[English] 日本語
Yorodumi
- PDB-9q6d: CryoEM structure of decameric COMMD-like protein MBK5214510 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9q6d
TitleCryoEM structure of decameric COMMD-like protein MBK5214510 from Flavobacteriaceae bacterium
ComponentsCOMMD-like protein MBK5214510
KeywordsUNKNOWN FUNCTION / COMMD / homooligomer
Biological speciesFlavobacteriaceae bacterium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.77 Å
AuthorsCollins, B.M. / Healy, M.D. / Liu, M. / Cater, R.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking
Authors: Collins, B.M. / Healy, M.D. / Liu, M.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510
C: COMMD-like protein MBK5214510
D: COMMD-like protein MBK5214510
E: COMMD-like protein MBK5214510
F: COMMD-like protein MBK5214510
G: COMMD-like protein MBK5214510
H: COMMD-like protein MBK5214510
I: COMMD-like protein MBK5214510
J: COMMD-like protein MBK5214510


Theoretical massNumber of molelcules
Total (without water)277,51510
Polymers277,51510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 220 / Label seq-ID: 21 - 240

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.809465176364, 0.587150588589, 0.00450716916928), (0.587154184907, -0.809474879778, 0.000618186668427), (0.00401140888767, 0.00214600265924, -0.999989651582)-46.0721708422, 140.185887474, 227.442301862
2given(0.307610497892, -0.951488151957, 0.0067880978475), (0.951449544364, 0.307500385321, -0.0136849390336), (0.0109337146471, 0.0106681635139, 0.999883315278)187.866645364, -28.1404801086, -1.95484332079
3given(-0.325663089637, 0.945480621819, -0.00315369841147), (0.945323773516, 0.325667205966, 0.0174308399975), (0.0175075775898, 0.0026953151257, -0.999843097692)43.328921859, -33.1243318445, 226.253940649
4given(-0.813567832596, -0.581348942103, 0.0118654659253), (0.58143440912, -0.813574446183, 0.00553610066778), (0.00643503360232, 0.0114029835905, 0.99991427748)273.63251262, 140.370195515, -1.6778328931
5given(-0.999973045462, -0.000166838338203, 0.0073403347965), (-0.000195082603287, 0.999992580203, -0.00384726928829), (-0.0073396384607, -0.00384859755855, -0.999965658412)228.599951993, 0.411196209287, 229.013126612
6given(-0.806885958806, 0.590706393273, -0.00100320917053), (-0.590698897181, -0.806864363177, 0.00668672592954), (0.00314043802813, 0.00598801981361, 0.999977140373)139.874337241, 274.561711828, -0.821862199139
7given(-0.304493431676, -0.952091223018, 0.0283910746135), (-0.951789296733, 0.305289270517, 0.029926508861), (-0.0371602568801, -0.0179098955587, -0.999148813215)255.890673879, 185.410839438, 232.615387408
8given(0.297896574585, 0.954390940849, -0.0198887625748), (-0.954240599054, 0.298290548019, 0.0211572228702), (0.0261248917287, 0.0126760004931, 0.999578315613)-26.9615476522, 187.10948827, -3.22849481254
9given(0.797708466356, -0.603043255945, -0.00018483294638), (-0.603002919616, -0.797658580551, 0.0113255378909), (-0.00697722283068, -0.00892302265528, -0.999935846956)91.7428887422, 274.010615803, 229.413097854

-
Components

#1: Protein
COMMD-like protein MBK5214510


Mass: 27751.531 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacteriaceae bacterium (bacteria) / Production host: Escherichia coli (E. coli)
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Decameric cryoEM structure of MBK5214510 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Flavobacteriaceae bacterium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48201 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 319.28 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002418160
ELECTRON MICROSCOPYf_angle_d0.556424300
ELECTRON MICROSCOPYf_chiral_restr0.03512750
ELECTRON MICROSCOPYf_plane_restr0.00193150
ELECTRON MICROSCOPYf_dihedral_angle_d5.68752310
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints5.19994980951E-13
ens_1d_3BBELECTRON MICROSCOPYNCS constraints3.68002801569E-10
ens_1d_4BBELECTRON MICROSCOPYNCS constraints3.82629249577E-13
ens_1d_5BBELECTRON MICROSCOPYNCS constraints4.67978007577E-13
ens_1d_6BBELECTRON MICROSCOPYNCS constraints4.25479328142E-13
ens_1d_7BBELECTRON MICROSCOPYNCS constraints5.23660617671E-13
ens_1d_8BBELECTRON MICROSCOPYNCS constraints4.59061263575E-13
ens_1d_9BBELECTRON MICROSCOPYNCS constraints5.50462899453E-13
ens_1d_10BBELECTRON MICROSCOPYNCS constraints2.06379236143E-11

+
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