[English] 日本語
Yorodumi
- PDB-4oaf: Crystal structure of the cytosolic domain of mouse MiD51 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oaf
TitleCrystal structure of the cytosolic domain of mouse MiD51
ComponentsMitochondrial dynamic protein MID51
KeywordsTRANSFERASE / nucleotidyl transferase fold
Function / homology
Function and homology information


positive regulation of mitochondrial fusion / mitochondrial fission / positive regulation of mitochondrial fission / positive regulation of protein targeting to membrane / ADP binding / GDP binding / cellular response to hypoxia / mitochondrial outer membrane / mitochondrion / identical protein binding
Similarity search - Function
Mitochondrial dynamics protein MID49/MID51 / : / Mitochondrial dynamics protein MID51-like, C-terminal domain / Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain ...Mitochondrial dynamics protein MID49/MID51 / : / Mitochondrial dynamics protein MID51-like, C-terminal domain / Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitochondrial dynamics protein MID51
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLoson, O.C. / Kaiser, J.T. / Chan, D.C.
CitationJournal: Structure / Year: 2014
Title: The Mitochondrial Fission Receptor MiD51 Requires ADP as a Cofactor.
Authors: Loson, O.C. / Liu, R. / Rome, M.E. / Meng, S. / Kaiser, J.T. / Shan, S.O. / Chan, D.C.
History
DepositionJan 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial dynamic protein MID51
B: Mitochondrial dynamic protein MID51
C: Mitochondrial dynamic protein MID51
D: Mitochondrial dynamic protein MID51


Theoretical massNumber of molelcules
Total (without water)149,0114
Polymers149,0114
Non-polymers00
Water8,089449
1
A: Mitochondrial dynamic protein MID51
C: Mitochondrial dynamic protein MID51


Theoretical massNumber of molelcules
Total (without water)74,5062
Polymers74,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial dynamic protein MID51
D: Mitochondrial dynamic protein MID51


Theoretical massNumber of molelcules
Total (without water)74,5062
Polymers74,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.075, 78.592, 102.310
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Mitochondrial dynamic protein MID51 / Mitochondrial dynamic protein of 51 kDa homolog / Mitochondrial elongation factor 1 / Smith-Magenis ...Mitochondrial dynamic protein of 51 kDa homolog / Mitochondrial elongation factor 1 / Smith-Magenis syndrome chromosomal region candidate gene 7 protein-like


