[English] 日本語
Yorodumi
- PDB-5znz: Structure of mDR3 DD with MBP tag mutant-I387V -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5znz
TitleStructure of mDR3 DD with MBP tag mutant-I387V
ComponentsMaltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
KeywordsAPOPTOSIS / TNFRSF25 / TRADD / NF-kappa B
Function / homology
Function and homology information


TNFs bind their physiological receptors / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...TNFs bind their physiological receptors / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / apoptotic process / signal transduction / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 25 / Tumor necrosis factor receptor 25, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain ...Tumour necrosis factor receptor 25 / Tumor necrosis factor receptor 25, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily, member 25 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsJin, T. / Yin, X.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structure and activation mechanism of DR3 death domain.
Authors: Yin, X. / Li, W. / Ma, H. / Zeng, W. / Peng, C. / Li, Y. / Liu, M. / Chen, Q. / Zhou, R. / Jin, T.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 4, 2019Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
B: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
C: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
D: Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,92330
Polymers205,4254
Non-polymers2,49826
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12760 Å2
ΔGint-369 kcal/mol
Surface area70990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.400, 144.870, 177.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Maltose-binding periplasmic protein,Tumor necrosis factor receptor superfamily, member 25 / MBP tag / MBP / MMBP / Maltodextrin-binding protein / Tumor necrosis factor receptor superfamily / ...MBP tag / MBP / MMBP / Maltodextrin-binding protein / Tumor necrosis factor receptor superfamily / member 25 / isoform CRA_b


Mass: 51356.250 Da / Num. of mol.: 4
Mutation: D108A,K109A,E198A,N199A,K265A,E385A,K388A,D389A,I387V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Mus musculus (house mouse)
Strain: K12 / Gene: malE, b4034, JW3994, Tnfrsf25, mCG_4090 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: B1AWN9
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.5 M ammonium sulfate, 0.1 M MES 5.5

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 75446 / % possible obs: 99.5 % / Redundancy: 6.53 % / CC1/2: 0.999 / Net I/σ(I): 17.51
Reflection shellResolution: 2.55→2.7 Å / CC1/2: 0.806

-
Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMP

1omp


Resolution: 2.55→47.527 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2738 3773 5 %
Rwork0.2336 --
obs-75404 99.48 %
Refinement stepCycle: LAST / Resolution: 2.55→47.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13987 0 130 2 14119
LS refinement shellResolution: 2.55→2.641 Å
Refinement TLS params.Method: refined / Origin x: 45.1365 Å / Origin y: -3.772 Å / Origin z: -43.6477 Å
111213212223313233
T0.7206 Å2-0.0131 Å20.0353 Å2-0.5959 Å2-0.0001 Å2--0.5833 Å2
L-0.0358 °2-0.0645 °20.019 °2-0.3854 °20.0342 °2--0.3151 °2
S-0.0527 Å °0.0004 Å °-0.0237 Å °0.0332 Å °0.0263 Å °-0.0062 Å °0.0064 Å °-0.0696 Å °0.0193 Å °
Refinement TLS groupSelection details: all

+
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