[English] 日本語
Yorodumi
- PDB-2uwi: Structure of CrmE, a poxvirus TNF receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uwi
TitleStructure of CrmE, a poxvirus TNF receptor
ComponentsCRME PROTEIN
KeywordsRECEPTOR / POXVIRUS TNF RECEPTOR / RECEPTOR IMMUNOMODULATOR / TNF ALPHA RECEPTOR
Function / homology
Function and homology information


Tumor necrosis factor receptor, N-terminal, viral / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGraham, S.C. / Bahar, M.W. / Abrescia, N.G. / Smith, G.L. / Stuart, D.I. / Grimes, J.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of Crme, a Virus-Encoded Tumour Necrosis Factor Receptor.
Authors: Graham, S.C. / Bahar, M.W. / Abrescia, N.G. / Smith, G.L. / Stuart, D.I. / Grimes, J.M.
History
DepositionMar 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRME PROTEIN
B: CRME PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,7442
Polymers31,7442
Non-polymers00
Water3,459192
1
A: CRME PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,8721
Polymers15,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CRME PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,8721
Polymers15,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.380, 56.490, 122.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CRME PROTEIN / CYTOKINE RESPONSE MODIFIER E


Mass: 15872.030 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH DOMAINS 1-3, RESIDUES 22-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: LISTER / Plasmid: PDEST14CRME / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: Q8UYL3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRDS 1-3 OF CRME, C-TERMINAL HIS TAGGED CONSTRUCT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.86 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 NL PROTEIN (6 MG/ML CRME IN 20 MM TRIS 150 MM NACL PH 8.0) AND 100 NL RESERVOIR (0.1 M CITRATE PH 5.0 PLUS 30% W/V PEG 6000) SITTING DROPS AT 20C EQUILIBRATED AGAINST 100 UL RESERVOIRS.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2006 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 20089 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTERTNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→39.193 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINED IN BUSTER TNT BETA VERSION 2.1.1 SIDECHAINS OF RESIDUES A 24 (GLN), A52 (LYS), A53 (TYR), A148 (ARG), B24 (GLN), B86 (ASN), B148 (ARG) WERE NOT VISIBLE IN ELECTRON DENSITY AND WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1014 5 %RANDOM
Rwork0.2101 ---
obs-19013 --
Refinement stepCycle: LAST / Resolution: 2→39.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 192 2092
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

+
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