[English] 日本語
Yorodumi
- PDB-7pv1: Crystal structure of the dimeric mitofilin domain of Mic60 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pv1
TitleCrystal structure of the dimeric mitofilin domain of Mic60 in complex with the CHCH domain of Mic19
ComponentsMICOS complex subunit MIC60 fused to MIC19
KeywordsSTRUCTURAL PROTEIN / MICOS / dimer / mitochondria / fusion protein
Function / homologyProtein of unknown function DUF1690 / Protein of Unknown function (DUF1690) / Mitochondrial inner membrane protein Mitofilin / Mitochondrial inner membrane protein / MICOS complex / cristae formation / MICOS complex subunit mic19 / MICOS complex subunit MIC60
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsFunck, K. / Bock-Bierbaum, T. / 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MICOS complex subunit MIC60 fused to MIC19
B: MICOS complex subunit MIC60 fused to MIC19
C: MICOS complex subunit MIC60 fused to MIC19
D: MICOS complex subunit MIC60 fused to MIC19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9047
Polymers68,3214
Non-polymers5833
Water1448
1
A: MICOS complex subunit MIC60 fused to MIC19
B: MICOS complex subunit MIC60 fused to MIC19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5494
Polymers34,1612
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-31 kcal/mol
Surface area16040 Å2
MethodPISA
2
C: MICOS complex subunit MIC60 fused to MIC19
D: MICOS complex subunit MIC60 fused to MIC19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3553
Polymers34,1612
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-34 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.197, 85.371, 61.497
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 5 and (name N...
21(chain B and (resid 4 through 5 or resid 7...
31(chain C and ((resid 4 through 5 and (name N...
41(chain D and ((resid 4 through 5 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALA(chain A and ((resid 4 through 5 and (name N...AA4 - 54 - 5
12THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
13THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
14THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
15THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
21ARGARGALAALA(chain B and (resid 4 through 5 or resid 7...BB4 - 54 - 5
22LEULEUPHEPHE(chain B and (resid 4 through 5 or resid 7...BB7 - 117 - 11
23ARGARGGLYGLY(chain B and (resid 4 through 5 or resid 7...BB13 - 2513 - 25
24GLYGLYGLYGLY(chain B and (resid 4 through 5 or resid 7...BB2727
25ASPASPASPASP(chain B and (resid 4 through 5 or resid 7...BB2929
26THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
27THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
28THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
29THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
31ARGARGALAALA(chain C and ((resid 4 through 5 and (name N...CC4 - 54 - 5
32GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
33GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
34GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
35GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
41ARGARGALAALA(chain D and ((resid 4 through 5 and (name N...DD4 - 54 - 5
42PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146
43PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146
44PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146
45PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146

-
Components

#1: Protein
MICOS complex subunit MIC60 fused to MIC19 / Mitofilin


Mass: 17080.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0073820, CTHT_0012250 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SHY5, UniProt: G0S140
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) Jeffamine ED-2001, 0.1 M HEPES/NaOH pH 7.0.

-
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: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→40.738 Å / Num. obs: 20339 / % possible obs: 98.8 % / Redundancy: 4.028 % / Biso Wilson estimate: 68.373 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.13 / Χ2: 0.81 / Net I/σ(I): 9.16 / Num. measured all: 81921
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
2.5-2.654.0091.6550.7512949330732300.3941.91197.7
2.65-2.833.8581.0491.2311809310130610.571.21998.7
2.83-3.064.180.6092.2612102290328950.8090.799.7
3.06-3.354.1330.3314.2310871265226300.930.3899.2
3.35-3.743.8730.1498.619183240723710.9840.17398.5
3.74-4.314.2230.08116.029062215221460.9940.09399.7
4.31-5.273.9930.05522.177167181617950.9960.06498.8
5.27-7.424.0580.04823.185710142314070.9980.05598.9
7.42-40.7383.8160.02443.7630688198040.9990.02898.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PV0

