[English] 日本語
Yorodumi
- PDB-4d2m: Vaccinia Virus F1L bound to Bim BH3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d2m
TitleVaccinia Virus F1L bound to Bim BH3
Components
  • BCL-2-LIKE PROTEIN 11
  • PROTEIN F1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / host cell mitochondrial outer membrane / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / host cell mitochondrial outer membrane / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / symbiont-mediated suppression of host apoptosis / ear development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mammary gland development / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / B cell homeostasis / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / FLT3 Signaling / endomembrane system / response to endoplasmic reticulum stress / thymus development / cell-matrix adhesion / post-embryonic development / kidney development / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / microtubule binding / regulation of apoptotic process / spermatogenesis / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / membrane / cytosol
Similarity search - Function
Orthopoxvirus protein F1 / Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like ...Orthopoxvirus protein F1 / Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 11 / Apoptosis regulator OPG045
Similarity search - Component
Biological speciesVACCINIA VIRUS ANKARA
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKvansakul, M. / Colman, P.M.
CitationJournal: J.Virol. / Year: 2014
Title: Structural Insight Into Bh3-Domain Binding of Vaccinia Virus Anti-Apoptotic F1L.
Authors: Campbell, S. / Thibault, J. / Mehta, N. / Colman, P.M. / Barry, M. / Kvansakul, M.
History
DepositionMay 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Atomic model
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN F1
B: BCL-2-LIKE PROTEIN 11
C: PROTEIN F1
D: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9429
Polymers49,6824
Non-polymers2605
Water2,216123
1
A: PROTEIN F1
B: BCL-2-LIKE PROTEIN 11
C: PROTEIN F1
D: BCL-2-LIKE PROTEIN 11
hetero molecules

A: PROTEIN F1
B: BCL-2-LIKE PROTEIN 11
C: PROTEIN F1
D: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,88418
Polymers99,3648
Non-polymers52010
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area24260 Å2
ΔGint-285.7 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.503, 56.503, 232.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1189-

CL

21C-1188-

CL

-
Components

#1: Protein PROTEIN F1


Mass: 21566.379 Da / Num. of mol.: 2 / Fragment: RESIDUES 18-186 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS ANKARA / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: O57173
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH


Mass: 3274.691 Da / Num. of mol.: 2 / Fragment: RESIDUES 141-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYZS / References: UniProt: O43521
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 6.2
Details: 0.2M KCL, 15 % PEG400, 1.44 % MPD AND 0.1M AMMONIUM CITRATE PH 6.2.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→46.54 Å / Num. obs: 23011 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 35.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 12 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VTY

2vty


Resolution: 2.1→37.788 Å / SU ML: 0.24 / σ(F): 1.9 / Phase error: 26.06 / Stereochemistry target values: ML
Details: RESIDUE C156 HARBOURS A COVALENT MODIFICATION THAT WAS INTERPRETED AS BME.
RfactorNum. reflection% reflection
Rfree0.255 1181 5.1 %
Rwork0.2148 --
obs0.2168 23008 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→37.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 12 123 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032674
X-RAY DIFFRACTIONf_angle_d0.6263607
X-RAY DIFFRACTIONf_dihedral_angle_d12.8751007
X-RAY DIFFRACTIONf_chiral_restr0.026404
X-RAY DIFFRACTIONf_plane_restr0.002453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.32291460.24652618X-RAY DIFFRACTION100
2.1956-2.31130.28641560.2392641X-RAY DIFFRACTION100
2.3113-2.45610.2731370.22132727X-RAY DIFFRACTION100
2.4561-2.64570.26861620.2252654X-RAY DIFFRACTION100
2.6457-2.91190.22641560.2082702X-RAY DIFFRACTION100
2.9119-3.3330.2661360.22042754X-RAY DIFFRACTION100
3.333-4.19840.24671440.1992772X-RAY DIFFRACTION100
4.1984-37.79360.2411440.2142959X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / 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)
15.679-0.8081-0.39451.87980.49382.0212-0.0104-0.150.2064-0.4171-0.08810.26420.0251-0.24530.17080.4404-0.0665-0.09460.26890.00030.24555.271615.6293-16.6723
22.3834-0.33060.33462.8322-0.11962.91290.05390.0916-0.3169-0.2235-0.0566-0.08860.28280.01360.02920.4086-0.03250.07470.2404-0.03520.261921.5845-0.1327-13.2535
34.2844-0.37932.50091.6320.08233.60980.35180.2276-1.4053-0.3263-0.5054-0.76021.41250.53260.63590.79930.04410.03440.29050.03370.785423.8839-12.1752-12.9796
45.1036-1.1320.23361.6172-0.57691.9379-0.0288-0.72840.4486-0.0507-0.1105-0.0615-0.54120.13190.12470.5705-0.10560.0550.3242-0.0450.301320.965310.8431-16.7805
52.2848-0.6808-0.51752.8043-0.0532.59790.02890.08760.3242-0.2473-0.00090.011-0.2823-0.0155-0.04170.4316-0.0491-0.03910.29670.01320.31614.760926.6355-13.127
62.3265-0.6401-0.41191.8178-0.85663.07450.1760.22950.8271-0.2804-0.4853-0.1974-0.9456-0.38550.29120.90290.1218-0.02220.34330.00090.70752.875638.8158-12.4239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 51 THROUGH 81 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 82 THROUGH 186 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 53 THROUGH 74 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 51 THROUGH 81 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 82 THROUGH 186 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 53 THROUGH 73 )

+
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