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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nxu
TitleCrystal structure of the cytosolic domain of human MiD51
ComponentsMitochondrial dynamic protein MID51
KeywordsTRANSFERASE / protein-nucleotide complex / nucleotidyltransferase / protein-protein interaction / ADP / GDP / Drp1 / membrane-anchored
Function / homology
Function and homology information


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-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like ...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-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Mitochondrial dynamics protein MIEF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRichter, V. / Kvansakul, M. / Ryan, M.T.
CitationJournal: J.Cell Biol. / Year: 2014
Title: Structural and functional analysis of MiD51, a dynamin receptor required for mitochondrial fission.
Authors: Richter, V. / Palmer, C.S. / Osellame, L.D. / Singh, A.P. / Elgass, K. / Stroud, D.A. / Sesaki, H. / Kvansakul, M. / Ryan, M.T.
History
DepositionDec 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,56814
Polymers155,2914
Non-polymers2,27710
Water6,143341
1
A: Mitochondrial dynamic protein MID51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3463
Polymers38,8231
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial dynamic protein MID51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3423
Polymers38,8231
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitochondrial dynamic protein MID51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6306
Polymers38,8231
Non-polymers8075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mitochondrial dynamic protein MID51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2502
Polymers38,8231
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Mitochondrial dynamic protein MID51
hetero molecules

D: Mitochondrial dynamic protein MID51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5965
Polymers77,6452
Non-polymers9503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_546x,y-1,z+11
Buried area4160 Å2
ΔGint-43 kcal/mol
Surface area29520 Å2
MethodPISA
6
C: Mitochondrial dynamic protein MID51
hetero molecules

B: Mitochondrial dynamic protein MID51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9729
Polymers77,6452
Non-polymers1,3277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4390 Å2
ΔGint-48 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.573, 79.265, 79.375
Angle α, β, γ (deg.)65.44, 84.18, 63.35
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 38822.656 Da / Num. of mol.: 4 / Fragment: unp residues 119-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: candidate 7-like, MID51, MIEF1, SMCR7L, Smith-Magenis syndrome chromosome region
Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9NQG6
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 8000, 0.1M HEPES, 10% 2-propanol, 0.2M ammonium sulfate, 0.01M ADP, 0.01M manganese chloride , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 62135 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.7 / Num. unique all: 62135