Mass: 37252.750 Da / Num. of mol.: 4 / Fragment: Cytosolic domain, unp residues 134-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mid51, MiD51 (aka SMCR7L), Mief1, Smcr7l / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8BGV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPE, 700 mM Potassium sodium tartrate tetrahydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2012 / Details: K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.872→39.296 Å / Num. all: 110262 / Num. obs: 110262 / % possible obs: 93.4 % / Redundancy: 2.8 % / Rsym value: 0.103 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.87-1.972.50.0210.42.066174.8
1.97-2.092.90.0210.61.349198.4
2.09-2.242.80.0210.70.857197
2.24-2.422.90.0211.50.5196.8
2.42-2.652.90.0212.40.315197.3
2.65-2.962.90.0214.20.177196
2.96-3.422.90.0218.70.084196.9
3.42-4.192.90.02115.70.042195.4
4.19-5.922.80.02117.80.032194.3
5.92-39.2962.90.02118.90.024193.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.02 Å39.3 Å
Translation4.02 Å39.3 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.005 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1783 2.85 %
Rwork0.2039 --
obs0.2054 69897 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.3462 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10121 0 0 449 10570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710334
X-RAY DIFFRACTIONf_angle_d1.14114109
X-RAY DIFFRACTIONf_dihedral_angle_d13.9253785
X-RAY DIFFRACTIONf_chiral_restr0.0731658
X-RAY DIFFRACTIONf_plane_restr0.0051816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.34081380.27954692X-RAY DIFFRACTION93
2.255-2.3160.33661410.25924877X-RAY DIFFRACTION97
2.316-2.38410.29051460.24914937X-RAY DIFFRACTION98
2.3841-2.4610.30941440.23574920X-RAY DIFFRACTION98
2.461-2.54890.31241430.22644871X-RAY DIFFRACTION97
2.5489-2.65090.28351430.21454867X-RAY DIFFRACTION96
2.6509-2.77150.29651390.22264711X-RAY DIFFRACTION93
2.7715-2.91760.28841440.20194929X-RAY DIFFRACTION97
2.9176-3.10020.2391460.19244927X-RAY DIFFRACTION97
3.1002-3.33940.23731420.19094848X-RAY DIFFRACTION96
3.3394-3.6750.22591410.18214766X-RAY DIFFRACTION94
3.675-4.20570.28381440.17964912X-RAY DIFFRACTION97
4.2057-5.29490.20231410.18024793X-RAY DIFFRACTION94
5.2949-32.00870.2531430.22134852X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.73910.48121.10756.12125.57748.49310.25380.3859-0.31960.46050.4235-0.49490.97981.2026-0.34930.54210.0981-0.11040.4028-0.01940.307-28.8869-2.8785-34.0916
22.1506-1.71480.63277.15220.89892.70990.1238-0.41970.32210.7891-0.3371-0.1437-0.53350.13510.23690.5563-0.0885-0.02060.4391-0.03740.3099-37.709422.7686-15.6963
30.7727-1.2920.4681.6696-0.17540.9089-0.2398-0.0850.07460.03560.1491-0.2168-0.17010.02710.05060.2592-0.03-0.01240.23850.02740.2612-46.744827.2947-32.6315
42.8305-0.82050.5611.9387-1.40873.6303-0.23290.14510.50810.1656-0.2452-0.3425-0.07070.30990.41640.28390.0172-0.01830.1857-0.01780.338-39.808436.5304-27.2772
53.1788-1.48170.6732.8054-0.34972.3720.1868-0.5710.01820.2118-0.1407-1.13840.19870.24780.0310.3805-0.0535-0.11980.45230.10030.5947-26.96720.6598-20.9077
61.07061.4874-0.00042.4782-0.73992.63050.05530.2521-0.0705-0.0502-0.17880.1885-0.0506-0.12010.15170.37540.01210.00590.18880.00820.3553-44.903923.4541-37.8836
72.3109-0.0283-0.32591.68840.80152.85820.12-0.23870.04170.1195-0.18340.1760.40130.08130.04010.43860.03570.04190.2104-0.01630.2019-39.1924.5047-39.7655
82.3302-1.5126-0.39225.47931.83632.33650.02610.4309-0.0563-0.2316-0.0521-0.05380.2548-0.0542-0.05460.4097-0.0280.01360.2435-0.0180.1854-37.69925.339-49.2943
91.0961-0.27840.60981.3485-0.06722.5596-0.05530.118-0.05590.3883-0.1129-0.08940.43070.07660.1510.6370.0495-0.04420.23620.0070.3406-49.394917.3838-2.6275
104.8110.62512.87365.2639-0.15562.1819-0.05880.5193-0.14480.0231-0.0255-0.20490.02530.53340.28580.59160.0267-0.02430.47580.00860.4418-49.91818.57833.278
111.6777-0.41681.16711.2079-1.29712.871-0.0612-0.1513-0.06520.1890.0570.017-0.5267-0.39970.00440.54930.0738-0.02580.3077-0.01630.2423-59.469640.6875-12.5203
121.7706-0.63640.41283.49150.36593.1812-0.02250.0478-0.56160.00220.11110.74150.3711-0.5061-0.10580.4913-0.0197-0.05930.3726-0.04620.4674-58.092116.9731-6.9301
131.84011.6504-2.70983.0137-0.3618.133-0.0396-0.4032-0.11240.2157-0.63380.9879-0.9163-1.35430.46410.52130.1679-0.13740.8102-0.15690.6717-62.854637.79780.2845
147.8315-1.72041.92053.2562-2.23093.2360.0064-0.2114-0.3756-0.4903-0.2686-0.4002-0.0963-0.17940.30010.6110.1057-0.05120.36880.00750.3286-45.826332.71063.4571
153.46070.28220.19434.98831.71733.74170.2045-0.0869-0.0030.3928-0.1163-0.27110.37370.4309-0.09840.61150.0712-0.05150.35170.0450.282-43.989726.844215.7962
