[English] 日本語
Yorodumi
- PDB-6ccu: Complex between a GID4 fragment and a short peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ccu
TitleComplex between a GID4 fragment and a short peptide
Components
  • Glucose-induced degradation protein 4 homolog
  • Short peptide
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC
Function / homologyVacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / Regulation of pyruvate metabolism / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cytosol / 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: Nat. Chem. Biol. / Year: 2018
Title: Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway.
Authors: Dong, C. / Zhang, H. / Li, L. / Tempel, W. / Loppnau, P. / Min, J.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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: Short peptide


Theoretical massNumber of molelcules
Total (without water)22,2497
Polymers22,2492
Non-polymers05
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.045, 43.669, 99.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 21739.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7
#2: Protein/peptide Short peptide


Mass: 509.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.18 Å3/Da / Density % sol: 37.39 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 0.03M Citric acid

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→43.67 Å / Num. obs: 20007 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Net I/σ(I): 14.7 / Num. measured all: 128263 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.736.51.7886820104410440.6710.7511.9421.199.2
9-43.675.40.0299451760.9990.0140.03349.299.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: early version of model from PDB entry 6CCR

6ccr


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.827 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2359 908 5 %
Rwork0.1909 --
obs0.193 17417 99.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.7 Å2 / Biso mean: 31.715 Å2 / Biso min: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-0 Å2
2--2.02 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 5 47 1411
Biso mean--34.15 34.46 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191417
X-RAY DIFFRACTIONr_bond_other_d0.0020.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9141922
X-RAY DIFFRACTIONr_angle_other_deg0.94632757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69323.94471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.921152
X-RAY DIFFRACTIONr_chiral_restr0.0940.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_mcbond_it1.0571.915673
X-RAY DIFFRACTIONr_mcbond_other1.0571.914672
X-RAY DIFFRACTIONr_mcangle_it1.6732.86837
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 57 -
Rwork0.312 1257 -
all-1314 -
obs--99.85 %
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)
12.9050.14950.50651.5070.43532.8580.0268-0.24480.0732-0.052-0.0330.0441-0.057-0.13660.00620.02070.0084-0.00130.13790.00910.0053-8.1403-9.30812.2368
20.59410.397-1.38947.1877-0.81357.70430.0373-0.09680.03860.2761-0.05720.1892-0.133-0.02060.01990.1494-0.0054-0.00760.1908-0.03180.1285-14.8328-4.264823.8725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 289
2X-RAY DIFFRACTION2B1 - 4

+
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