[English] 日本語
Yorodumi
- PDB-2efc: Ara7-GDP/AtVps9a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2efc
TitleAra7-GDP/AtVps9a
Components
  • Similarity to vacuolar protein sorting-associated protein VPS9
  • Small GTP-binding protein-like
KeywordsTRANSPORT PROTEIN / GEF / GTPase / Vps9 / Rab5 / nucleotide
Function / homology
Function and homology information


cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / molecular sequestering activity / embryo development ending in seed dormancy / vacuole organization / late endosome to vacuole transport / multivesicular body membrane / small molecule binding ...cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / molecular sequestering activity / embryo development ending in seed dormancy / vacuole organization / late endosome to vacuole transport / multivesicular body membrane / small molecule binding / GTPase activator activity / guanyl-nucleotide exchange factor activity / intracellular protein transport / early endosome membrane / early endosome / endosome / GTPase activity / GTP binding / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 ...Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / small GTPase Rab1 family profile. / Serum Albumin; Chain A, Domain 1 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Ras subfamily of RAS small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Vacuolar protein sorting-associated protein 9A / Ras-related protein RABF2b
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsUejima, T. / Ihara, K. / Goh, T. / Ito, E. / Sunada, M. / Ueda, T. / Nakano, A. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system
Authors: Uejima, T. / Ihara, K. / Goh, T. / Ito, E. / Sunada, M. / Ueda, T. / Nakano, A. / Wakatsuki, S.
History
DepositionFeb 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Similarity to vacuolar protein sorting-associated protein VPS9
B: Small GTP-binding protein-like
C: Similarity to vacuolar protein sorting-associated protein VPS9
D: Small GTP-binding protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9986
Polymers100,1114
Non-polymers8862
Water5,963331
1
A: Similarity to vacuolar protein sorting-associated protein VPS9
B: Small GTP-binding protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4993
Polymers50,0562
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-21 kcal/mol
Surface area19070 Å2
MethodPISA, PQS
2
C: Similarity to vacuolar protein sorting-associated protein VPS9
D: Small GTP-binding protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4993
Polymers50,0562
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-21 kcal/mol
Surface area19040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.377, 58.474, 68.714
Angle α, β, γ (deg.)81.68, 86.89, 72.97
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Similarity to vacuolar protein sorting-associated protein VPS9 / AtVps9a / Hypothetical protein At3g19770


Mass: 30168.316 Da / Num. of mol.: 2 / Fragment: Vps9 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3)pLysS / References: UniProt: Q9LT31
#2: Protein Small GTP-binding protein-like / Ara7 / AT4g19640/F24J7_190


Mass: 19887.432 Da / Num. of mol.: 2 / Fragment: GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9SN68
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 200mM lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→100 Å / Num. all: 123703 / Num. obs: 48167 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 10.6
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.3 / % possible all: 78.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: nucleotide-free Ara7/AtVps9a which was solved by MAD

Resolution: 2.09→68.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.572 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.294 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27419 2448 5.1 %RANDOM
Rwork0.22139 ---
obs0.22409 45719 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.644 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20.53 Å2-0.07 Å2
2---0.37 Å2-0.41 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.09→68.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 56 331 6867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226662
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9649010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04625.127316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.966151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.421532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025014
X-RAY DIFFRACTIONr_nbd_refined0.2120.23349
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2416
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.214
X-RAY DIFFRACTIONr_mcbond_it0.6731.54212
X-RAY DIFFRACTIONr_mcangle_it1.15326592
X-RAY DIFFRACTIONr_scbond_it1.57332775
X-RAY DIFFRACTIONr_scangle_it2.5834.52418
LS refinement shellResolution: 2.09→2.145 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 147 -
Rwork0.265 2557 -
obs--72.09 %

+
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