[English] 日本語
Yorodumi
- PDB-7pdj: R12E vFLIP mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pdj
TitleR12E vFLIP mutant
ComponentsFLICE inhibitory protein
KeywordsVIRAL PROTEIN / KSHV virus / tandem DED protein / NF-kappaB activation / IKK kinase binding / IKKgamma
Function / homologyDeath effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Caspase activation via Death Receptors in the presence of ligand / Death-like domain superfamily / regulation of apoptotic process / FLICE inhibitory protein
Function and homology information
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsBarrett, T.E.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)LiDo London Consortium DTP United Kingdom
Wellcome Trust209250/Z/17/Z United Kingdom
Sarcoma UKSUK203.2017 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Mechanistic insights into the activation of the IKK kinase complex by the Kaposi's sarcoma herpes virus oncoprotein vFLIP.
Authors: Bagneris, C. / Senthil Kumar, S.L. / Baratchian, M. / Britt, H.M. / Assafa, T.E. / Thalassinos, K. / Collins, M.K. / Barrett, T.E.
History
DepositionAug 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FLICE inhibitory protein
B: FLICE inhibitory protein
C: FLICE inhibitory protein
D: FLICE inhibitory protein
E: FLICE inhibitory protein
F: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)131,2646
Polymers131,2646
Non-polymers00
Water00
1
D: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FLICE inhibitory protein


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.402, 69.324, 131.887
Angle α, β, γ (deg.)90, 89.85, 90
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
FLICE inhibitory protein / K13 / ORF71 / ORF71 protein / ORF71/K13 / Putative apoptosis inhibitor protein


Mass: 21877.367 Da / Num. of mol.: 6 / Mutation: R12E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF71, HHV8GK18_gp80 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 star / References: UniProt: Q76RF1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.125 M Na HEPES pH 7.0, 1 % PEG 8000 and 3% methanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2019
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 4.2→132 Å / Num. obs: 8076 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 63 Å2 / CC1/2: 0.5 / Rpim(I) all: 0.59 / Net I/σ(I): 2.5
Reflection shellResolution: 4.2→4.7 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2287 / CC1/2: 0.21 / Rpim(I) all: 2.4 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CL3

3cl3


Resolution: 4.2→65.94 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.776 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 1.043
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 790 -RANDOM
Rwork0.2234 ---
obs0.228 8075 99.7 %-
Displacement parametersBiso mean: 74.93 Å2
Baniso -1Baniso -2Baniso -3
1--13.92 Å20 Å212.4755 Å2
2--0.2311 Å20 Å2
3---13.6889 Å2
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refinement stepCycle: LAST / Resolution: 4.2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 0 0 7092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077213HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.919868HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2295SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1214HARMONIC5
X-RAY DIFFRACTIONt_it7213HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1010SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5130SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion20.45
LS refinement shellResolution: 4.2→4.23 Å
RfactorNum. reflection% reflection
Rfree0.3933 17 -
Rwork0.2269 --
obs0.2411 208 100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.6999-0.0648-0.27162.7519-0.8331.72030.2654-0.15190.1577-0.1519-0.08490.19240.15770.1924-0.18050.11290.13820.01880.1448-0.0066-0.0581-4.114618.0498180.6616
24.569-2.91381.27623.5281-1.26824.7366-0.0482-0.16380.0854-0.1638-0.07050.32830.08540.32830.1188-0.04350.04440.1520.304-0.1085-0.034214.466847.7718157.1212
32.27251.5119-0.82284.7839-0.23253.0201-0.00010.0471-0.00250.04710.1651-0.0108-0.0025-0.0108-0.1649-0.1510.05020.10990.25840.0993-0.0789-17.584656.4922136.5431
43.53992.911-0.08965.60310.21993.95690.05110.1527-0.29880.15270.1336-0.3328-0.2988-0.3328-0.1848-0.0740.1040.12040.16790.10470.0357-21.846849.0027171.0786
56.77430.1555-1.4190.1994-0.80183.7603-0.36140.54430.43480.54430.1814-0.06090.4348-0.06090.180.21570.1139-0.04010.2754-0.0304-0.13831.156225.8246150.4765
61.4106-0.25181.08644.4629-0.38943.70150.10670.1296-0.17310.1296-0.26910.265-0.17310.2650.16230.0576-0.0530.11160.27040.0198-0.173113.347449.6265194.0053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 170
2X-RAY DIFFRACTION2{ B|* }B4 - 170
3X-RAY DIFFRACTION3{ C|* }C0 - 170
4X-RAY DIFFRACTION4{ D|* }D0 - 170
5X-RAY DIFFRACTION5{ E|* }E3 - 169
6X-RAY DIFFRACTION6{ F|* }F0 - 170

+
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://pdbjlvh1.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