[English] 日本語
Yorodumi
- PDB-6awl: Crystal structure of human Coq9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6awl
TitleCrystal structure of human Coq9
ComponentsUbiquinone biosynthesis protein COQ9, mitochondrial
KeywordsBIOSYNTHETIC PROTEIN / TetR family / Coenzyme Q biosynthesis / lipid binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Mitochondrial Protein Partnership / MPP
Function / homology
Function and homology information


Ubiquinol biosynthesis / ubiquinone biosynthesis complex / ubiquinone biosynthetic process / mitochondrial electron transport, NADH to ubiquinone / mitochondrial inner membrane / lipid binding / protein homodimerization activity / mitochondrion
Similarity search - Function
Ubiquinone biosynthesis protein COQ9 / : / Ubiquinone biosynthesis protein COQ9, N-terminal domain / COQ9 / COQ9
Similarity search - Domain/homology
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Ubiquinone biosynthesis protein COQ9, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBingman, C.A. / Lohman, D.C. / Smith, R.W. / Pagliarini, D.J. / Mitochondrial Protein Partnership (MPP)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U01GM094622-01 United States
CitationJournal: Mol. Cell / Year: 2019
Title: An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis.
Authors: Lohman, D.C. / Aydin, D. / Von Bank, H.C. / Smith, R.W. / Linke, V. / Weisenhorn, E. / McDevitt, M.T. / Hutchins, P. / Wilkerson, E.M. / Wancewicz, B. / Russell, J. / Stefely, M.S. / Beebe, ...Authors: Lohman, D.C. / Aydin, D. / Von Bank, H.C. / Smith, R.W. / Linke, V. / Weisenhorn, E. / McDevitt, M.T. / Hutchins, P. / Wilkerson, E.M. / Wancewicz, B. / Russell, J. / Stefely, M.S. / Beebe, E.T. / Jochem, A. / Coon, J.J. / Bingman, C.A. / Dal Peraro, M. / Pagliarini, D.J.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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: Ubiquinone biosynthesis protein COQ9, mitochondrial
B: Ubiquinone biosynthesis protein COQ9, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0014
Polymers71,1002
Non-polymers9012
Water3,693205
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: there seems to be an inter-chain swap of helix 10 in the crystal.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-30 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.110, 97.390, 63.650
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquinone biosynthesis protein COQ9, mitochondrial


Mass: 35549.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COQ9, C16orf49, HSPC326, PSEC0129 / Production host: Escherichia coli (E. coli) / References: UniProt: O75208
#2: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 1.65 Å3/Da / Density % sol: 25.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein was dissolved at 4.89 mg/mL in a buffer containing 10 mM HEPES pH 7.5, 100 mM NaCl, 0.3 mM TCEP. 200 nL of protein was mixed with 200 nL of reservoir in a SD2 plate. The reservoir ...Details: Protein was dissolved at 4.89 mg/mL in a buffer containing 10 mM HEPES pH 7.5, 100 mM NaCl, 0.3 mM TCEP. 200 nL of protein was mixed with 200 nL of reservoir in a SD2 plate. The reservoir consisted of 21% w/v PEG 3350, 0.25 M NaCl, and 0.1 M bistris pH 6.5. Crystals were cryopreserved in 35% PEG 3350, 0.2 M NaCl and 0.1 M bistris buffer, pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2016
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→48.69 Å / Num. obs: 31242 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 36.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09055 / Rpim(I) all: 0.04409 / Net I/σ(I): 12.38
Reflection shellResolution: 2→2.071 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 3066 / CC1/2: 0.48 / Rpim(I) all: 0.658 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RHP

4rhp


Resolution: 2→48.69 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 25.65
RfactorNum. reflection% reflection
Rfree0.2454 2000 6.41 %
Rwork0.1974 --
obs0.2003 31212 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.2 Å2
Refinement stepCycle: LAST / Resolution: 2→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 46 205 3499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033433
X-RAY DIFFRACTIONf_angle_d0.6614657
X-RAY DIFFRACTIONf_dihedral_angle_d12.6852064
X-RAY DIFFRACTIONf_chiral_restr0.038512
X-RAY DIFFRACTIONf_plane_restr0.004600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30551410.30752061X-RAY DIFFRACTION100
2.05-2.10550.33841430.2852098X-RAY DIFFRACTION100
2.1055-2.16740.28221410.26352052X-RAY DIFFRACTION100
2.1674-2.23740.30141430.25392096X-RAY DIFFRACTION100
2.2374-2.31730.27541420.2372055X-RAY DIFFRACTION100
2.3173-2.41010.28521420.22552092X-RAY DIFFRACTION100
2.4101-2.51980.3021440.21512098X-RAY DIFFRACTION100
2.5198-2.65260.25451410.21012069X-RAY DIFFRACTION100
2.6526-2.81880.27191430.21032078X-RAY DIFFRACTION100
2.8188-3.03640.24421440.21282095X-RAY DIFFRACTION100
3.0364-3.34190.28221430.19692094X-RAY DIFFRACTION100
3.3419-3.82540.23881430.17852095X-RAY DIFFRACTION100
3.8254-4.81890.19821440.15832108X-RAY DIFFRACTION100
4.8189-48.70940.19731460.17752121X-RAY DIFFRACTION100

+
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