs: 32436 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rrim(I) all: 0.034 / Net I/σ(I): 6
Reflection shellResolution: 2.67→2.83 Å / Num. unique obs: 4627 / CC1/2: 0.446 / Rrim(I) all: 0.26

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-OCT-2021)refinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→46.41 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.7 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.69 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1608 5 %RANDOM
Rwork0.236 ---
obs0.2376 32148 97 %-
Displacement parametersBiso mean: 68.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.6916 Å20 Å25.089 Å2
2---9.3792 Å20 Å2
3---6.6876 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.67→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6450 0 165 122 6737
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086731HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19186HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2312SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1183HARMONIC5
X-RAY DIFFRACTIONt_it6731HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion19.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5136SEMIHARMONIC4
LS refinement shellResolution: 2.67→2.71 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4356 -4.98 %
Rwork0.3828 611 -
all0.3857 643 -
obs--39.18 %
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)
14.0803-0.53910.15311.94660.19598.236-0.0060.01930.13290.1232-0.1065-0.1016-0.2890.38470.1125-0.1762-0.0603-0.0912-0.08020.0181-0.253316.51540.04543.6418
24.5346-0.48261.31462.6241-0.25665.19510.12540.0828-0.02960.08750.0233-0.01920.1020.1854-0.1486-0.21210.0164-0.06530.1184-0.0133-0.26997.9203-2.0702-24.9671
39.1692-2.11691.98892.71230.04598.09560.1372-0.1405-0.2984-0.1380.06430.09460.082-0.2908-0.2015-0.3187-0.0316-0.08740.0990.0278-0.303332.9022-15.4303-48.0008
44.5502-0.20081.03863.526-1.4794.97460.01-0.25480.05570.12750.11690.11950.1593-0.2176-0.1269-0.26440.055-0.04490.0905-0.0111-0.241955.3068-18.5545-28.1574
56.543-1.5882.60742.1572-0.5536.85950.14230.4605-0.0187-0.0023-0.07270.2009-0.10180.4645-0.0695-0.20250.0032-0.07560.0848-0.0446-0.1987-3.65534.7416-51.299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

+
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