[English] 日本語
Yorodumi
- PDB-7xyu: Crystal structure of ZER1 bound to TFLH degron -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xyu
TitleCrystal structure of ZER1 bound to TFLH degron
ComponentsProtein zer-1 homolog
KeywordsLIGASE / E3
Function / homology
Function and homology information


Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process
Similarity search - Function
: / Protein zer-1 homolog-like, C-terminal domain / : / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Leucine-rich repeat domain superfamily / Armadillo-like helical / Alpha Horseshoe ...: / Protein zer-1 homolog-like, C-terminal domain / : / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Leucine-rich repeat domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein zer-1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDong, C. / Yan, X. / Li, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900865 China
National Natural Science Foundation of China (NSFC)32071193 China
National Natural Science Foundation of China (NSFC)81874039 China
CitationJournal: Nat Commun / Year: 2022
Title: CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation.
Authors: Li, Y. / Zhao, Y. / Yan, X. / Ye, C. / Weirich, S. / Zhang, B. / Wang, X. / Song, L. / Jiang, C. / Jeltsch, A. / Dong, C. / Mi, W.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein zer-1 homolog
A: Protein zer-1 homolog
C: Protein zer-1 homolog
D: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)116,7314
Polymers116,7314
Non-polymers00
Water41423
1
B: Protein zer-1 homolog
D: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)58,3662
Polymers58,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-12 kcal/mol
Surface area20210 Å2
MethodPISA
2
A: Protein zer-1 homolog
C: Protein zer-1 homolog


Theoretical massNumber of molelcules
Total (without water)58,3662
Polymers58,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-12 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.779, 67.779, 418.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))
21(chain B and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))
31(chain C and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))AB516 - 6211 - 106
12ALAALAGLYGLY(chain A and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))AB625 - 650110 - 135
13PROPROASNASN(chain A and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))AB654 - 756139 - 241
21THRTHRLEULEU(chain B and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))BA516 - 6211 - 106
22ALAALAGLYGLY(chain B and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))BA625 - 650110 - 135
23PROPROASNASN(chain B and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))BA654 - 756139 - 241
31THRTHRLEULEU(chain C and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))CC516 - 6211 - 106
32ALAALAGLYGLY(chain C and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))CC625 - 650110 - 135
33PROPROASNASN(chain C and (resid 516 through 621 or resid 625 through 650 or resid 654 through 756))CC654 - 756139 - 241
41THRTHRASNASNchain DDD516 - 7561 - 241

-
Components

#1: Protein
Protein zer-1 homolog / Hzyg / Zyg-11 homolog B-like protein / Zyg11b-like protein


Mass: 29182.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZER1, C9orf60, ZYG, ZYG11BL / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z7L7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.16 M Sodium Malonate pH 7.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.7→48.05 Å / Num. obs: 29654 / % possible obs: 99.94 % / Redundancy: 2 % / Rmerge(I) obs: 0.01634 / Net I/σ(I): 33.3
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.1203 / Num. unique obs: 2990

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EP3

7ep3


Resolution: 2.7→44.9 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3037 1397 4.71 %
Rwork0.2482 28251 -
obs0.2508 29648 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.14 Å2 / Biso mean: 84.6125 Å2 / Biso min: 41.04 Å2
Refinement stepCycle: final / Resolution: 2.7→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7827 0 0 23 7850
Biso mean---73.78 -
Num. residues----963
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2828X-RAY DIFFRACTION8.555TORSIONAL
12B2828X-RAY DIFFRACTION8.555TORSIONAL
13C2828X-RAY DIFFRACTION8.555TORSIONAL
14D2828X-RAY DIFFRACTION8.555TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.80.40591300.336928622992
2.8-2.910.42951430.338427882931
2.91-3.040.40281340.313428392973
3.04-3.20.33311440.296528312975
3.2-3.40.36161420.284128172959
3.4-3.660.31251370.280328002937
3.66-4.030.29191440.251428392983
4.03-4.620.2731280.222328302958
4.62-5.810.26881460.240128182964
5.81-44.90.27981490.228272976
Refinement TLS params.Method: refined / Origin x: 20.2893 Å / Origin y: -53.0466 Å / Origin z: -13.7777 Å
111213212223313233
T0.2172 Å20.1849 Å20.0221 Å2-0.9114 Å20.0096 Å2--0.4533 Å2
L0.3535 °20.4192 °2-0.4637 °2-2.3235 °2-1.3966 °2--1.7536 °2
S0.0675 Å °-0.0416 Å °-0.0543 Å °-0.2526 Å °-0.4222 Å °-0.206 Å °0.1553 Å °0.3122 Å °0.1282 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB516 - 759
2X-RAY DIFFRACTION1allA516 - 760
3X-RAY DIFFRACTION1allC516 - 757
4X-RAY DIFFRACTION1allD516 - 756
5X-RAY DIFFRACTION1allS1 - 23

+
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