[English] 日本語
Yorodumi
- PDB-4zi3: BART-like domain of BARTL1/CCDC104 aa1-133 in complex with Arl3FL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zi3
TitleBART-like domain of BARTL1/CCDC104 aa1-133 in complex with Arl3FL bound to GppNHp in P1 21 1
Components
  • (Cilia- and flagella-associated protein ...) x 2
  • ADP-ribosylation factor-like protein 3
KeywordsHYDROLASE / Arf-like GTPase / GTP-binding / BART-like domain / cilia
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / protein localization to ciliary membrane / intraciliary transport / ciliary transition zone / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / Golgi to plasma membrane transport / protein localization to cilium / motile cilium ...Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / protein localization to ciliary membrane / intraciliary transport / ciliary transition zone / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / Golgi to plasma membrane transport / protein localization to cilium / motile cilium / ciliary base / smoothened signaling pathway / small GTPase-mediated signal transduction / cytoplasmic microtubule / axoneme / mitotic cytokinesis / cilium assembly / ciliary basal body / kidney development / spindle microtubule / cilium / GDP binding / microtubule cytoskeleton / protein transport / midbody / microtubule binding / Golgi membrane / GTPase activity / centrosome / GTP binding / Golgi apparatus / magnesium ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cilia- and flagella-associated protein 36 / Adp-ribosylation factor-like protein 2-binding protein fold / ADP-ribosylation factor-like 2-binding protein, domain / BART domain / BART domain superfamily / The ARF-like 2 binding protein BART / ADP-ribosylation factor-like protein 2/3 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type ...Cilia- and flagella-associated protein 36 / Adp-ribosylation factor-like protein 2-binding protein fold / ADP-ribosylation factor-like 2-binding protein, domain / BART domain / BART domain superfamily / The ARF-like 2 binding protein BART / ADP-ribosylation factor-like protein 2/3 / small GTPase Arf family 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 / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cilia- and flagella-associated protein 36 / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLokaj, M. / Koerner, C. / Koesling, S. / Wittinghofer, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC) Advanced GrantARCID; No. 268782 Germany
CitationJournal: Structure / Year: 2015
Title: The Interaction of CCDC104/BARTL1 with Arl3 and Implications for Ciliary Function.
Authors: Lokaj, M. / Kosling, S.K. / Koerner, C. / Lange, S.M. / van Beersum, S.E. / van Reeuwijk, J. / Roepman, R. / Horn, N. / Ueffing, M. / Boldt, K. / Wittinghofer, A.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
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: Cilia- and flagella-associated protein 36
D: Cilia- and flagella-associated protein 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2458
Polymers74,1524
Non-polymers1,0934
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-66 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 67.720, 98.470
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 21582.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arl3 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUL7

-
Cilia- and flagella-associated protein ... , 2 types, 2 molecules CD

#2: Protein Cilia- and flagella-associated protein 36 / Coiled-coil domain-containing protein 104 / BARTL1/CCDC104


Mass: 15570.520 Da / Num. of mol.: 1 / Fragment: UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cfap36, Ccdc104 / Plasmid: pGex4T1 Gateway / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C6E0
#3: Protein Cilia- and flagella-associated protein 36 / Coiled-coil domain-containing protein 104 / BARTL1/CCDC104


Mass: 15416.351 Da / Num. of mol.: 1 / Fragment: UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cfap36, Ccdc104 / Plasmid: pGex4T1 Gateway / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C6E0

-
Non-polymers , 3 types, 278 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


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


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1 M LiCl, 0.1 M Tris pH8.5, 20 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→28.95 Å / Num. all: 51617 / Num. obs: 44692 / % possible obs: 99.2 % / Redundancy: 3.35 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.28
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.24 % / Mean I/σ(I) obs: 3.72 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZI2

4zi2


Resolution: 2→28.95 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2235 5 %Random
Rwork0.1893 ---
obs0.192 44692 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 66 274 5168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085157
X-RAY DIFFRACTIONf_angle_d1.1457008
X-RAY DIFFRACTIONf_dihedral_angle_d16.3971964
X-RAY DIFFRACTIONf_chiral_restr0.048792
X-RAY DIFFRACTIONf_plane_restr0.005899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.29641380.2672641X-RAY DIFFRACTION99
2.0435-2.0910.33581400.25272645X-RAY DIFFRACTION100
2.091-2.14330.2911380.2472629X-RAY DIFFRACTION100
2.1433-2.20120.32711390.22912638X-RAY DIFFRACTION100
2.2012-2.2660.26961380.21292618X-RAY DIFFRACTION100
2.266-2.33910.28311420.20472694X-RAY DIFFRACTION100
2.3391-2.42260.2351380.21052635X-RAY DIFFRACTION100
2.4226-2.51960.29291390.19692636X-RAY DIFFRACTION100
2.5196-2.63420.2441390.21082640X-RAY DIFFRACTION100
2.6342-2.7730.26281390.21132643X-RAY DIFFRACTION100
2.773-2.94650.23931410.20782683X-RAY DIFFRACTION100
2.9465-3.17380.25931400.20932659X-RAY DIFFRACTION100
3.1738-3.49270.23281400.18512653X-RAY DIFFRACTION100
3.4927-3.9970.25441410.16682672X-RAY DIFFRACTION100
3.997-5.03140.20711390.15362653X-RAY DIFFRACTION99
5.0314-28.95530.19331440.16572718X-RAY DIFFRACTION99

+
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