[English] 日本語
Yorodumi
- PDB-6ley: Structure of Sil1G bound FEM1C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ley
TitleStructure of Sil1G bound FEM1C
ComponentsProtein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1
KeywordsPROTEIN BINDING / ubiquitination E3 ligase
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / cotranslational protein targeting to membrane / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ubiquitin ligase complex / intracellular protein transport / unfolded protein binding / protein folding / Neddylation ...adenyl-nucleotide exchange factor activity / cotranslational protein targeting to membrane / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ubiquitin ligase complex / intracellular protein transport / unfolded protein binding / protein folding / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular space / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Nucleotide exchange factor Fes1 / : / Nucleotide exchange factor Fes1 / : / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...Nucleotide exchange factor Fes1 / : / Nucleotide exchange factor Fes1 / : / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Protein fem-1 homolog C / Nucleotide exchange factor SIL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChen, X. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase.
Authors: Chen, X. / Liao, S. / Makaros, Y. / Guo, Q. / Zhu, Z. / Krizelman, R. / Dahan, K. / Tu, X. / Yao, X. / Koren, I. / Xu, C.
History
DepositionNov 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1
B: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1


Theoretical massNumber of molelcules
Total (without water)91,2302
Polymers91,2302
Non-polymers00
Water2,900161
1
A: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1


Theoretical massNumber of molelcules
Total (without water)45,6151
Polymers45,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1


Theoretical massNumber of molelcules
Total (without water)45,6151
Polymers45,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.497, 95.973, 147.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein fem-1 homolog C,Peptide from Nucleotide exchange factor SIL1 / FEM1c / FEM1-gamma / BiP-associated protein / BAP


Mass: 45615.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FEM1C fused with SIL1G peptide, linked with linker residues GGGSGGGSGGGSGGGS.
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785, SIL1, UNQ545/PRO836 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JP0, UniProt: Q9H173
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 4.01 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 6.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→147.48 Å / Num. obs: 54296 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 12.9
Reflection shellResolution: 2.39→2.45 Å / Num. unique obs: 5321 / CC1/2: 0.826

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBF

6lbf


Resolution: 2.39→80.44 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2767 5.1 %
Rwork0.1976 51529 -
obs0.1992 54296 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.83 Å2 / Biso mean: 73.4135 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.39→80.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5587 0 0 161 5748
Biso mean---58.82 -
Num. residues----759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.39-2.43080.30781380.2713250499
2.4308-2.4750.30241330.25942546100
2.475-2.52260.27311220.2562564100
2.5226-2.57410.29581690.24572504100
2.5741-2.630.31271300.24212542100
2.63-2.69120.24041100.22372557100
2.6912-2.75850.27881460.22362552100
2.7585-2.83310.23921310.22052575100
2.8331-2.91650.2591500.22482519100
2.9165-3.01060.271190.23362600100
3.0106-3.11820.25331530.22682523100
3.1182-3.24310.26661510.22312562100
3.2431-3.39070.29281510.22782572100
3.3907-3.56950.20531310.20152591100
3.5695-3.79310.22521320.17552582100
3.7931-4.08590.20861380.16812597100
4.0859-4.49710.1751310.15562615100
4.4971-5.14770.21261410.17382620100
5.1477-6.48520.21351290.20432672100
6.4852-80.440.20871620.1907273299
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)
11.34370.7433-0.04122.2006-0.0671.24530.03210.2461-0.0081-0.2212-0.0849-0.22290.050.03720.0650.29450.09230.02880.4139-0.00770.373613.9770.14932.948
22.23530.4808-0.48231.3516-0.52491.0793-0.0637-0.29240.10820.3794-0.0014-0.0914-0.0179-0.01590.06130.6160.05940.04170.3817-0.03350.394727.046-10.6644.246
35.3550.8913-4.76440.1864-0.79944.24-0.79790.6015-0.6408-0.891-0.4659-0.01970.9187-0.11961.08481.0150.07750.03221.1560.07380.979716.0524.5927.223
41.59130.31362.81480.12760.5574.9792-0.0847-0.4136-0.19120.0006-0.32430.19270.0159-0.34730.36991.5388-0.186-0.20240.9015-0.00020.853133.539-8.3939.941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:390 )A2 - 390
2X-RAY DIFFRACTION2( CHAIN B AND RESID 5:390 )B5 - 390
3X-RAY DIFFRACTION3( CHAIN A AND RESID 411:417 )A411 - 417
4X-RAY DIFFRACTION4( CHAIN B AND RESID 412:417 )B412 - 417

+
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