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- PDB-6h1n: Crystal Structure of a Zebra-fish pro-survival protein NRZ-apo -

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Basic information

Entry
Database: PDB / ID: 6h1n
TitleCrystal Structure of a Zebra-fish pro-survival protein NRZ-apo
ComponentsBCL2-like 10 (Apoptosis facilitator)
KeywordsAPOPTOSIS / Bcl-2 family / pro-survival protein
Function / homology
Function and homology information


epiboly / regulation of release of sequestered calcium ion into cytosol / somitogenesis / extrinsic apoptotic signaling pathway in absence of ligand / gastrulation / release of cytochrome c from mitochondria / calcium-mediated signaling / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / mitochondrial outer membrane ...epiboly / regulation of release of sequestered calcium ion into cytosol / somitogenesis / extrinsic apoptotic signaling pathway in absence of ligand / gastrulation / release of cytochrome c from mitochondria / calcium-mediated signaling / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / mitochondrial outer membrane / positive regulation of apoptotic process / negative regulation of apoptotic process / mitochondrion
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / BCL2-like 10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research CouncilFT130101349 Australia
CitationJournal: Cell Death Dis / Year: 2018
Title: A structural investigation of NRZ mediated apoptosis regulation in zebrafish.
Authors: Suraweera, C.D. / Caria, S. / Jarva, M. / Hinds, M.G. / Kvansakul, M.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jan 17, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL2-like 10 (Apoptosis facilitator)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3433
Polymers17,1881
Non-polymers1552
Water68538
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, protein was eluted as a monomer in gel filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.177, 48.177, 75.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein BCL2-like 10 (Apoptosis facilitator) / Nr13


Mass: 17188.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: bcl2l10, mcl1l, nr13 / Production host: Escherichia coli (E. coli) / Variant (production host): Codon Plus / References: UniProt: Q8UWD5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.0 M magnesium sulphate hydrate, 0.1 M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.18 Å / Num. obs: 11653 / % possible obs: 99.93 % / Redundancy: 6.9 % / Biso Wilson estimate: 42.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.029 / Rrim(I) all: 0.056 / Net I/σ(I): 18.3
Reflection shellResolution: 2→8.94 Å / Redundancy: 6.9 % / Num. unique obs: 834 / CC1/2: 0.615 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Coot0.8.8 ELmodel building
Aimless7.0.046data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FBX

6fbx


Resolution: 2→48.177 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2237 615 5.28 %
Rwork0.1903 --
obs0.192 11653 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 9 38 1209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121216
X-RAY DIFFRACTIONf_angle_d1.2691640
X-RAY DIFFRACTIONf_dihedral_angle_d20.661722
X-RAY DIFFRACTIONf_chiral_restr0.048170
X-RAY DIFFRACTIONf_plane_restr0.008215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.20140.29351560.2462739X-RAY DIFFRACTION100
2.2014-2.520.26961500.22412751X-RAY DIFFRACTION100
2.52-3.17480.24391680.21992738X-RAY DIFFRACTION100
3.1748-48.1910.19561410.16752810X-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)
16.9086-2.3516-0.73985.4734-0.53214.3525-0.1499-0.484-0.27440.19660.2050.6047-0.4927-0.3217-0.04730.5525-0.0217-0.00780.3813-0.01730.2737-10.5932-9.59271.4928
26.67231.1341-3.07192.9512-1.69214.5176-0.0285-0.0702-0.32650.121-0.203-0.22490.19720.50390.24170.380.03380.0110.3587-0.00850.28210.1501-16.6129-6.0475
36.9461-3.6108-1.8075.9202-2.0192.9754-0.393-0.73280.92521.13340.2566-0.3939-0.52570.76520.22250.5319-0.0187-0.02810.5371-0.06760.4402-1.4528-6.7868-0.531
47.2314-1.3991-0.79775.4725-2.04746.31270.14230.8706-0.31430.0981-0.30390.7691-0.0567-0.3237-0.00330.3344-0.05-0.03740.4793-0.06840.3749-16.4905-15.0927-8.7555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 150 )

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