[English] 日本語
Yorodumi
- PDB-3bh7: Crystal structure of the RP2-Arl3 complex bound to GDP-AlF4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bh7
TitleCrystal structure of the RP2-Arl3 complex bound to GDP-AlF4
Components
  • ADP-ribosylation factor-like protein 3
  • Protein XRP2
KeywordsSIGNALING PROTEIN / Protein-Protein complex / GTPase Activating protein and GTPase / Retinitis pigmentosa / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Disease mutation / Membrane / Palmitate / Phosphoprotein / Sensory transduction / Vision / METAL BINDING PROTEIN
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / periciliary membrane compartment / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / protein localization to cilium / Golgi to plasma membrane transport ...Trafficking of myristoylated proteins to the cilium / Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / periciliary membrane compartment / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / photoreceptor connecting cilium / protein localization to cilium / Golgi to plasma membrane transport / smoothened signaling pathway / small GTPase-mediated signal transduction / ciliary transition zone / mitotic cytokinesis / cilium assembly / axoneme / cytoplasmic microtubule / visual perception / centriole / kidney development / GTPase activator activity / spindle microtubule / : / GDP binding / microtubule cytoskeleton / protein transport / protein folding / cytoplasmic vesicle / midbody / microtubule binding / cilium / ciliary basal body / Golgi membrane / GTPase activity / centrosome / GTP binding / Golgi apparatus / magnesium ion binding / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein XRP2 / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / ADP-ribosylation factor-like protein 2/3 / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. ...Protein XRP2 / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / ADP-ribosylation factor-like protein 2/3 / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Nucleoside diphosphate kinase-like domain / Small GTPase Arf domain profile. / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain superfamily / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Pectate Lyase C-like / ARF-like small GTPases; ARF, ADP-ribosylation factor / 3 Solenoid / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Protein XRP2 / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVeltel, S. / Gasper, R. / Wittinghofer, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3
Authors: Veltel, S. / Gasper, R. / Eisenacher, E. / Wittinghofer, A.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribosylation factor-like protein 3
B: Protein XRP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7825
Polymers58,2122
Non-polymers5703
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-21.1 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.698, 77.943, 97.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

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


Mass: 18384.799 Da / Num. of mol.: 1 / Fragment: residues 14-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ARL3 / Plasmid: pGEX4T5-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9WUL7
#2: Protein Protein XRP2


Mass: 39827.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RP2 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O75695

-
Non-polymers , 4 types, 222 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.4M potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→19.73 Å / Num. all: 44554 / Num. obs: 44554 / % possible obs: 98.7 % / Observed criterion σ(I): 5.3 / Redundancy: 4.1 % / Biso Wilson estimate: 30.076 Å2 / Rsym value: 0.042 / Net I/σ(I): 20.03
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 6262 / Rsym value: 0.323 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KSG, 2BX6

1ksg

2bx6


Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.731 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26194 2228 5 %RANDOM
Rwork0.23185 ---
obs0.23336 42324 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 34 219 3998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223873
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9635254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02124.946184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35515671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5691521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022918
X-RAY DIFFRACTIONr_nbd_refined0.1940.21834
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2241
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.215
X-RAY DIFFRACTIONr_mcbond_it0.5281.52455
X-RAY DIFFRACTIONr_mcangle_it0.87923840
X-RAY DIFFRACTIONr_scbond_it1.10831633
X-RAY DIFFRACTIONr_scangle_it1.7424.51411
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 161 -
Rwork0.27 3066 -
obs-3066 100 %

+
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