[English] 日本語
Yorodumi
- PDB-7puz: Crystal structure of the Mic60 coiled coil domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7puz
TitleCrystal structure of the Mic60 coiled coil domain
ComponentsMICOS complex subunit MIC60
KeywordsSTRUCTURAL PROTEIN / MICOS / coiled coil / mitochondria
Function / homologyMitochondrial inner membrane protein Mitofilin / Mitochondrial inner membrane protein / MICOS complex / cristae formation / MICOS complex subunit MIC60
Function and homology information
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.842 Å
AuthorsBock-Bierbaum, T. / Funck, K. / Daumke, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2013-CoG-616024 Germany
German Research Foundation (DFG)FOR2848/P06 Germany
CitationJournal: Sci Adv / Year: 2022
Title: Structural insights into crista junction formation by the Mic60-Mic19 complex.
Authors: Bock-Bierbaum, T. / Funck, K. / Wollweber, F. / Lisicki, E. / von der Malsburg, K. / von der Malsburg, A. / Laborenz, J. / Noel, J.K. / Hessenberger, M. / Jungbluth, S. / Bernert, C. / Kunz, ...Authors: Bock-Bierbaum, T. / Funck, K. / Wollweber, F. / Lisicki, E. / von der Malsburg, K. / von der Malsburg, A. / Laborenz, J. / Noel, J.K. / Hessenberger, M. / Jungbluth, S. / Bernert, C. / Kunz, S. / Riedel, D. / Lilie, H. / Jakobs, S. / van der Laan, M. / Daumke, O.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MICOS complex subunit MIC60


Theoretical massNumber of molelcules
Total (without water)20,0241
Polymers20,0241
Non-polymers00
Water00
1
A: MICOS complex subunit MIC60

A: MICOS complex subunit MIC60

A: MICOS complex subunit MIC60

A: MICOS complex subunit MIC60


Theoretical massNumber of molelcules
Total (without water)80,0954
Polymers80,0954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area17660 Å2
ΔGint-137 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.194, 54.194, 134.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein MICOS complex subunit MIC60 / Mitofilin


Mass: 20023.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: MIC60, KLTH0H09724g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5E325

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17.5 % PEG 1500, 0.1 M MMT buffer pH 7.1, 0.1 M D-Sorbitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.84→44.681 Å / Num. obs: 5166 / % possible obs: 99.7 % / Redundancy: 13.499 % / Biso Wilson estimate: 81.653 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.168 / Χ2: 0.916 / Net I/σ(I): 13.11 / Num. measured all: 69737
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.84-3.0114.022.5420.99112308098010.7732.63899
3.01-3.2214.3011.5941.69107547527520.7071.654100
3.22-3.4813.4990.9352.9695037047040.850.972100
3.48-3.8113.8970.3577.8490756536530.9870.371100
3.81-4.2513.8490.1715.0384346106090.9970.17699.8
4.25-4.912.9720.08825.0770185425410.9990.09299.8
4.9-5.9913.6050.08124.41643547347310.084100
5.99-8.3912.1640.0629.76459837837810.063100
8.39-44.68110.5490.03650.7426902592550.9990.03898.5

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealized alpha helices

Resolution: 2.842→44.681 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 259 5.02 %
Rwork0.2442 4897 -
obs0.2466 5156 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.54 Å2 / Biso mean: 94.4275 Å2 / Biso min: 52.5 Å2
Refinement stepCycle: final / Resolution: 2.842→44.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 0 0 1127
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.842-3.58040.35581240.33622358
3.5804-44.6810.27241350.21912539
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)
10.51920.8502-3.20370.111-2.59958.4198-0.2097-0.2373-0.1734-0.433-0.09160.07941.24420.71620.38251.2926-0.03150.15641.0830.13160.627755.12741.900763.9775
28.21832.1932-4.2463.5558-4.96298.73030.0407-0.0062-0.3180.6826-1.0116-0.8762-0.49690.77490.5950.58660.0024-0.03070.6914-0.04570.486939.5522-6.352121.1092
38.83761.1253-3.43496.572-2.13245.5259-0.4119-0.07260.0008-0.7948-0.814-1.73280.50421.9361.00360.68190.08290.03010.9896-0.01220.782447.3598-7.266114.1917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 235 through 332 )A235 - 332
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 357 )A333 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 384 )A358 - 384

+
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