[English] 日本語
Yorodumi
- PDB-2xu6: MDV1 coiled coil domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xu6
TitleMDV1 coiled coil domain
ComponentsMDV1 COILED COIL
KeywordsPROTEIN BINDING / MITOCHONDRIAL OUTER MEMBRANE / ADAPTER PROTEIN / ORGANELLE DIVISION
Function / homology
Function and homology information


peroxisome fission / mitochondrial genome maintenance / mitochondrial fission / positive regulation of mitochondrial fission / ubiquitin binding / mitochondrial outer membrane / mitochondrion
Similarity search - Function
Mitochondrial division protein 1 / Mitochondrial division protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...Mitochondrial division protein 1 / Mitochondrial division protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial division protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKoirala, S. / Bui, H.T. / Schubert, H.L. / Eckert, D.M. / Hill, C.P. / Kay, M.S. / Shaw, J.M.
CitationJournal: J.Cell Biol. / Year: 2010
Title: Molecular Architecture of a Dynamin Adaptor: Implications for Assembly of Mitochondrial Fission Complexes
Authors: Koirala, S. / Bui, H.T. / Schubert, H.L. / Eckert, D.M. / Hill, C.P. / Kay, M.S. / Shaw, J.M.
History
DepositionOct 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MDV1 COILED COIL
B: MDV1 COILED COIL


Theoretical massNumber of molelcules
Total (without water)17,0732
Polymers17,0732
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-30.2 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.380, 41.380, 227.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.789, 0.613, 0.042), (0.613, -0.79, 0.022), (0.047, 0.009, -0.999)
Vector: -9.15117, 12.50437, 211.679)

-
Components

#1: Protein MDV1 COILED COIL


Mass: 8536.310 Da / Num. of mol.: 2 / Fragment: COILED COIL, RESIDUES 231-300 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P47025
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEMET DERIVATIVE L248M, L281M ADDITIONAL MET RESIDUES ADDED FOR SEMET PHASING.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 % / Description: NONE
Crystal growpH: 7.5
Details: 16% PEG 3350 0.1 M BIS-TRIS-PROPANE, PH 7.5 0.4 M NACL

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97982
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2009 / Details: RH COATED FLAT MIRROR.
RadiationMonochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL ASYMMETRIC CUT 4.9650 DEG
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 2.7→38 Å / Num. obs: 10392 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 60.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0062refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→38 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.906 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.704 / ESU R Free: 0.382
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.31381 278 4.6 %RANDOM
Rwork0.2704 ---
obs0.27251 5730 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 0 21 1052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221114
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9941512
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3175146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77828.0667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.87515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.464155
X-RAY DIFFRACTIONr_chiral_restr0.0940.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02838
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.5667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37621096
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2273447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1334.5404
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 22 -
Rwork0.39 419 -
obs--99.55 %

+
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