[English] 日本語
Yorodumi
- PDB-3qc8: Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qc8
TitleCrystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change
Components
  • FAS-associated factor 1
  • Transitional endoplasmic reticulum ATPase
KeywordsPROTEIN BINDING / UBX domain / FAF1 / p97 / VCP
Function / homology
Function and homology information


Fas signaling pathway / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / protein kinase regulator activity / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex ...Fas signaling pathway / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / protein kinase regulator activity / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / deubiquitinase activator activity / positive regulation of oxidative phosphorylation / cytoplasm protein quality control / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / regulation of protein catabolic process / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / NAD+ metabolic process / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / ubiquitin-specific protease binding / regulation of synapse organization / polyubiquitin modification-dependent protein binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / intracellular membrane-bounded organelle / autophagosome maturation / MHC class I protein binding / HSF1 activation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / mitophagy / NF-kappaB binding / interstrand cross-link repair / ATP metabolic process / proteasome complex / protein unfolding / endoplasmic reticulum unfolded protein response / ribosome-associated ubiquitin-dependent protein catabolic process / Attachment and Entry / ERAD pathway / heat shock protein binding / Protein methylation / translesion synthesis / negative regulation of smoothened signaling pathway / positive regulation of DNA replication / viral genome replication / negative regulation of protein localization to chromatin / macroautophagy / negative regulation of canonical NF-kappaB signal transduction / rescue of stalled cytosolic ribosome / lipid droplet / Josephin domain DUBs / autophagy / ubiquitin binding / establishment of protein localization / proteasomal protein catabolic process / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein-containing complex assembly / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / Hh mutants are degraded by ERAD / Dengue Virus Genome Translation and Replication / Translesion Synthesis by POLH / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / ABC-family protein mediated transport / cytoplasmic stress granule / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / double-strand break repair / Aggrephagy / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / azurophil granule lumen / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / KEAP1-NFE2L2 pathway / nuclear envelope / site of double-strand break / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / secretory granule lumen / protein phosphatase binding / ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry
Similarity search - Function
FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Vcp-like ATPase; Chain A, domain 2 - #10 / Domain present in ubiquitin-regulatory proteins / UBX domain ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Vcp-like ATPase; Chain A, domain 2 - #10 / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / AAA ATPase, CDC48 family / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48), N-terminal domain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48) domain 2 / Cell division protein 48 (CDC48), domain 2 / : / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, K.H. / Kang, W. / Suh, S.W. / Yang, J.K.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of FAF1 UBX domain in complex with p97/VCP N domain reveals a conformational change in the conserved FcisP touch-turn motif of UBX domain
Authors: Kim, K.H. / Kang, W. / Suh, S.W. / Yang, J.K.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers30,1222
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-4 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.070, 72.740, 130.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 20286.295 Da / Num. of mol.: 1 / Fragment: N domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072
#2: Protein FAS-associated factor 1 / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 9835.250 Da / Num. of mol.: 1 / Fragment: UBX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25%(w/v) PEG3350, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 14425 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.32 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.969 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24978 724 5 %RANDOM
Rwork0.21645 ---
all0.21813 14425 --
obs0.21813 13670 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 0 130 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222057
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9942780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9485248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06923.33396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691521
X-RAY DIFFRACTIONr_chiral_restr0.1180.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211542
X-RAY DIFFRACTIONr_mcbond_it1.481.51255
X-RAY DIFFRACTIONr_mcangle_it2.59622054
X-RAY DIFFRACTIONr_scbond_it3.53802
X-RAY DIFFRACTIONr_scangle_it5.4824.5726
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 49 -
Rwork0.353 979 -
obs--100 %

+
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