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- PDB-9uhd: Structure of FAM92A BAR domain -

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Basic information

Entry
Database: PDB / ID: 9uhd
TitleStructure of FAM92A BAR domain
ComponentsCBY1-interacting BAR domain-containing protein 1
KeywordsLIPID BINDING PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


sperm annulus / inner mitochondrial membrane organization / ciliary transition zone / limb morphogenesis / positive regulation of smoothened signaling pathway / cilium assembly / centriole / spermatogenesis / mitochondrial inner membrane / cilium ...sperm annulus / inner mitochondrial membrane organization / ciliary transition zone / limb morphogenesis / positive regulation of smoothened signaling pathway / cilium assembly / centriole / spermatogenesis / mitochondrial inner membrane / cilium / ciliary basal body / mitochondrion / nucleus / cytoplasm
Similarity search - Function
CBY1-interacting BAR domain-containing protein/FAM92 / CBY1-interacting BAR domain-containing protein 1/2, BAR domain / FAM92 protein / AH/BAR domain superfamily
Similarity search - Domain/homology
CBY1-interacting BAR domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsXu, X. / Ren, J. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471271 China
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Dimerization of the BAR domain-containing protein FAM92A modulates lipid binding and interaction with CBY1.
Authors: Xu, X. / Ren, J. / Li, J.
History
DepositionApr 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 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: CBY1-interacting BAR domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)25,2331
Polymers25,2331
Non-polymers00
Water2,684149
1
A: CBY1-interacting BAR domain-containing protein 1

A: CBY1-interacting BAR domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)50,4652
Polymers50,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5210 Å2
ΔGint-46 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.270, 132.270, 67.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-377-

HOH

21A-421-

HOH

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Components

#1: Protein CBY1-interacting BAR domain-containing protein 1


Mass: 25232.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cibar1, Fam92a, Fam92a1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BP22
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 6.78 Å3/Da / Density % sol: 81.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 15% w/v polyethylene glycol 3350, 10 mM magnesium chloride hexahydrate and 5 mM nickel (II) chloride hexahydrate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.21→58.32 Å / Num. obs: 34469 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / Χ2: 0.99 / Net I/σ(I): 17.5 / Num. measured all: 677791
Reflection shellResolution: 2.21→2.27 Å / % possible obs: 99.9 % / Redundancy: 20.1 % / Rmerge(I) obs: 2.499 / Num. measured all: 50858 / Num. unique obs: 2526 / CC1/2: 0.713 / Rpim(I) all: 0.571 / Rrim(I) all: 2.564 / Χ2: 1.02 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→58.32 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1762 5.12 %
Rwork0.188 --
obs0.1894 34418 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 0 149 1886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131756
X-RAY DIFFRACTIONf_angle_d1.1442362
X-RAY DIFFRACTIONf_dihedral_angle_d4.541235
X-RAY DIFFRACTIONf_chiral_restr0.065270
X-RAY DIFFRACTIONf_plane_restr0.011312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.39831270.35112478X-RAY DIFFRACTION99
2.27-2.340.27331660.27252460X-RAY DIFFRACTION100
2.34-2.410.27991420.2452461X-RAY DIFFRACTION100
2.41-2.50.26281290.23182505X-RAY DIFFRACTION100
2.5-2.60.28141370.22742494X-RAY DIFFRACTION100
2.6-2.720.24771300.19622506X-RAY DIFFRACTION100
2.72-2.860.20461400.17792475X-RAY DIFFRACTION100
2.86-3.040.20841150.18392512X-RAY DIFFRACTION100
3.04-3.270.22361230.18922536X-RAY DIFFRACTION100
3.27-3.60.21551340.17662516X-RAY DIFFRACTION100
3.6-4.120.20081350.16772548X-RAY DIFFRACTION100
4.12-5.190.18761190.15242558X-RAY DIFFRACTION100
5.2-58.320.18261650.18992607X-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)
10.20751.15960.65728.46764.9732.2788-0.03410.03030.0090.0007-0.16860.6930.0403-0.10160.17040.388-0.0181-0.01050.34140.02230.366664.237-13.72714.209
20.57091.76260.98526.2573.71362.045-0.0013-0.1264-0.0333-0.5549-0.13640.0657-0.2705-0.18050.07910.4138-0.0237-0.01350.39390.03840.368864.227-17.5124.715
30.76931.28370.90334.32892.75452.0266-0.12150.11520.017-0.31520.2837-0.0653-0.23050.2081-0.27370.3538-0.01720.03370.39620.02270.353272.382-20.1585.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:61 )A2 - 61
2X-RAY DIFFRACTION2( CHAIN A AND RESID 62:140 )A62 - 140
3X-RAY DIFFRACTION3( CHAIN A AND RESID 141:214 )A141 - 214

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