[English] 日本語
Yorodumi
- PDB-7fgm: The complex crystals structure of the FAF1 UBL1_L-Hsp70 NBD with ... -

+
Open data


ID or keywords:

Loading...

-
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


Fas signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / : / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity ...Fas signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / : / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / protein kinase regulator activity / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / regulation of protein catabolic process / mRNA catabolic process / : / regulation of protein ubiquitination / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / NF-kappaB binding / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / regulation of cell adhesion / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / transcription regulator inhibitor activity / heat shock protein binding / ERAD pathway / inclusion body / negative regulation of protein ubiquitination / negative regulation of canonical NF-kappaB signal transduction / protein folding chaperone / centriole / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of DNA replication / ubiquitin binding / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / negative regulation of cell growth / G protein-coupled receptor binding / PKR-mediated signaling / histone deacetylase binding / disordered domain specific binding / positive regulation of protein catabolic process / transcription corepressor activity / unfolded protein binding / nuclear envelope / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / virus receptor activity / protein refolding / cellular response to oxidative stress / blood microparticle / vesicle / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / nuclear speck / positive regulation of apoptotic process / cadherin binding / receptor ligand activity / ribonucleoprotein complex / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / focal adhesion / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / centrosome / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space
Similarity search - Function
FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / ATPase, nucleotide binding domain / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more