[English] 日本語
Yorodumi
- PDB-1wmg: Crystal structure of the UNC5H2 death domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wmg
TitleCrystal structure of the UNC5H2 death domain
Componentsnetrin receptor Unc5h2
KeywordsAPOPTOSIS / six helix bundle / death domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


netrin receptor activity / anterior/posterior axon guidance / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process ...netrin receptor activity / anterior/posterior axon guidance / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process / plasma membrane / cytosol
Similarity search - Function
UNC5B, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas ...UNC5B, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas / Thrombospondin type 1 domain / Death domain profile. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SULFITE ION / Netrin receptor UNC5B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHanda, N. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structure of the UNC5H2 death domain
Authors: Handa, N. / Kukimoto-Niino, M. / Akasaka, R. / Murayama, K. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Nunokawa, E. / Tanaka, A. / Hayashizaki, Y. / Kigawa, ...Authors: Handa, N. / Kukimoto-Niino, M. / Akasaka, R. / Murayama, K. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Nunokawa, E. / Tanaka, A. / Hayashizaki, Y. / Kigawa, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: netrin receptor Unc5h2
B: netrin receptor Unc5h2
C: netrin receptor Unc5h2
D: netrin receptor Unc5h2
E: netrin receptor Unc5h2
F: netrin receptor Unc5h2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,06616
Polymers67,2176
Non-polymers84910
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.878, 47.207, 121.177
Angle α, β, γ (deg.)90.00, 119.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-7-

HOH

-
Components

#1: Protein
netrin receptor Unc5h2


Mass: 11202.854 Da / Num. of mol.: 6 / Fragment: Death domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / References: UniProt: Q8K1S3
#2: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.4 Å3/Da / Density % sol: 47.9 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 285 K / Method: liquid diffusion / pH: 6.5
Details: MES, magnesium sulfate, pH 6.5, LIQUID DIFFUSION, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.979006, 0.979363, 0.964000
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Apr 6, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790061
20.9793631
30.9641
ReflectionResolution: 2.1→50 Å / Num. obs: 71778 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.59 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.069
Reflection shellResolution: 2.1→2.18 Å / Rsym value: 0.241 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→39.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 824690.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: The structure was refined also with ARP/wARP. The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3282 5 %RANDOM
Rwork0.229 ---
obs0.229 65800 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5025 Å2 / ksol: 0.399766 e/Å3
Displacement parametersBiso mean: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.14 Å20 Å29.07 Å2
2---9.32 Å20 Å2
3----2.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 43 185 4298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 495 5.1 %
Rwork0.303 9301 -
obs--83.3 %

+
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://pdbjlc1.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