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- PDB-7cnu: Crystal structure of DLC2 in complex with BMF peptide -

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Basic information

Entry
Database: PDB / ID: 7cnu
TitleCrystal structure of DLC2 in complex with BMF peptide
Components
  • Bcl-2-modifying factor
  • Dynein light chain 2, cytoplasmic
KeywordsMOTOR PROTEIN / Dynein light chain 2 / Bcl-2-modifying factor
Function / homology
Function and homology information


myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / ciliary tip / Intraflagellar transport / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / myosin complex / anoikis ...myosin V complex / Activation of BMF and translocation to mitochondria / 9+0 non-motile cilium / ciliary tip / Intraflagellar transport / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / myosin complex / anoikis / dynein intermediate chain binding / Macroautophagy / positive regulation of release of cytochrome c from mitochondria / microtubule-based process / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / negative regulation of autophagy / RHO GTPases Activate Formins / positive regulation of protein-containing complex assembly / cilium / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / cellular response to UV / mitochondrial outer membrane / postsynapse / microtubule / cytoskeleton / positive regulation of apoptotic process / centrosome / glutamatergic synapse / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Bcl-2-modifying factor / Bcl-2-modifying factor, apoptosis / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily
Similarity search - Domain/homology
Dynein light chain 2, cytoplasmic / Bcl-2-modifying factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWen, Y. / Shao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870132 China
CitationJournal: Cell Death Differ. / Year: 2022
Title: Non-canonical phosphorylation of Bmf by p38 MAPK promotes its apoptotic activity in anoikis.
Authors: Zhi, Z. / Ouyang, Z. / Ren, Y. / Cheng, Y. / Liu, P. / Wen, Y. / Shao, Y.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain 2, cytoplasmic
B: Dynein light chain 2, cytoplasmic
C: Bcl-2-modifying factor
E: Dynein light chain 2, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)35,7854
Polymers35,7854
Non-polymers00
Water1,20767
1
A: Dynein light chain 2, cytoplasmic
C: Bcl-2-modifying factor


Theoretical massNumber of molelcules
Total (without water)13,2842
Polymers13,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-4 kcal/mol
Surface area5660 Å2
MethodPISA
2
B: Dynein light chain 2, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)11,2511
Polymers11,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5130 Å2
MethodPISA
3
E: Dynein light chain 2, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)11,2511
Polymers11,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.243, 38.701, 44.699
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dynein light chain 2, cytoplasmic / 8 kDa dynein light chain b / DLC8b / Dynein light chain LC8-type 2


Mass: 11250.780 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL2, DLC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FJ2
#2: Protein/peptide Bcl-2-modifying factor


Mass: 2033.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMF / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LC9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium chloride 0.1 M HEPES 7.0 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→41.93 Å / Num. obs: 19215 / % possible obs: 98.98 % / Redundancy: 5.6 % / CC1/2: 0.997 / Net I/σ(I): 11.78
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 1908 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XQQ

2xqq


Resolution: 2→41.93 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.969 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22565 1923 10 %RANDOM
Rwork0.19325 ---
obs0.19645 17305 99.27 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.342 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0 Å21.42 Å2
2--3.19 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 0 67 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192205
X-RAY DIFFRACTIONr_bond_other_d0.0010.022001
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.8672965
X-RAY DIFFRACTIONr_angle_other_deg1.0732.9354660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98825.225111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57415402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.908154
X-RAY DIFFRACTIONr_chiral_restr0.0950.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022432
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_mcbond_it2.662.6181052
X-RAY DIFFRACTIONr_mcbond_other2.6312.6161050
X-RAY DIFFRACTIONr_mcangle_it3.4723.9031308
X-RAY DIFFRACTIONr_mcangle_other3.4383.9021308
X-RAY DIFFRACTIONr_scbond_it4.3893.1721153
X-RAY DIFFRACTIONr_scbond_other4.3893.1711153
X-RAY DIFFRACTIONr_scangle_other6.6034.5411657
X-RAY DIFFRACTIONr_long_range_B_refined8.38930.5722379
X-RAY DIFFRACTIONr_long_range_B_other8.3830.3632367
LS refinement shellResolution: 2→2.049 Å
RfactorNum. reflection% reflection
Rfree0.32 140 -
Rwork0.279 1259 -
obs--97.15 %
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)
16.8786-0.4890.3042.1738-0.40755.80810.05130.364-0.9018-0.1841-0.00290.20720.3153-0.4532-0.04830.0928-0.03850.0010.0623-0.06240.2677-12.6379.61916.14
21.4977-0.4813-1.046620.01423.9061.529-0.10160.2353-0.112-0.64460.1282-0.1711-0.0520.0244-0.02660.21250.01260.00060.203-0.04590.2540.1299.43312.477
35.3511-0.53130.10522.44380.05163.8046-0.1042-0.04730.46320.11250.0504-0.3898-0.37030.19820.05380.1046-0.0115-0.02470.0224-0.00980.1175-22.55726.645-4.79
43.74290.550.63834.50981.37545.8081-0.0044-0.16020.06890.36590.1155-0.3401-0.05290.6644-0.1110.1261-0.0014-0.02950.0981-0.01120.0334-41.6665.55911.851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 88
2X-RAY DIFFRACTION2C3 - 11
3X-RAY DIFFRACTION3B6 - 89
4X-RAY DIFFRACTION4E5 - 89

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