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- PDB-7fgn: The crystal structure of the FAF1 UBL1 -

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Basic information

Entry
Database: PDB / ID: 7fgn
TitleThe crystal structure of the FAF1 UBL1
ComponentsFAS-associated factor 1
KeywordsCHAPERONE
Function / homology
Function and homology information


ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / ERAD pathway / NF-kappaB binding / regulation of cell adhesion ...ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / ERAD pathway / NF-kappaB binding / regulation of cell adhesion / heat shock protein binding / positive regulation of DNA replication / ubiquitin binding / positive regulation of protein-containing complex assembly / positive regulation of protein catabolic process / nuclear envelope / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of apoptotic process / protein domain specific binding / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. ...: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.199 Å
AuthorsKim, E.E. / ParK, J.K. / Shin, S.C.
CitationJournal: J Mol Cell Biol / Year: 2022
Title: The complex of Fas-associated factor 1 with Hsp70 stabilizes the adherens junction integrity by suppressing RhoA activation
Authors: Song, S. / Park, J.K. / Shin, S.C. / Lee, J.J. / Hong, S.K. / Song, I.K. / Kim, B. / Song, E.J. / Lee, K.J. / Kim, E.E.
History
DepositionJul 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 9, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)8,9091
Polymers8,9091
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4890 Å2
Unit cell
Length a, b, c (Å)65.028, 65.028, 33.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-316-

HOH

31A-317-

HOH

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Components

#1: Protein FAS-associated factor 1 / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 8909.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1, UBXD12, UBXN3A, CGI-03 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50 mM Bis-Tris pH 6.5 50 mM (NH4)2SO4 30 % v/v pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.199→50 Å / Num. obs: 23078 / % possible obs: 99.7 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.05 / Χ2: 0.951 / Net I/σ(I): 19.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.2-1.249.30.21622560.567199.6
1.24-1.299.80.17922610.594199.9
1.29-1.3510.40.15722630.634199.8
1.35-1.4211.20.12222590.665199.6
1.42-1.51120.09622910.733199.9
1.51-1.63130.07822930.827199.7
1.63-1.7913.60.06422950.9671100
1.79-2.0514.20.05423141.256199.9
2.05-2.5914.60.04723741.377199.9
2.59-1013.60.04124721.362198.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.199→29.825 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1184 5.14 %
Rwork0.2221 21868 -
obs0.2232 23052 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.95 Å2 / Biso mean: 14.6011 Å2 / Biso min: 3.9 Å2
Refinement stepCycle: final / Resolution: 1.199→29.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 118 719
Biso mean---20.49 -
Num. residues----75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.199-1.25330.26491260.2612265999
1.2533-1.31940.27331460.25662671100
1.3194-1.40210.26351590.24682694100
1.4021-1.51030.26441760.23692678100
1.5103-1.66230.23091460.22442710100
1.6623-1.90280.23541530.21732745100
1.9028-2.39720.26461410.21832791100
2.3972-100.22771370.2098292099

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