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- PDB-8ceg: BAR domain protein FAM92A1 essential for mitochondrial membrane r... -

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Basic information

Entry
Database: PDB / ID: 8ceg
TitleBAR domain protein FAM92A1 essential for mitochondrial membrane remodeling
ComponentsCBY1-interacting BAR domain-containing protein 1
KeywordsLIPID BINDING PROTEIN / BAR domain / mitochondria / membrane binding
Function / homology
Function and homology information


membrane tubulation / inner mitochondrial membrane organization / ciliary transition zone / limb morphogenesis / membrane organization / positive regulation of smoothened signaling pathway / ciliary base / mitochondrial crista / cilium assembly / centriole ...membrane tubulation / inner mitochondrial membrane organization / ciliary transition zone / limb morphogenesis / membrane organization / positive regulation of smoothened signaling pathway / ciliary base / mitochondrial crista / cilium assembly / centriole / ciliary basal body / phospholipid binding / mitochondrial inner membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.03 Å
AuthorsKajander, T. / Fudo, S. / Yan, Z. / Zhao, H.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland266846 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Nat Commun / Year: 2024
Title: Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition.
Authors: Wang, L. / Yang, Z. / Satoshi, F. / Prasanna, X. / Yan, Z. / Vihinen, H. / Chen, Y. / Zhao, Y. / He, X. / Bu, Q. / Li, H. / Zhao, Y. / Jiang, L. / Qin, F. / Dai, Y. / Zhang, N. / Qin, M. / ...Authors: Wang, L. / Yang, Z. / Satoshi, F. / Prasanna, X. / Yan, Z. / Vihinen, H. / Chen, Y. / Zhao, Y. / He, X. / Bu, Q. / Li, H. / Zhao, Y. / Jiang, L. / Qin, F. / Dai, Y. / Zhang, N. / Qin, M. / Kuang, W. / Zhao, Y. / Jokitalo, E. / Vattulainen, I. / Kajander, T. / Zhao, H. / Cen, X.
History
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: 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

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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
B: CBY1-interacting BAR domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)51,1262
Polymers51,1262
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Asymmetric unit contains the biological relevant oligomer (dimer).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-46 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.044, 54.915, 57.505
Angle α, β, γ (deg.)88.32, 67.40, 63.86
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25563.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIBAR1, FAM92A, FAM92A1 / Production host: Escherichia coli (E. coli) / References: UniProt: A1XBS5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Citrate, 6% tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.89998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89998 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 30902 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11
Reflection shellResolution: 2.03→2.08 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2177 / CC1/2: 0.731 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
autoPROCdata processing
Arcimboldo1.0.16phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.03→28.92 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1567 5.08 %
Rwork0.1848 --
obs0.1872 30855 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 0 156 3381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.155
X-RAY DIFFRACTIONf_dihedral_angle_d16.7451229
X-RAY DIFFRACTIONf_chiral_restr0.057511
X-RAY DIFFRACTIONf_plane_restr0.013573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.090.32361420.2622554X-RAY DIFFRACTION94
2.09-2.170.30681510.24182649X-RAY DIFFRACTION97
2.17-2.260.35671380.2252640X-RAY DIFFRACTION97
2.26-2.360.29031210.21882689X-RAY DIFFRACTION97
2.36-2.480.24631290.19322680X-RAY DIFFRACTION97
2.48-2.640.21731330.19212683X-RAY DIFFRACTION98
2.64-2.840.22191640.17952669X-RAY DIFFRACTION98
2.84-3.130.26761560.19062686X-RAY DIFFRACTION98
3.13-3.580.24671500.18632686X-RAY DIFFRACTION99
3.58-4.510.19081420.15542692X-RAY DIFFRACTION98
4.51-28.920.1851410.17072660X-RAY DIFFRACTION97
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)
11.2197-0.18231.21343.4309-4.27727.32180.2122-0.1339-0.0945-0.35690.00610.14910.6692-0.0476-0.17460.46440.0352-0.07390.262-0.01540.195677.187728.282227.8585
20.0633-0.25730.58881.2309-2.63895.9376-0.0820.49550.3184-0.71070.2164-0.120.8277-0.1066-0.02320.7398-0.0575-0.00870.63380.14810.380177.059140.0819-3.9306
30.65990.0756-0.46632.3174-3.80155.644-0.1049-0.094-0.04610.07070.33150.0563-0.2724-0.8109-0.15240.37430.0052-0.08550.35640.03810.22870.852742.623712.2849
40.7927-0.38530.83810.9919-1.21812.4070.01880.06220.008-0.0422-0.2108-0.19920.01720.25520.05390.40770.0101-0.08010.33380.04920.251884.522328.291341.4081
50.0385-0.21310.22030.3582-0.60460.5238-0.31150.06730.3130.0501-0.1864-0.5618-0.14080.19340.22540.50880.0947-0.06680.38920.1440.4274100.15392.196569.2934
60.0182-0.68190.74171.3194-1.84862.3013-0.3211-0.17960.14810.50240.0814-0.3813-0.5-0.2656-0.02380.53350.0234-0.12580.41320.07010.307983.49921.056258.3415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 213 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 95 )
5X-RAY DIFFRACTION5chain 'B' and (resid 96 through 140 )
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 213 )

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