[English] 日本語
Yorodumi
- PDB-7w3n: Crystal structure of Ufm1 fused to UFBP1 UFIM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w3n
TitleCrystal structure of Ufm1 fused to UFBP1 UFIM
ComponentsUFBP1 peptide,Ubiquitin-fold modifier 1
KeywordsLIGASE / ER-phagy / Ufm1 / E3 ligase / Ufmylation
Function / homology
Function and homology information


positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of intracellular estrogen receptor signaling pathway ...positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of intracellular estrogen receptor signaling pathway / positive regulation of proteasomal protein catabolic process / cartilage development / reticulophagy / negative regulation of protein import into nucleus / ubiquitin-like protein ligase binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RHOA GTPase cycle / response to endoplasmic reticulum stress / regulation of protein stability / brain development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of cell migration / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
DDRGK domain containing protein / DDRGK domain / DDRGK / Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Ubiquitin-fold modifier 1 / DDRGK domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNoda, N.N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Science and TechnologyJPMJCR20E3 Japan
CitationJournal: Nat Commun / Year: 2022
Title: The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3.
Authors: Ishimura, R. / El-Gowily, A.H. / Noshiro, D. / Komatsu-Hirota, S. / Ono, Y. / Shindo, M. / Hatta, T. / Abe, M. / Uemura, T. / Lee-Okada, H.C. / Mohamed, T.M. / Yokomizo, T. / Ueno, T. / ...Authors: Ishimura, R. / El-Gowily, A.H. / Noshiro, D. / Komatsu-Hirota, S. / Ono, Y. / Shindo, M. / Hatta, T. / Abe, M. / Uemura, T. / Lee-Okada, H.C. / Mohamed, T.M. / Yokomizo, T. / Ueno, T. / Sakimura, K. / Natsume, T. / Sorimachi, H. / Inada, T. / Waguri, S. / Noda, N.N. / Komatsu, M.
History
DepositionNov 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _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: UFBP1 peptide,Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)10,0831
Polymers10,0831
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.411, 53.411, 82.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein UFBP1 peptide,Ubiquitin-fold modifier 1 / Dashurin / UFM1-binding and PCI domain-containing protein 1


Mass: 10082.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ufm1 fused to UFBP1 / Source: (gene. exp.) Homo sapiens (human) / Gene: DDRGK1, C20orf116, UFBP1, UFM1, C13orf20, BM-002 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96HY6, UniProt: P61960
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 28% 2-propanol, 3% PEG 200, 0.1M MES at pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→27.4144 Å / Num. obs: 18508 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 34.9
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.478 / Num. unique obs: 1850

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKH

5hkh


Resolution: 1.6→27.4144 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 991 5.37 %
Rwork0.181 --
obs0.182 18456 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→27.4144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms680 0 0 151 831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015695
X-RAY DIFFRACTIONf_angle_d1.426945
X-RAY DIFFRACTIONf_dihedral_angle_d14.033425
X-RAY DIFFRACTIONf_chiral_restr0.099112
X-RAY DIFFRACTIONf_plane_restr0.009122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.68440.23051330.21222452X-RAY DIFFRACTION100
1.6844-1.78990.23891460.20642456X-RAY DIFFRACTION100
1.7899-1.92810.2231450.19252445X-RAY DIFFRACTION100
1.9281-2.12210.21031250.16722480X-RAY DIFFRACTION100
2.1221-2.4290.18981460.17352493X-RAY DIFFRACTION100
2.429-3.05960.19891500.19362497X-RAY DIFFRACTION100
3.0596-27.41440.19091460.17372642X-RAY DIFFRACTION100
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)
14.7893-3.8524-4.23024.97892.87195.20440.0213-0.6706-0.26850.0562-0.11950.0736-0.14020.44050.07510.1536-0.0025-0.01750.3402-0.00470.1268-48.596128.4832-8.9017
21.90221.22861.35111.8556-0.28982.10930.14140.088-0.22620.0727-0.1399-0.28450.00680.3113-0.03660.103-0.01120.00250.21140.02660.1492-16.559719.0755-9.7039
34.43330.06440.55083.9912-1.25594.9086-0.06220.2858-0.4380.0440.12350.07890.42910.1571-0.06060.12890.01350.01010.1474-0.02430.1176-25.64813.1677-12.1176
42.0241-0.2058-0.22574.22552.42053.9588-0.172-0.1921-0.67240.5379-0.09670.04460.91720.70460.16720.35670.11790.09510.25370.03880.3138-18.88779.0435-5.2817
57.48490.190.67052.0818-1.8767.62420.0066-0.12370.34980.3510.04510.1264-0.37820.09120.00140.19680.01270.02030.1871-0.00260.1519-27.26316.51620.4426
60.7720.93631.47725.97413.03688.3592-0.5377-0.75120.7320.48020.35490.5375-0.4163-0.737-0.01860.18550.12560.04950.3582-0.01290.1963-31.862921.588-3.6855
73.0764-4.30231.969.42750.5636.9918-0.2023-0.3729-0.37280.53880.0771-0.01070.25430.54280.10950.20850.00520.04450.28510.05270.2148-19.427316.2924-3.5682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -8 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 17 )
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 51 )
5X-RAY DIFFRACTION5chain 'A' and (resid 52 through 62 )
6X-RAY DIFFRACTION6chain 'A' and (resid 63 through 70 )
7X-RAY DIFFRACTION7chain 'A' and (resid 71 through 79 )

+
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://pdbjlvh1.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