[English] 日本語
Yorodumi
- PDB-4goj: The Crystal Structure of full length Arl3GppNHp in complex with U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4goj
TitleThe Crystal Structure of full length Arl3GppNHp in complex with UNC119a
Components
  • ADP-ribosylation factor-like protein 3
  • Protein unc-119 homolog A
KeywordsSIGNALING PROTEIN / Small G protein Arl / GDI-like solubilizing factors / Cilia
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / negative regulation of caveolin-mediated endocytosis / photoreceptor cell development / negative regulation of clathrin-dependent endocytosis / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport ...Trafficking of myristoylated proteins to the cilium / negative regulation of caveolin-mediated endocytosis / photoreceptor cell development / negative regulation of clathrin-dependent endocytosis / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport / lipoprotein transport / small GTPase-mediated signal transduction / smoothened signaling pathway / positive regulation of protein tyrosine kinase activity / mitotic cytokinesis / axoneme / cilium assembly / phototransduction / spindle midzone / intercellular bridge / cytoplasmic microtubule / visual perception / kidney development / spindle microtubule / endocytosis / spindle pole / GDP binding / protein transport / nervous system development / midbody / microtubule binding / chemical synaptic transmission / ciliary basal body / cilium / Golgi membrane / GTPase activity / synapse / lipid binding / centrosome / GTP binding / magnesium ion binding / Golgi apparatus / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / ADP-ribosylation factor-like protein 2/3 / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Small GTPase Arf domain profile. / Coagulation Factor XIII; Chain A, domain 1 / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type ...: / ADP-ribosylation factor-like protein 2/3 / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Small GTPase Arf domain profile. / Coagulation Factor XIII; Chain A, domain 1 / 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 / Rab subfamily of small GTPases / Distorted Sandwich / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein unc-119 homolog A / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIsmail, S. / Xiang-Chen, Y. / Miertzschke, M. / Vetter, I. / Koerner, C. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2012
Title: Structural basis for Arl3-specific release of myristoylated ciliary cargo from UNC119.
Authors: Ismail, S.A. / Chen, Y.X. / Miertzschke, M. / Vetter, I.R. / Koerner, C. / Wittinghofer, A.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / 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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_sheet.number_strands / _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: ADP-ribosylation factor-like protein 3
B: ADP-ribosylation factor-like protein 3
C: Protein unc-119 homolog A
D: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0258
Polymers96,9324
Non-polymers1,0934
Water3,135174
1
A: ADP-ribosylation factor-like protein 3
C: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0124
Polymers48,4662
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-18 kcal/mol
Surface area15700 Å2
MethodPISA
2
B: ADP-ribosylation factor-like protein 3
D: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0124
Polymers48,4662
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-18 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.750, 103.300, 119.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ADP-ribosylation factor-like protein 3


Mass: 21469.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arl3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUL7
#2: Protein Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 26996.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.4 M Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 29, 2012
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.97 Å / Num. all: 51107 / Num. obs: 51107 / % possible obs: 99.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.06
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.395 / Num. unique all: 6574 / Rsym value: 0.383 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0093refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BH6, 3GQQ

3bh6

3gqq


Resolution: 2.1→29.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.065 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24832 2556 5 %RANDOM
Rwork0.21357 ---
obs0.21533 48550 99.62 %-
all-48550 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5453 0 66 174 5693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225661
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9717668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38723.915281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51715991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661541
X-RAY DIFFRACTIONr_chiral_restr0.0820.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214273
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 168 -
Rwork0.259 3294 -
obs--99.68 %

+
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