[English] 日本語
Yorodumi
- PDB-1yu9: GppNHp-Bound Rab4A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yu9
TitleGppNHp-Bound Rab4A
ComponentsGTP-binding proteinG protein
KeywordsPROTEIN TRANSPORT / Rab GTPase / Rab4 / vesicular trafficking
Function / homology
Function and homology information


Rab protein signal transduction / postsynaptic recycling endosome / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / antigen processing and presentation / vesicle-mediated transport ...Rab protein signal transduction / postsynaptic recycling endosome / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / antigen processing and presentation / vesicle-mediated transport / small monomeric GTPase / G protein activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / recycling endosome membrane / GDP binding / protein transport / early endosome membrane / vesicle / GTPase activity / GTP binding / perinuclear region of cytoplasm / extracellular exosome
Similarity search - Function
Rab4 / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain ...Rab4 / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsEathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
CitationJournal: Nature / Year: 2005
Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
History
DepositionFeb 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4135
Polymers19,6741
Non-polymers7394
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: GTP-binding protein
hetero molecules

A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,82610
Polymers39,3492
Non-polymers1,4778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4020 Å2
ΔGint-87 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.808, 68.808, 90.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein GTP-binding protein / G protein


Mass: 19674.312 Da / Num. of mol.: 1 / Fragment: GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab4a / Plasmid: PGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL cells / References: UniProt: P20338
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / 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.: 237 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, MES, Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2002
RadiationMonochromator: confocal blue optic device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 13803 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 15.1
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2011 / Rsym value: 0.282 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rab3a polyalanine

Resolution: 2.07→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19547 665 -Random
Rwork0.15631 ---
all0.179 25209 --
obs0.1582 12656 98.58 %-
Displacement parametersBiso mean: 16.527 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.07→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 43 237 1664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.222
X-RAY DIFFRACTIONr_angle_other_deg0.795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99
X-RAY DIFFRACTIONr_chiral_restr0.071
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined0.204
X-RAY DIFFRACTIONr_nbd_other0.182
X-RAY DIFFRACTIONr_nbtor_refined0.176
X-RAY DIFFRACTIONr_nbtor_other0.081
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.157
X-RAY DIFFRACTIONr_metal_ion_refined0.037
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.136
X-RAY DIFFRACTIONr_symmetry_vdw_other0.186
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.176
X-RAY DIFFRACTIONr_mcbond_it0.876
X-RAY DIFFRACTIONr_mcbond_other0.115
X-RAY DIFFRACTIONr_mcangle_it0.963
X-RAY DIFFRACTIONr_scbond_it1.543
X-RAY DIFFRACTIONr_scangle_it2.425
LS refinement shellResolution: 2.067→2.116 Å
RfactorNum. reflection% reflection
Rfree0.225 52 -
Rwork0.172 --
obs-12780 91.16 %

+
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