162.6771-1.24161.38482.86040.59542.25640.0693-0.36780.07480.6104-0.1149-0.15670.3874-0.1225-0.02750.6293-0.0376-0.00410.3295-0.00850.2019-53.261231.105820.955
172.4180.7829-2.354.0382-4.77176.44470.03140.1469-0.4378-0.13190.1535-0.24210.7908-1.0678-0.27750.7317-0.138-0.07780.2620.06150.337-10.38481.4758-15.0253
184.54781.5987-0.59638.6026-1.64691.84250.28320.33150.6165-0.18990.06090.3869-0.37360.0717-0.12570.6379-0.01240.0630.4311-0.00330.1885-3.113225.4447-34.8767
191.65331.24380.77151.87760.3571.2795-0.0920.0505-0.0370.08130.1398-0.0936-0.1048-0.0459-0.03850.52510.06330.07720.2612-0.00230.25047.676633.0491-18.5856
202.18741.98750.78682.88021.46711.339-0.14760.21870.4115-0.3470.07520.4592-0.5664-0.35630.16670.57090.08720.00290.40270.06090.2418-3.338.1651-26.7678
217.40854.54972.82636.44721.72315.0226-0.41760.7706-0.81250.07560.39290.6302-0.1217-0.57230.21690.3058-0.00810.05490.3861-0.060.4834-10.182326.3692-26.4165
223.7839-1.3897-2.34373.75640.97525.2938-0.08060.12190.17420.26890.0901-0.57430.3537-0.1055-0.02660.5047-0.01210.00610.2559-0.00110.25214.350531.6522-11.6928
231.49910.3383-0.61762.3713-1.71953.026-0.0280.065-0.1163-0.0334-0.0835-0.09220.39890.12970.07570.5734-0.00580.01390.24090.03540.20071.909810.9609-7.3848
244.214-0.77620.30725.205-0.54442.12720.5235-0.0247-0.24290.8030.43681.0208-0.7426-0.34630.37710.46380.03250.15540.30710.04860.2349-11.855210.60241.1983
254.46161.15430.40031.50942.32794.15070.0487-0.0141-0.3981-0.7448-0.12270.00180.5175-0.151-0.10480.5789-0.0962-0.02260.1873-0.01620.21423.700219.3513-70.9074
260.13420.50620.91733.27942.79213.3724-0.0309-0.01-0.0149-0.01230.0192-0.01710.32410.0011-0.01390.3822-0.0087-0.00530.2453-0.0220.254711.585224.7347-43.0872
271.62590.23790.86441.68791.02722.0039-0.22680.01320.1155-0.0580.1269-0.0841-0.71890.00440.10940.3708-0.0043-0.00030.15640.00970.170320.316249.1603-39.213
281.81430.84831.07863.40410.22291.54160.01390.1838-0.57270.01520.2518-0.38720.54150.472-0.25070.45930.095-0.01020.2371-0.00110.323520.595720.9193-42.849
294.5801-1.4345-2.34762.00440.97174.62560.0169-0.3492-0.20730.3956-0.07450.0003-0.02590.43990.090.4434-0.0522-0.00460.18480.01740.118619.376343.5733-49.634
306.29561.38024.04191.54072.60854.97320.23870.8232-0.69490.4288-0.1782-0.02950.1880.0244-0.01040.5977-0.06570.02910.1699-0.01180.32780.719635.8456-56.2665
311.09891.42810.03533.24460.67682.9831-0.05140.10870.0866-0.4608-0.00140.1598-0.0827-0.03870.02490.3752-0.0211-0.00430.1588-0.00440.17877.275135.7129-67.7645
321.64481.14491.8552.74650.50282.5053-0.30510.6993-0.1106-1.16210.4832-0.65840.2020.4957-0.00740.96850.00510.16080.370.02810.311716.250930.5617-77.1155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 134:154 )D134 - 154
2X-RAY DIFFRACTION2( CHAIN D AND RESID 155:179 )D155 - 179
3X-RAY DIFFRACTION3( CHAIN D AND RESID 180:243 )D180 - 243
4X-RAY DIFFRACTION4( CHAIN D AND RESID 244:277 )D244 - 277
5X-RAY DIFFRACTION5( CHAIN D AND RESID 278:314 )D278 - 314
6X-RAY DIFFRACTION6( CHAIN D AND RESID 315:348 )D315 - 348
7X-RAY DIFFRACTION7( CHAIN D AND RESID 349:394 )D349 - 394
8X-RAY DIFFRACTION8( CHAIN D AND RESID 395:463 )D395 - 463
9X-RAY DIFFRACTION9( CHAIN B AND RESID 134:189 )B134 - 189
10X-RAY DIFFRACTION10( CHAIN B AND RESID 190:203 )B190 - 203
11X-RAY DIFFRACTION11( CHAIN B AND RESID 204:274 )B204 - 274
12X-RAY DIFFRACTION12( CHAIN B AND RESID 275:322 )B275 - 322
13X-RAY DIFFRACTION13( CHAIN B AND RESID 323:337 )B323 - 337
14X-RAY DIFFRACTION14( CHAIN B AND RESID 338:350 )B338 - 350
15X-RAY DIFFRACTION15( CHAIN B AND RESID 351:403 )B351 - 403
16X-RAY DIFFRACTION16( CHAIN B AND RESID 404:463 )B404 - 463
17X-RAY DIFFRACTION17( CHAIN C AND RESID 134:151 )C134 - 151
18X-RAY DIFFRACTION18( CHAIN C AND RESID 152:177 )C152 - 177
19X-RAY DIFFRACTION19( CHAIN C AND RESID 178:243 )C178 - 243
20X-RAY DIFFRACTION20( CHAIN C AND RESID 244:292 )C244 - 292
21X-RAY DIFFRACTION21( CHAIN C AND RESID 294:316 )C294 - 316
22X-RAY DIFFRACTION22( CHAIN C AND RESID 317:342 )C317 - 342
23X-RAY DIFFRACTION23( CHAIN C AND RESID 343:440 )C343 - 440
24X-RAY DIFFRACTION24( CHAIN C AND RESID 441:463 )C441 - 463
25X-RAY DIFFRACTION25( CHAIN A AND RESID 134:148 )A134 - 148
26X-RAY DIFFRACTION26( CHAIN A AND RESID 149:208 )A149 - 208
27X-RAY DIFFRACTION27( CHAIN A AND RESID 209:265 )A209 - 265
28X-RAY DIFFRACTION28( CHAIN A AND RESID 266:316 )A266 - 316
29X-RAY DIFFRACTION29( CHAIN A AND RESID 317:339 )A317 - 339
30X-RAY DIFFRACTION30( CHAIN A AND RESID 340:355 )A340 - 355
31X-RAY DIFFRACTION31( CHAIN A AND RESID 356:440 )A356 - 440
32X-RAY DIFFRACTION32( CHAIN A AND RESID 441:462 )A441 - 462

+
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