[English] 日本語
Yorodumi
- PDB-5x4l: Crystal structure of the UBX domain of human UBXD7 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x4l
TitleCrystal structure of the UBX domain of human UBXD7 in complex with p97 N domain
Components
  • Transitional endoplasmic reticulum ATPase
  • UBX domain-containing protein 7
KeywordsHYDROLASE/PROTEIN BINDING / UBXD7 / p97 / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


: / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control ...: / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / : / aggresome assembly / mitotic spindle disassembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / stress granule disassembly / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / ATP metabolic process / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / Attachment and Entry / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / establishment of protein localization / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / ABC-family proteins mediated transport / autophagy / positive regulation of protein catabolic process / cytoplasmic stress granule / Aggrephagy / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / protein-containing complex
Similarity search - Function
UBX domain-containing protein 2/7 / UAS / : / UAS / Thioredoxin-like / : / UBA-like domain / Domain present in ubiquitin-regulatory proteins / Vcp-like ATPase; Chain A, domain 2 - #10 / UBX domain ...UBX domain-containing protein 2/7 / UAS / : / UAS / Thioredoxin-like / : / UBA-like domain / Domain present in ubiquitin-regulatory proteins / Vcp-like ATPase; Chain A, domain 2 - #10 / UBX domain / UBX domain / UBX domain profile. / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / 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 / : / UBA-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
UBX domain-containing protein 7 / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsJiang, T. / Li, Z. / Wang, Y. / Xu, M.
Funding support China, 1items
OrganizationGrant numberCountry
Strategic Priority Research ProgramXDB08010301 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structures of the UBX domain of human UBXD7 and its complex with p97 ATPase
Authors: Li, Z.H. / Wang, Y. / Xu, M. / Jiang, T.
History
DepositionFeb 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: UBX domain-containing protein 7
D: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)59,6934
Polymers59,6934
Non-polymers00
Water3,801211
1
A: Transitional endoplasmic reticulum ATPase
C: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transitional endoplasmic reticulum ATPase
D: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)29,8462
Polymers29,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.046, 84.822, 109.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 20212.734 Da / Num. of mol.: 2 / Fragment: UNP residues 23-196
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, vesicle-fusing ATPase
#2: Protein UBX domain-containing protein 7


Mass: 9633.721 Da / Num. of mol.: 2 / Fragment: UNP residues 410-489 / Mutation: L472M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBXN7, KIAA0794, UBXD7 / Production host: Escherichia coli (E. coli) / References: UniProt: O94888
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M Calcium acetate hydrate pH7.5, 20% v/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.4→45.92 Å / Num. obs: 23521 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Net I/σ(I): 27

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ7

3qq7


Resolution: 2.402→45.92 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1182 5.04 %
Rwork0.185 --
obs0.1874 23453 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 0 211 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094062
X-RAY DIFFRACTIONf_angle_d1.2655484
X-RAY DIFFRACTIONf_dihedral_angle_d15.1941608
X-RAY DIFFRACTIONf_chiral_restr0.048620
X-RAY DIFFRACTIONf_plane_restr0.006717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4022-2.51150.29431380.21052725X-RAY DIFFRACTION99
2.5115-2.64390.2471500.20922734X-RAY DIFFRACTION100
2.6439-2.80950.25951440.2072730X-RAY DIFFRACTION100
2.8095-3.02640.24091470.2082776X-RAY DIFFRACTION100
3.0264-3.33090.2671370.19382771X-RAY DIFFRACTION100
3.3309-3.81260.23311510.18062780X-RAY DIFFRACTION100
3.8126-4.80270.19671560.1512816X-RAY DIFFRACTION100
4.8027-45.9280.23011590.18742939X-RAY DIFFRACTION100

+
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