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- PDB-5vmo: Crystal structure of grouper iridovirus GIV66:Bim complex -

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Basic information

Entry
Database: PDB / ID: 5vmo
TitleCrystal structure of grouper iridovirus GIV66:Bim complex
Components
  • Bak protein
  • Bcl-2 interacting mediator of cell death
KeywordsVIRAL PROTEIN/apoptosis / Apoptosis / Bcl-2 / iridovirus / grouper / VIRAL PROTEIN-apoptosis complex
Function / homology
Function and homology information


symbiont-mediated suppression of host apoptosis / regulation of apoptotic process / membrane
Similarity search - Function
Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2 interacting mediator of cell death / BCL2-like 11 / Bak protein
Similarity search - Component
Biological speciesGrouper iridovirus
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBanjara, S. / Kvansakul, M.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Grouper iridovirus GIV66 is a Bcl-2 protein that inhibits apoptosis by exclusively sequestering Bim.
Authors: Banjara, S. / Mao, J. / Ryan, T.M. / Caria, S. / Kvansakul, M.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bak protein
B: Bcl-2 interacting mediator of cell death
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,66910
Polymers17,9972
Non-polymers6738
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-17 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.800, 71.800, 56.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Bak protein


Mass: 14943.972 Da / Num. of mol.: 1 / Fragment: UNP residues 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grouper iridovirus / Gene: GIV66 / Plasmid: pGEX-6P3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5GAF0
#2: Protein/peptide Bcl-2 interacting mediator of cell death


Mass: 3052.530 Da / Num. of mol.: 1 / Fragment: UNP residues 117-142 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish) / References: UniProt: B2KKY9, UniProt: B8JK68*PLUS
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5, 20 % PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→41.84 Å / Num. obs: 18346 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.575 / Num. unique obs: 901 / CC1/2: 0.48 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VMN

5vmn


Resolution: 1.7→35.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1997 927 5.06 %
Rwork0.1603 --
obs0.1622 18317 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 44 119 1279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181186
X-RAY DIFFRACTIONf_angle_d1.6231587
X-RAY DIFFRACTIONf_dihedral_angle_d17.928718
X-RAY DIFFRACTIONf_chiral_restr0.083177
X-RAY DIFFRACTIONf_plane_restr0.011200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.78980.24981140.23072481X-RAY DIFFRACTION100
1.7898-1.90190.23281380.20492466X-RAY DIFFRACTION100
1.9019-2.04870.20691520.16112440X-RAY DIFFRACTION100
2.0487-2.25490.17711460.13242466X-RAY DIFFRACTION100
2.2549-2.58110.18851390.13482480X-RAY DIFFRACTION100
2.5811-3.25160.19011080.15712524X-RAY DIFFRACTION100
3.2516-35.9080.20361300.16482533X-RAY DIFFRACTION100
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)
16.5879-2.4732-1.35657.5486-1.46295.55410.05860.47850.1549-0.90760.0196-0.1617-0.4505-0.2685-0.09050.2527-0.01890.03380.14980.0150.109723.8377-5.2382-1.351
21.59671.22780.94985.584.13834.3776-0.4622-0.3586-0.44750.15360.3958-0.69440.73480.41050.11840.20470.06050.06540.2722-0.00140.267932.7871-3.43774.2978
31.950.2611-1.01981.97340.22351.9890.1633-0.3657-0.06230.3687-0.1402-0.1324-0.14930.1414-0.0760.1533-0.0108-0.03570.15480.02840.102225.688910.850112.0684
45.2962.6292-1.80193.1036-1.94642.2605-0.0214-0.258-0.3030.0098-0.0647-0.17320.1620.09450.10030.11620.01310.00010.09120.02170.115927.72494.40927.5962
55.49483.37-1.43778.5213-5.244.0741-0.0666-0.077-0.17710.18680.19610.3031-0.0093-0.4131-0.14890.12810.02010.00710.09760.010.149216.82713.78114.0706
65.1249-0.3121-2.91525.79811.95653.9573-0.1805-0.2441-0.21920.21910.0994-0.32570.29490.2147-0.00480.1658-0.01120.02390.14630.03730.122933.67599.1189-5.0574
73.376-2.1817-1.54885.50220.53954.81050.0678-0.56320.36610.33290.0045-0.3957-0.04510.60090.03620.2082-0.0149-0.07130.20520.0020.159531.722313.100712.691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 98 )
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 118 )
7X-RAY DIFFRACTION7chain 'B' and (resid 117 through 140 )

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