7pv0


Resolution: 2.497→40.738 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1017 5 %
Rwork0.232 19305 -
obs0.2334 20322 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.76 Å2 / Biso mean: 80.0625 Å2 / Biso min: 32.38 Å2
Refinement stepCycle: final / Resolution: 2.497→40.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 93 8 4486
Biso mean--106.42 58.92 -
Num. residues----553
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2055X-RAY DIFFRACTION11.88TORSIONAL
12B2055X-RAY DIFFRACTION11.88TORSIONAL
13C2055X-RAY DIFFRACTION11.88TORSIONAL
14D2055X-RAY DIFFRACTION11.88TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4972-2.62880.45691430.4075271197
2.6288-2.79350.37731440.3481274999
2.7935-3.00910.33871450.31162746100
3.0091-3.31180.35371450.2911275299
3.3118-3.79070.22781450.2336275199
3.7907-4.77470.20551470.19692796100
4.7747-40.7380.22821480.1836280099
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)
17.0849-2.94612.34829.3223-2.92177.51580.08270.6655-0.794-1.1910.15950.1560.8563-0.0839-0.34350.715-0.1402-0.05790.6023-0.1650.626229.144659.316340.8642
28.88990.79766.00254.81170.08747.3652-0.0057-1.13440.24070.0725-0.31280.20040.9443-1.5941-0.18190.3219-0.02350.07210.29860.09860.580435.264657.26972.6129
36.47892.1327-5.19152.54-2.23544.31881.3598-0.88260.25950.7337-0.240.45880.5255-2.71211.43431.39540.1111-0.38591.4636-0.32211.092645.028961.796296.4423
44.05490.6042.78516.88411.23874.49590.0547-1.5661.14870.5836-0.1078-0.03140.053-1.5398-0.06580.57160.0070.06210.8592-0.05790.665335.253165.535883.8145
56.5805-2.97093.39913.8461-1.74935.10350.58480.91481.2787-0.044-0.6422-0.6907-0.23140.7327-0.12590.4353-0.0335-0.00530.47620.03470.694856.650183.772671.7506
61.9373.40710.95217.8957-1.57757.0061-0.25730.09861.14520.3437-0.0014-0.5536-0.47770.0554-0.0480.5494-0.0390.05690.5686-0.19370.492953.975486.544981.2758
79.75951.09184.01071.61790.78953.1503-0.0303-0.41920.166-0.0156-0.09890.0422-0.1596-0.26740.01240.28560.03520.03840.32660.00860.426634.363478.488571.0546
85.2044-2.0441-1.95525.692-0.97243.8184-0.2145-0.6767-0.8786-0.4002-0.05230.43250.6612-0.4572-0.8890.47020.04680.18190.52140.14861.105411.858368.861362.4907
93.9065-0.1023.61871.232.06367.1668-0.31850.1972-0.7742-0.133-0.00010.12570.4549-0.235-0.14530.45410.07770.02630.6233-0.03930.771919.196869.899355.7046
107.39921.02961.04548.2817-0.22054.6555-0.3712-1.0053-0.81180.9186-0.92180.65142.1708-2.16210.24380.591-0.12070.10520.63240.05550.712334.131847.992181.8566
114.7417-4.2436-4.71025.65815.88376.1491-0.43021.6616-0.6952-2.30171.4205-1.0292-1.890.34550.67690.9401-0.06690.11440.9558-0.24510.994838.347648.021465.5525
122.60820.93221.66292.2978-0.51452.02590.2294-0.0025-1.8668-0.68010.3143-0.97841.78181.12630.74070.93280.03960.10410.56520.16641.02343.848644.079678.7288
137.5437-0.30091.76022.74450.02463.1884-0.4053-0.0212-1.10090.7916-0.1157-1.615-0.34191.37890.91660.56480.0497-0.07430.54450.1190.859347.48352.480978.8491
145.8696-0.80060.57448.5489-2.89815.22740.0467-0.36390.2436-0.4809-0.0839-0.11820.6343-0.50240.02980.5069-0.01140.04730.3883-0.08440.524435.795363.801950.1107
