- PDB-1mk3: SOLUTION STRUCTURE OF HUMAN BCL-W PROTEIN -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1mk3
Title
SOLUTION STRUCTURE OF HUMAN BCL-W PROTEIN
Components
Apoptosis regulator Bcl-W
Keywords
APOPTOSIS / Bcl-w protein / apoptotis
Function / homology
Function and homology information
negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / cellular response to glycine / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to estradiol stimulus / response to ischemia ...negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / cellular response to glycine / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to estradiol stimulus / response to ischemia / cellular response to amyloid-beta / intrinsic apoptotic signaling pathway in response to DNA damage / disordered domain specific binding / spermatogenesis / regulation of apoptotic process / mitochondrial outer membrane / protein heterodimerization activity / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function
Apoptosis regulator, Bcl-W / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH1 motif, conserved site ...Apoptosis regulator, Bcl-W / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
structures with the least restraint violations,structures with the lowest energy
Representative
Model #1
closest to the average,lowest energy
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Components
#1: Protein
ApoptosisregulatorBcl-W / Bcl-w
Mass: 19659.885 Da / Num. of mol.: 1 / Mutation: P116V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92843
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
HN(CA)CB
1
2
1
CBCA(CO)HN
1
3
1
13C,15N-edited NOESY
1
4
1
HNCO
1
5
2
15N-edited NOESY
1
6
2
HNHA
1
7
3
IPAP-HSQC
NMR details
Text: The structure was determined using triple-resonance NMR spectroscopy
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.4 mM Bcl-w protein U-15N,13C, 20 mM phosphate buffer
90% H2O/10% D2O
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1.3 mM Bcl-w protein U-15N, 20 mM phosphate buffer
90% H2O/10% D2O
3
0.5 mM Bcl-w protein U-15N, 6 MG/ML PF1-PHAGE
90% H2O/10% D2O
Sample conditions
Ionic strength: 10 mM NaCl / pH: 7.3 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DRX
Bruker
DRX
500
1
Varian INOVA
Varian
INOVA
800
2
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Processing
NMR software
Name
Version
Developer
Classification
CNS
Brunger
collection
CNS
Brunger
processing
CNS
Brunger
dataanalysis
CNS
1.1
Brungeretal.
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: Structure refined by using standard protocol in CNS with restraints from NOE distances, backbone torsion angles, hydrogen bonds and residual dipolar couplings
NMR representative
Selection criteria: closest to the average,lowest energy
NMR ensemble
Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10
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