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- PDB-9wt3: NRBF2 coiled coil domain promotes autophagy by strengthening asso... -

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Basic information

Entry
Database: PDB / ID: 9wt3
TitleNRBF2 coiled coil domain promotes autophagy by strengthening association with Vps15 in the PI3KC3 complex
ComponentsNuclear receptor-binding factor 2
KeywordsSTRUCTURAL PROTEIN / PI3KC3 complex / NRBF2 / Autophagy
Function / homology
Function and homology information


regulation of lipid kinase activity / Nuclear Receptor transcription pathway / phosphatidylinositol 3-kinase complex, class III / autophagosome / response to endoplasmic reticulum stress / nuclear receptor binding / autophagy / cytoplasmic vesicle / transcription regulator complex / transcription coactivator activity ...regulation of lipid kinase activity / Nuclear Receptor transcription pathway / phosphatidylinositol 3-kinase complex, class III / autophagosome / response to endoplasmic reticulum stress / nuclear receptor binding / autophagy / cytoplasmic vesicle / transcription regulator complex / transcription coactivator activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Nuclear receptor-binding factor 2, C-terminal / Nuclear receptor-binding factor 2, MIT domain / Nuclear receptor-binding factor 2 / Nuclear receptor-binding factor 2, autophagy regulator / MIT domain of nuclear receptor-binding factor 2
Similarity search - Domain/homology
Nuclear receptor-binding factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLi, N. / Zhao, Y.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)15105216 Hong Kong
CitationJournal: Autophagy / Year: 2025
Title: NRBF2 homodimerization by its coiled-coil domain strengthens association with the PtdIns3K complex mediated by the mit domain to promote autophagy.
Authors: Li, N. / Li, X. / Qiu, X. / Pan, X. / Wu, S. / Chen, J. / Liu, R. / Lu, J. / Yue, Z. / Zhao, Y.
History
DepositionSep 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor-binding factor 2
B: Nuclear receptor-binding factor 2
C: Nuclear receptor-binding factor 2
D: Nuclear receptor-binding factor 2
E: Nuclear receptor-binding factor 2
F: Nuclear receptor-binding factor 2
G: Nuclear receptor-binding factor 2
H: Nuclear receptor-binding factor 2


Theoretical massNumber of molelcules
Total (without water)45,5978
Polymers45,5978
Non-polymers00
Water4,756264
1
A: Nuclear receptor-binding factor 2
B: Nuclear receptor-binding factor 2


Theoretical massNumber of molelcules
Total (without water)11,3992
Polymers11,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-17 kcal/mol
Surface area6940 Å2
MethodPISA
2
C: Nuclear receptor-binding factor 2
D: Nuclear receptor-binding factor 2


Theoretical massNumber of molelcules
Total (without water)11,3992
Polymers11,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-20 kcal/mol
Surface area6960 Å2
MethodPISA
3
E: Nuclear receptor-binding factor 2
H: Nuclear receptor-binding factor 2


Theoretical massNumber of molelcules
Total (without water)11,3992
Polymers11,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-14 kcal/mol
Surface area6780 Å2
MethodPISA
4
F: Nuclear receptor-binding factor 2
G: Nuclear receptor-binding factor 2


Theoretical massNumber of molelcules
Total (without water)11,3992
Polymers11,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-16 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.529, 132.810, 87.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide
Nuclear receptor-binding factor 2 / NRBF-2


Mass: 5699.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrbf2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VCQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 3.916 M NaCl and 0.1 M Tris buffer (pH 7.0)

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→87.29 Å / Num. obs: 23604 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 33.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 12 % / Rmerge(I) obs: 0.148 / Num. unique obs: 3380 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house SeMet derivative model

Resolution: 2.25→43.68 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.03 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1161 4.9 %RANDOM
Rwork0.21583 ---
obs0.21818 22419 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.25→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 0 264 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122944
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163179
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9393899
X-RAY DIFFRACTIONr_angle_other_deg0.5831.8547315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5885348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.077532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07710697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
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_it2.6152.7841416
X-RAY DIFFRACTIONr_mcbond_other2.6122.7841416
X-RAY DIFFRACTIONr_mcangle_it3.7954.9481756
X-RAY DIFFRACTIONr_mcangle_other3.7944.9511757
X-RAY DIFFRACTIONr_scbond_it4.2613.5081528
X-RAY DIFFRACTIONr_scbond_other4.263.5111529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.986.1372144
X-RAY DIFFRACTIONr_long_range_B_refined8.52427.13418
X-RAY DIFFRACTIONr_long_range_B_other8.52527.113419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.253→2.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 92 -
Rwork0.209 1619 -
obs--99.53 %

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