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- PDB-2vm6: Human Bcl2-A1 in complex with Bim-BH3 peptide -

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Basic information

Entry
Database: PDB / ID: 2vm6
TitleHuman Bcl2-A1 in complex with Bim-BH3 peptide
Components
  • BCL-2-LIKE PROTEIN 11
  • BCL-2-RELATED PROTEIN A1
KeywordsIMMUNE SYSTEM / B-CELL LYMPHOMA2 / ANTIAPOPTOTIC / BIM / BFL-1 / BCL2A1 / BCL-2A1 / MEMBRANE / APOPTOSIS
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / 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 ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / 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 / ear development / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / tube formation / positive regulation of T cell apoptotic process / regulation of organ growth / Regulation of MITF-M-dependent genes involved in apoptosis / mitochondrial fusion / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / BH domain binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / positive regulation of IRE1-mediated unfolded protein response / B cell homeostasis / endomembrane system / positive regulation of cell cycle / Nuclear events stimulated by ALK signaling in cancer / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / kidney development / positive regulation of protein-containing complex assembly / : / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / channel activity / spermatogenesis / microtubule binding / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / negative regulation of apoptotic process / protein kinase binding / apoptotic process / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Bcl-2-related protein A1 / 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 / Apoptosis regulator, Bcl-2, BH1 motif, conserved site ...Bcl-2-related protein A1 / 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 / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 11 / Bcl-2-related protein A1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHerman, M.D. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Herman, M.D. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: FEBS Lett. / Year: 2008
Title: Completing the Family Portrait of the Anti- Apoptotic Bcl-2 Proteins: Crystal Structure of Human Bfl-1 in Complex with Bim.
Authors: Herman, M.D. / Nyman, T. / Welin, M. / Lehtio, L. / Flodin, S. / Tresaugues, L. / Kotenyova, T. / Flores, A. / Nordlund, P.
History
DepositionJan 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 25, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: BCL-2-RELATED PROTEIN A1
B: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4603
Polymers20,3642
Non-polymers961
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-22.6 kcal/mol
Surface area10260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.800, 70.800, 208.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2019-

HOH

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Components

#1: Protein BCL-2-RELATED PROTEIN A1 / PROTEIN BFL-1 / HEMOPOIETIC-SPECIFIC EARLY RESPONSE PROTEIN / PROTEIN GRS / BCL-2A1 / A1


Mass: 17246.617 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: Q16548
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH


Mass: 3117.497 Da / Num. of mol.: 1 / Fragment: RESIDUES 141-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: O43521
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.1M BIS, TRIS PH 5.8, 2M AMSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 27, 2007 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 10576 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 30.27
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.75 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.977 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 25-30 ARE DISORDERED, FIRST SER IS FROM VECTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 503 4.8 %RANDOM
Rwork0.194 ---
obs0.196 10075 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 5 38 1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9391920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80424.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77215254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9451510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021083
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2715
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21012
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.5872
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38721353
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1573652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3074.5567
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 40
Rwork0.193 708
Refinement TLS params.Method: refined / Origin x: -5.59 Å / Origin y: 20.223 Å / Origin z: 52.343 Å
111213212223313233
T-0.0312 Å20.0533 Å20.0299 Å2--0.118 Å20.0149 Å2---0.1535 Å2
L4.2234 °20.0842 °20.9229 °2-2.9115 °2-0.0071 °2--1.345 °2
S0.2037 Å °0.1462 Å °-0.1986 Å °-0.3558 Å °-0.1641 Å °0.0423 Å °-0.0705 Å °-0.0767 Å °-0.0396 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 149
2X-RAY DIFFRACTION1B141 - 165

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