[English] 日本語
Yorodumi
- PDB-4ts6: Crystal structure of the RIM C2A domain from Drosophila. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ts6
TitleCrystal structure of the RIM C2A domain from Drosophila.
ComponentsRab3 interacting molecule variant 2
KeywordsTRANSPORT PROTEIN / C2A domain
Function / homology
Function and homology information


exocytosis / intracellular protein transport / small GTPase binding / synapse / membrane / metal ion binding
Similarity search - Function
Rim-like / : / RIM2-alpha zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...Rim-like / : / RIM2-alpha zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Rab3 interacting molecule variant 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsHatzopoulos, G.N. / Shiroma, J. / Vakonakis, I.
CitationJournal: Brain / Year: 2022
Title: The human cognition-enhancing CORD7 mutation increases active zone number and synaptic release.
Authors: Paul, M.M. / Dannhauser, S. / Morris, L. / Mrestani, A. / Hubsch, M. / Gehring, J. / Hatzopoulos, G.N. / Pauli, M. / Auger, G.M. / Bornschein, G. / Scholz, N. / Ljaschenko, D. / Muller, M. / ...Authors: Paul, M.M. / Dannhauser, S. / Morris, L. / Mrestani, A. / Hubsch, M. / Gehring, J. / Hatzopoulos, G.N. / Pauli, M. / Auger, G.M. / Bornschein, G. / Scholz, N. / Ljaschenko, D. / Muller, M. / Sauer, M. / Schmidt, H. / Kittel, R.J. / DiAntonio, A. / Vakonakis, I. / Heckmann, M. / Langenhan, T.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 7, 2024Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rab3 interacting molecule variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0442
Polymers14,9521
Non-polymers921
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-0 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.080, 38.700, 131.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Rab3 interacting molecule variant 2


Mass: 14952.046 Da / Num. of mol.: 1 / Fragment: Residues 836-962
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rim / Production host: Escherichia coli (E. coli) / References: UniProt: V5M2P5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-lithium citrate, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.92→65.68 Å / Num. obs: 13188 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.806 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.066 / Net I/σ(I): 12.39 / Num. measured all: 90891
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.92-1.970.6940.6431.976649176317560.75199.6
1.97-2.020.8710.3973.096723176917690.462100
2.02-2.080.8770.3373.796314166416620.39499.9
2.08-2.150.9140.2924.326499171117090.3499.9
2.15-2.220.9650.2135.75791152015190.24899.9
2.22-2.290.960.1886.766072159315920.21999.9
2.29-2.380.9730.1567.885510144614440.18299.9
2.38-2.480.9780.1398.945513145514540.16299.9
2.48-2.590.9850.11510.445177136913650.13599.7
2.59-2.720.9910.08813.164900129912990.102100
2.72-2.860.9920.07814.994720125412490.09199.6
2.86-3.040.9950.06217.954399117711700.07299.4
3.04-3.250.9970.04921.854226114411360.05799.3
3.25-3.510.9970.04324.533763102810200.0599.2
3.51-3.840.9970.03927.1634459409280.04598.7
3.84-4.290.9980.03727.9931118538450.04499.1
4.29-4.960.9970.03329.1327457707600.03998.7
4.96-6.070.9990.02728.3624376366320.03199.4
6.07-8.590.9990.02628.7719265015000.0399.8
8.590.9990.02528.689712812690.02995.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless3.11data scaling
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MrBUMPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BWQ

2bwq


Resolution: 1.92→65.68 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8336 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 648 4.93 %
Rwork0.1843 12492 -
obs0.186 13140 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.22 Å2 / Biso mean: 37.6901 Å2 / Biso min: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.92→65.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 6 94 1117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071058
X-RAY DIFFRACTIONf_angle_d1.191436
X-RAY DIFFRACTIONf_chiral_restr0.086159
X-RAY DIFFRACTIONf_plane_restr0.004184
X-RAY DIFFRACTIONf_dihedral_angle_d13.69392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9201-2.06830.2951370.22672418
2.0683-2.27650.24711200.19622486
2.2765-2.60590.20931320.19542442
2.6059-3.28320.2551200.19092517
3.28320.1881390.17042629
Refinement TLS params.Method: refined / Origin x: 14.3144 Å / Origin y: 4.2403 Å / Origin z: -17.8546 Å
111213212223313233
T0.1424 Å2-0.0329 Å20.0283 Å2-0.2094 Å2-0.0483 Å2--0.2187 Å2
L2.5579 °2-0.7521 °2-0.7027 °2-2.9456 °21.0375 °2--3.2253 °2
S-0.0471 Å °-0.3888 Å °0.2443 Å °-0.0716 Å °0.176 Å °-0.3199 Å °-0.0017 Å °0.1437 Å °-0.1061 Å °
Refinement TLS groupSelection details: chain 'A' and (resid -1 through 962)

+
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