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- PDB-4qnq: Crystal Structure Analysis of full-length Bcl-XL in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4qnq
TitleCrystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS/APOPTOSIS inhibitor / ALPHA-HELICAL PROTEIN / APOPTOSIS / APOPTOSIS-APOPTOSIS inhibitor complex
Function / homology
Function and homology information


response to erythropoietin / cellular response to astaxanthin / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / The NLRP1 inflammasome / cellular response to erythropoietin / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / cellular response to prolactin ...response to erythropoietin / cellular response to astaxanthin / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / The NLRP1 inflammasome / cellular response to erythropoietin / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / cellular response to prolactin / BH domain binding / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis / positive regulation of mononuclear cell proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / regulation of long-term synaptic depression / response to cycloheximide / clathrin binding / positive regulation of ATP biosynthetic process / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to inorganic substance / cellular response to nitric oxide / ectopic germ cell programmed cell death / MDM2/MDM4 family protein binding / cellular response to interleukin-1 / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cAMP / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to organonitrogen compound / response to endoplasmic reticulum stress / mitochondrion organization / cellular response to dexamethasone stimulus / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / epithelial cell proliferation / response to cytokine / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / response to lead ion / response to virus / cellular response to gamma radiation / response to radiation / response to hydrogen peroxide / response to organic cyclic compound / cerebral cortex development / synaptic vesicle membrane / response to peptide hormone / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to xenobiotic stimulus / presynapse / GTPase binding / cellular response to tumor necrosis factor / cellular response to hypoxia / spermatogenesis / nuclear membrane / neuron apoptotic process / regulation of apoptotic process / in utero embryonic development / response to oxidative stress / mitochondrial outer membrane / negative regulation of neuron apoptotic process / response to lipopolysaccharide / mitochondrial inner membrane / response to hypoxia / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / centrosome / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / 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-X / Apoptosis regulator, Bcl-2/ BclX / 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, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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
Chem-1XJ / Bcl-2-like protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKorste, A. / Vetter, I.R. / Stoll, R.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263
Authors: Korste, A. / Vetter, I.R. / Stoll, R.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-like protein 1
B: Bcl-2-like protein 1
C: Bcl-2-like protein 1
D: Bcl-2-like protein 1
E: Bcl-2-like protein 1
F: Bcl-2-like protein 1
G: Bcl-2-like protein 1
H: Bcl-2-like protein 1
I: Bcl-2-like protein 1
J: Bcl-2-like protein 1
K: Bcl-2-like protein 1
L: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,95124
Polymers322,25612
Non-polymers11,69512
Water1,910106
1
A: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
G: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
I: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
J: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
K: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
L: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
B: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
H: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8292
Polymers26,8551
Non-polymers9751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.140, 85.810, 93.640
Angle α, β, γ (deg.)72.94, 67.42, 69.38
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 2 - 196 / Label seq-ID: 9 - 203

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

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Components

#1: Protein
Bcl-2-like protein 1 / / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 26854.664 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: B2CL1_RAT, Bcl2l1, Bclx, Blc2l / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P53563
#2: Chemical
ChemComp-1XJ / 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide / Navitoclax


Mass: 974.613 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C47H55ClF3N5O6S3 / Comment: anticancer, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.66 Å3/Da / Density % sol: 25.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 3350, 0.2 M Calcium Chloride, pH approx. 7.8, vapor diffusion, hanging drop, temperature 293K
PH range: approx. 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.06997 Å
DetectorType: PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06997 Å / Relative weight: 1
ReflectionResolution: 2.3→47.036 Å / Num. obs: 89549 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.89
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.360.541.39192.7
2.36-2.420.4981.57193.1
2.42-2.490.4081.89193.7
2.49-2.570.6182.41199.1
2.57-2.660.5012.96199.4
2.66-2.750.4563.34199.4
2.75-2.850.3514.19199.3
2.85-2.970.2685.25199.6
2.97-3.10.2186.03199.3
3.1-3.250.177.33199.1
3.25-3.430.1358.73199
3.43-3.640.10710.43197.4
3.64-3.890.09111.89196.8
3.89-4.20.07813.57197.4
4.2-4.60.0714.37197
4.6-5.140.06314.56196.7
5.14-5.940.06514.16198
5.94-7.270.0615.91198.6
7.27-10.290.05518.03198.3
10.290.05519.59197

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
DA+data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1r2d

1r2d


Resolution: 2.3→85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.207 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25286 4444 5 %RANDOM
Rwork0.20623 ---
obs0.20851 85104 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.27 Å2-1.14 Å2
2---0.17 Å21.21 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14043 0 780 106 14929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215246
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213081
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.98420724
X-RAY DIFFRACTIONr_angle_other_deg0.838329911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79551709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76523.927769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.979152317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5781596
X-RAY DIFFRACTIONr_chiral_restr0.080.22027
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1784.9776908
X-RAY DIFFRACTIONr_mcbond_other4.1764.9776907
X-RAY DIFFRACTIONr_mcangle_it6.3727.4398593
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2375.5028338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2160 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.860.5
2BMEDIUM POSITIONAL0.940.5
3CMEDIUM POSITIONAL0.760.5
4DMEDIUM POSITIONAL0.780.5
5EMEDIUM POSITIONAL0.70.5
6FMEDIUM POSITIONAL0.690.5
7GMEDIUM POSITIONAL0.810.5
8HMEDIUM POSITIONAL0.850.5
9IMEDIUM POSITIONAL0.770.5
10JMEDIUM POSITIONAL0.680.5
11KMEDIUM POSITIONAL0.730.5
12LMEDIUM POSITIONAL0.770.5
1AMEDIUM THERMAL10.932
2BMEDIUM THERMAL7.172
3CMEDIUM THERMAL7.392
4DMEDIUM THERMAL9.842
5EMEDIUM THERMAL7.52
6FMEDIUM THERMAL8.142
7GMEDIUM THERMAL9.582
8HMEDIUM THERMAL8.82
9IMEDIUM THERMAL9.222
10JMEDIUM THERMAL8.642
11KMEDIUM THERMAL7.082
12LMEDIUM THERMAL14.082
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 297 -
Rwork0.323 5938 -
obs--92.63 %

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