[English] 日本語
Yorodumi
- PDB-5l8e: Structure of UAF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l8e
TitleStructure of UAF1
Components
  • Unknown
  • WD repeat-containing protein 48
KeywordsSTRUCTURAL PROTEIN / WDR48 Activates USP1/12/46 B propellar
Function / homology
Function and homology information


regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / homeostasis of number of cells / embryonic organ development / single fertilization / positive regulation of double-strand break repair via homologous recombination ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / homeostasis of number of cells / embryonic organ development / single fertilization / positive regulation of double-strand break repair via homologous recombination / ubiquitin binding / positive regulation of epithelial cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / multicellular organism growth / late endosome / single-stranded DNA binding / double-stranded DNA binding / spermatogenesis / lysosome / Ub-specific processing proteases / intracellular membrane-bounded organelle / DNA damage response / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
WDR48/Bun107 / : / Domain of unknown function (DUF3337) / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...WDR48/Bun107 / : / Domain of unknown function (DUF3337) / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDharadhar, S. / Sixma, T.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
KWFNKI-2014-6858 Netherlands
KWFNKI-2008-4014 Netherlands
European Research Council249997 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2016
Title: A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme.
Authors: Dharadhar, S. / Clerici, M. / van Dijk, W.J. / Fish, A. / Sixma, T.K.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD repeat-containing protein 48
B: WD repeat-containing protein 48
C: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,12317
Polymers130,8333
Non-polymers1,28914
Water5,585310
1
A: WD repeat-containing protein 48
C: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2839
Polymers65,6382
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8398
Polymers65,1951
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.303, 131.601, 148.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein WD repeat-containing protein 48 / USP1-associated factor 1 / WD repeat endosomal protein / p80


Mass: 65194.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TAF3
#2: Protein/peptide Unknown


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350, 200mM Tri-Sodium Citrate, Bis-Tris Propane Cryo -30% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91997 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91997 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 64580 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYH

1vyh


Resolution: 2.3→49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.24 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22426 3201 5 %RANDOM
Rwork0.18539 ---
obs0.18731 61324 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 58.297 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å2-0 Å2
2---2.38 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8169 0 84 310 8563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198427
X-RAY DIFFRACTIONr_bond_other_d0.0020.028120
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.95111409
X-RAY DIFFRACTIONr_angle_other_deg0.849318667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42151036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23724.076368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.596151462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6131556
X-RAY DIFFRACTIONr_chiral_restr0.070.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021911
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4785.7174156
X-RAY DIFFRACTIONr_mcbond_other2.4785.7164155
X-RAY DIFFRACTIONr_mcangle_it4.1698.5545185
X-RAY DIFFRACTIONr_mcangle_other4.1698.5555186
X-RAY DIFFRACTIONr_scbond_it2.2945.9824271
X-RAY DIFFRACTIONr_scbond_other2.2935.9824272
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8168.8496224
X-RAY DIFFRACTIONr_long_range_B_refined6.25664.3559029
X-RAY DIFFRACTIONr_long_range_B_other6.25664.3619030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 226 -
Rwork0.309 4316 -
obs--96.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.96683.8591-4.45995.0801-5.83956.7291-0.1824-0.2333-0.3085-0.3233-0.2695-0.3640.33380.33350.45190.23510.1529-0.19010.2556-0.17810.285635.223210.214771.4706
200000000000000-00.0162000.016200.0162000
300000000000000-00.0162000.016200.0162000
400000000000000-00.0162000.016200.0162000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C25 - 360
2X-RAY DIFFRACTION2C12 - 24
3X-RAY DIFFRACTION2C361 - 560
4X-RAY DIFFRACTION3D25 - 360
5X-RAY DIFFRACTION4D12 - 24
6X-RAY DIFFRACTION4D361 - 560

+
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