[English] 日本語
Yorodumi
- PDB-6wzx: GID4 in complex with IGLWKS peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wzx
TitleGID4 in complex with IGLWKS peptide
Components
  • Glucose-induced degradation protein 4 homolog
  • ILE-GLY-LEU-TRP-LYS peptide
KeywordsPEPTIDE BINDING PROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homologyVacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Recognition of nonproline N-terminal residues by the Pro/N-degron pathway.
Authors: Dong, C. / Chen, S.J. / Melnykov, A. / Weirich, S. / Sun, K. / Jeltsch, A. / Varshavsky, A. / Min, J.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Glucose-induced degradation protein 4 homolog
B: Glucose-induced degradation protein 4 homolog
C: ILE-GLY-LEU-TRP-LYS peptide
D: ILE-GLY-LEU-TRP-LYS peptide


Theoretical massNumber of molelcules
Total (without water)40,61720
Polymers40,6174
Non-polymers016
Water1,00956
1
A: Glucose-induced degradation protein 4 homolog
C: ILE-GLY-LEU-TRP-LYS peptide


Theoretical massNumber of molelcules
Total (without water)20,30911
Polymers20,3092
Non-polymers09
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area8380 Å2
MethodPISA
2
B: Glucose-induced degradation protein 4 homolog
D: ILE-GLY-LEU-TRP-LYS peptide


Theoretical massNumber of molelcules
Total (without water)20,3099
Polymers20,3092
Non-polymers07
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-4 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.122, 51.190, 55.447
Angle α, β, γ (deg.)68.228, 89.119, 69.079
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog


Mass: 19604.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V3R / References: UniProt: Q8IVV7
#2: Protein/peptide ILE-GLY-LEU-TRP-LYS peptide


Mass: 703.850 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 16 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.96 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 3350 and 8% (v/v) Tacsimate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→51.02 Å / Num. obs: 40219 / % possible obs: 91.4 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.03 / Rrim(I) all: 0.044 / Net I/σ(I): 11.6 / Num. measured all: 81854 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.67-1.71.80.713363819720.5880.6490.9670.988.5
8.99-51.022.10.0245832760.9980.0210.03236.197.2

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CCR

6ccr


Resolution: 1.75→51.005 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.557 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2266 1737 4.95 %
Rwork0.1926 33356 -
all0.194 --
obs-35093 91.722 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.583 Å2-0.548 Å2-0.604 Å2
2---0.191 Å20.065 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.75→51.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 16 56 2797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132834
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182346
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6383849
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5765406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9485342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91122.549153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44115406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
X-RAY DIFFRACTIONr_nbd_refined0.2140.2479
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22103
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21322
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.27
X-RAY DIFFRACTIONr_nbd_other0.1820.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.050.210
X-RAY DIFFRACTIONr_mcbond_it1.3232.1491363
X-RAY DIFFRACTIONr_mcbond_other1.3222.151364
X-RAY DIFFRACTIONr_mcangle_it2.0363.2141699
X-RAY DIFFRACTIONr_mcangle_other2.0363.2141699
X-RAY DIFFRACTIONr_scbond_it1.5442.2681471
X-RAY DIFFRACTIONr_scbond_other1.5442.2691472
X-RAY DIFFRACTIONr_scangle_it2.4173.3512147
X-RAY DIFFRACTIONr_scangle_other2.4163.3522148
X-RAY DIFFRACTIONr_lrange_it4.20523.8873116
X-RAY DIFFRACTIONr_lrange_other4.19423.8083108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.3411170.30624840.30828250.7640.76492.07080.29
1.795-1.8450.3181210.29324060.29427500.8040.81291.89090.269
1.845-1.8980.2661300.25623440.25626880.8760.87592.03870.226
1.898-1.9560.2781020.23122710.23325900.8880.90791.62160.202
1.956-2.020.258990.20121830.20425370.9050.92789.94880.177
2.02-2.0910.2411140.19820630.224290.9150.92989.62540.175
2.091-2.170.2591170.20620790.20823430.9010.92793.7260.188
2.17-2.2580.2141140.219890.20122590.9380.93593.09430.184
2.258-2.3590.226990.19519520.19622130.9290.94292.67960.181
2.359-2.4730.272980.19617990.220470.9070.93392.67220.185
2.473-2.6070.252820.19416970.19720030.9260.93988.81680.188
2.607-2.7650.234880.19716030.19918600.9360.94190.9140.193
2.765-2.9550.203860.19215450.19217380.9430.94593.84350.194
2.955-3.1910.217770.19614440.19716400.930.93492.74390.207
3.191-3.4940.24640.19113010.19415060.9320.94390.63750.205
3.494-3.9040.2590.17711210.17813690.9490.95686.19430.198
3.904-4.5030.176710.14210660.14411970.960.9794.98750.17
4.503-5.5050.178400.159360.15210270.9640.97195.03410.187
5.505-7.740.255400.2126510.2147840.9370.9588.13780.268
7.74-51.0050.268190.2434090.2444390.9460.94697.49430.3
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)
13.07820.53920.58292.8366-0.16972.81960.033-0.25640.03130.201-0.1764-0.205-0.07840.03820.14330.1108-0.0469-0.11450.04120.04440.1207-22.8064-10.173114.6152
22.99720.12490.10463.25690.05872.3529-0.0480.03380.068-0.34730.03680.0941-0.0251-0.04980.01120.1062-0.0312-0.07760.0140.02640.0711-2.896-29.56870.2264
30.5671-0.0301-1.05260.11470.12852.02650.2346-0.0520.11060.1126-0.0742-0.0466-0.3160.0929-0.16040.2893-0.0078-0.03260.29850.04030.2637-16.0019-2.948724.7877
48.52120.161-0.65012.4947-0.18510.6801-0.10160.338-0.0769-0.19450.1872-0.29440.01180.1055-0.08570.1816-0.02690.0290.1672-0.02370.12025.8308-36.7369-10.7267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA125 - 289
2X-RAY DIFFRACTION2ALLB125 - 289
3X-RAY DIFFRACTION3ALLC1 - 5
4X-RAY DIFFRACTION4ALLD1 - 6

+
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