152.7627-3.07353.23825.2647-0.814410.0029-0.203-0.80441.2022-1.0056-0.2253-0.5096-0.18250.17380.44070.7186-0.1071-0.02330.53230.0490.751639.996877.20841.9755
163.9638-0.90241.25878.1175-2.14268.5391-0.2318-0.35661.1853-0.01340.3240.7327-0.5804-0.95710.09370.38690.0356-0.00370.5019-0.08310.487930.945877.114547.0374
172.59642.8232-0.36323.39031.01386.711-0.2681-1.56510.8821-0.1344-0.40870.59370.1336-0.52590.28960.38080.1282-0.09210.4836-0.01710.907312.485885.592965.2654
184.40872.45550.22152.32151.01660.8338-0.4464-1.54121.88450.3364-0.6202-0.7528-0.95651.2328-0.54730.5518-0.0753-0.26930.7082-0.05271.419530.460388.705266.3121
195.1111.9872-0.64363.2606-4.10176.6682-0.8459-0.6042.0135-0.43990.05950.0834-1.0147-0.60060.17970.70250.1511-0.090.4848-0.14961.058718.155393.389159.3156
203.62142.35363.52783.789-0.76227.92370.0760.41870.1935-1.22750.177-0.101-0.39610.04560.25350.64170.10550.09410.62470.03790.713620.006686.070853.1542
216.7992-0.78772.27195.18460.35123.54520.3531-0.0922-0.0232-0.19090.0973-0.2780.19050.13520.07540.3268-0.03880.08260.3970.00430.60147.06978.126367.9454
220.03250.0058-0.06560.2908-0.17290.1886-0.23191.5152-1.65671.11241.1807-0.61820.28642.30510.55960.88690.4206-0.0331.4896-0.2051.838668.476861.919778.6236
235.7874-2.27773.61964.57871.59695.27560.69361.45940.4275-1.4005-1.291-1.71841.08051.9326-0.16950.66720.01020.07880.76170.08391.009658.006168.765361.5971
246.0779-0.45194.2346.5535-0.73867.4820.41170.3985-0.81030.1861-0.4035-0.00820.9130.1686-0.50760.4023-0.07780.03290.5296-0.01150.687652.892464.468971.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 61 )A3 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 92 )A62 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 104 )A93 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 145 )A105 - 145
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 26 )C1 - 26
6X-RAY DIFFRACTION6chain 'C' and (resid 27 through 42 )C27 - 42
7X-RAY DIFFRACTION7chain 'C' and (resid 43 through 93 )C43 - 93
8X-RAY DIFFRACTION8chain 'C' and (resid 94 through 124 )C94 - 124
9X-RAY DIFFRACTION9chain 'C' and (resid 125 through 145 )C125 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 20 )B3 - 20
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 28 )B21 - 28
12X-RAY DIFFRACTION12chain 'B' and (resid 29 through 42 )B29 - 42
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 61 )B43 - 61
14X-RAY DIFFRACTION14chain 'B' and (resid 62 through 93 )B62 - 93
15X-RAY DIFFRACTION15chain 'B' and (resid 94 through 124 )B94 - 124
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 145 )B125 - 145
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 20 )D2 - 20
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 26 )D21 - 26
19X-RAY DIFFRACTION19chain 'D' and (resid 27 through 42 )D27 - 42
20X-RAY DIFFRACTION20chain 'D' and (resid 43 through 61 )D43 - 61
21X-RAY DIFFRACTION21chain 'D' and (resid 62 through 92 )D62 - 92
22X-RAY DIFFRACTION22chain 'D' and (resid 93 through 104 )D93 - 104
23X-RAY DIFFRACTION23chain 'D' and (resid 105 through 124 )D105 - 124
24X-RAY DIFFRACTION24chain 'D' and (resid 125 through 146 )D125 - 146

+
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