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- PDB-7fgm: The complex crystals structure of the FAF1 UBL1_L-Hsp70 NBD with ... -

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Basic information

Entry
Database: PDB / ID: 7fgm
TitleThe complex crystals structure of the FAF1 UBL1_L-Hsp70 NBD with ADP and phosphate
Components
  • FAS-associated factor 1
  • Heat shock 70 kDa protein 1A
KeywordsCHAPERONE/INHIBITOR / CHAPERONE-INHIBITOR COMPLEX
Function / homology
Function and homology information


ooplasm / positive regulation of endoribonuclease activity / denatured protein binding / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus ...ooplasm / positive regulation of endoribonuclease activity / denatured protein binding / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / regulation of protein catabolic process / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / NF-kappaB binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / regulation of cell adhesion / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of DNA replication / ubiquitin binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / positive regulation of protein catabolic process / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear envelope / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / blood microparticle / protein stabilization / nuclear speck / ribonucleoprotein complex / cadherin binding / positive regulation of apoptotic process / protein domain specific binding / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space
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 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Heat shock 70 kDa protein 1A / FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, E.E. / ParK, J.K. / Shin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock 70 kDa protein 1A
B: FAS-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0995
Polymers51,5532
Non-polymers5463
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-3 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.335, 103.335, 127.093
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Heat shock 70 kDa protein 1A / Heat shock 70 kDa protein 1 / HSP70-1 / HSP70.1


Mass: 42084.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV8
#2: Protein FAS-associated factor 1 / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 9467.923 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

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Non-polymers , 4 types, 357 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.81 Å3/Da / Density % sol: 67.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200 mM Imidazole-malate pH 8.5 12 % PEG 10,000

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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 210 / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40339 / % possible obs: 99.9 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.098 / Χ2: 0.776 / Net I/σ(I): 7 / Num. measured all: 656487
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.2813.10.32239570.46199.9
2.28-2.3713.70.29139810.4741100
2.37-2.4814.10.25839960.495199.9
2.48-2.6114.80.22439960.5261100
2.61-2.7715.50.17840020.5611100
2.77-2.9916.50.14440200.6161100
2.99-3.2917.70.10340100.689199.9
3.29-3.7618.90.07340460.8621100
3.76-4.7419.30.07540951.7441100
4.74-5018.90.04742360.888199.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3X

1s3x


Resolution: 2.2→30.763 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 2010 4.99 %
Rwork0.1745 38304 -
obs0.176 40314 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.22 Å2 / Biso mean: 24.6049 Å2 / Biso min: 9.51 Å2
Refinement stepCycle: final / Resolution: 2.2→30.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 33 354 3990
Biso mean--20.69 29.44 -
Num. residues----460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2003-2.25530.23771390.19552676
2.2553-2.31630.24341440.18732716
2.3163-2.38440.22491400.18762688
2.3844-2.46130.24391460.18562715
2.4613-2.54920.20661410.17592715
2.5492-2.65130.21791430.17542720
2.6513-2.77180.21281430.17232700
2.7718-2.91790.19581420.17632710
2.9179-3.10050.23151410.1892738
3.1005-3.33970.19981470.18112742
3.3397-3.67530.22931440.17872724
3.6753-4.20590.20581470.16232756
4.2059-5.29460.16051440.1532798
5.2946-30.7630.1731490.17162906

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