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.189 Å / SU ML: 0.27 / σ(F): 1.98 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 3090 4.97 %random
Rwork0.2161 ---
obs-62135 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10165 0 140 341 10646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610539
X-RAY DIFFRACTIONf_angle_d1.02814411
X-RAY DIFFRACTIONf_dihedral_angle_d15.9633848
X-RAY DIFFRACTIONf_chiral_restr0.0341676
X-RAY DIFFRACTIONf_plane_restr0.0041825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33590.31591150.29222720X-RAY DIFFRACTION97
2.3359-2.37420.31031340.28082616X-RAY DIFFRACTION97
2.3742-2.41520.30611500.27212718X-RAY DIFFRACTION98
2.4152-2.45910.28881450.26132619X-RAY DIFFRACTION97
2.4591-2.50640.27041440.26452696X-RAY DIFFRACTION97
2.5064-2.55750.28781480.25792660X-RAY DIFFRACTION98
2.5575-2.61310.28491420.24432648X-RAY DIFFRACTION97
2.6131-2.67390.3031430.25752698X-RAY DIFFRACTION98
2.6739-2.74070.3071280.26072706X-RAY DIFFRACTION98
2.7407-2.81480.27051160.24892692X-RAY DIFFRACTION98
2.8148-2.89760.30741580.24622685X-RAY DIFFRACTION98
2.8976-2.99110.25071400.23772667X-RAY DIFFRACTION98
2.9911-3.0980.2691360.22922685X-RAY DIFFRACTION98
3.098-3.2220.27381550.2192695X-RAY DIFFRACTION98
3.222-3.36850.25331400.22072679X-RAY DIFFRACTION98
3.3685-3.5460.20891480.20792686X-RAY DIFFRACTION98
3.546-3.7680.25881360.19982699X-RAY DIFFRACTION98
3.768-4.05870.23521480.19752681X-RAY DIFFRACTION98
4.0587-4.46660.21581200.17822705X-RAY DIFFRACTION98
4.4666-5.11170.21841460.17692667X-RAY DIFFRACTION97
5.1117-6.43560.24331570.21192697X-RAY DIFFRACTION99
6.4356-39.19470.18351410.18632726X-RAY DIFFRACTION99
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)
14.87820.5575-0.97051.3356-0.83752.98820.61520.87161.56550.3202-0.30340.2217-0.7548-0.1256-0.11750.37030.03990.0730.29360.12460.60311.4966-9.7281-17.4658
25.10051.6906-0.31175.5444-1.3312.79890.0331-0.23790.30870.76450.43910.7468-0.3964-0.7914-0.32360.330.16080.1090.53820.00550.4504-19.552-24.89840.0234
31.4545-0.33990.51822.43-1.24480.5057-0.0282-0.3149-0.59480.36350.32670.5946-0.061-0.2194-0.3130.3409-0.00540.05130.33180.0920.4817-8.676-44.4939-0.5185
42.2036-1.3278-0.78590.64530.02230.41590.1621-0.158-0.4923-0.44520.0760.64540.0199-0.4469-0.26660.35360.04130.00490.53810.23860.7387-24.9849-35.3441-5.2959
53.5603-1.6168-0.63016.3201-1.75023.2677-0.15670.25970.1457-0.34520.28650.5624-0.2967-0.8003-0.11030.25740.0302-0.03390.40280.08410.4567-17.8795-29.414-8.7245
62.36790.5461-1.28312.8411-0.85631.72970.0344-0.1056-0.05950.05430.01080.1572-0.01770.0427-0.00110.16820.034-0.02420.23130.02540.24010.7171-30.7485-9.3496
72.81770.8363-0.763.99910.23961.7189-0.08440.2751-0.0232-0.02680.1094-0.08270.10140.1696-0.01080.1897-0.00550.01860.23070.0040.191510.1832-26.7061-16.7191
82.0475-0.425-0.05812.01060.50521.86410.15350.08280.12060.20030.1511-0.5260.23850.358-0.30810.2368-0.017-0.0340.3798-0.00470.2612-25.2031-8.5285-30.0496
92.51910.6021-1.51911.94080.71691.8184-0.17760.5527-0.27670.08610.04390.07580.3098-0.18780.10160.3356-0.0545-0.01990.3538-0.02980.1783-45.2615-22.9351-35.0547
106.20331.70384.92822.37451.35753.88790.4493-0.6482-0.59380.3278-0.2641-0.87970.16830.5761-0.08240.39570.0366-0.12060.50950.05320.5449-20.2955-20.0377-24.7532
111.32280.5537-0.29622.76230.73951.65320.05220.11810.1977-0.14450.0402-0.0501-0.24410.1182-0.06490.2497-0.0277-0.01470.25570.03410.1977-39.33260.0074-25.5993
121.5683-1.85560.67853.76161.674.38580.3722-0.8020.20161.4827-0.4520.31620.3787-0.00910.30330.6081-0.045-0.01880.40410.02270.2506-38.74425.0047-8.0472
135.138-6.6258-1.43948.85531.8470.30960.182-0.09220.6712-0.4952-0.1095-1.16130.16080.1553-0.2030.2823-0.03120.02010.4840.01360.86849.41438.34897.1309
142.14630.7239-0.58342.082-0.15511.23220.0932-0.15060.03040.2120.0231-0.19080.05480.2646-0.07650.25560.0461-0.07270.2681-0.02230.1858-22.07379.397216.4812
154.1283.2181.50474.00811.06153.08180.29680.0990.16940.1723-0.14840.41430.1675-0.1197-0.07530.24740.0564-0.00770.1970.00370.274-38.6086.275213.5672
162.43880.41570.39453.73310.72150.9378-0.08620.51110.2758-0.50060.1952-0.1285-0.21260.2261-0.1250.37160.00650.00380.3929-0.02550.2307-21.013217.05059.8555
174.61971.0706-1.44223.1132-0.55431.5973-0.1179-0.3774-0.7877-0.1764-0.1045-0.99110.0870.51560.20950.31810.05120.04980.44970.00480.613-3.3365-1.94079.4134
184.01650.02060.32080.83351.11792.0964-0.44070.6895-0.4087-0.82590.0233-0.7661-0.18330.43090.20290.56980.04830.18430.4469-0.07730.5895-5.8639-3.6836-2.1228
193.55470.2692-1.16281.63610.76792.6954-0.03630.1014-0.219-0.23710.036-0.1128-0.2717-0.1941-0.02270.44420.02930.08480.32980.03490.32833.8267.7582-50.1236
201.1052-0.9874-0.08661.52381.4252.87020.2474-0.0881-0.14980.41740.3566-0.23750.02580.1278-0.54670.489-0.02340.20690.4036-0.02021.046711.8754-14.5413-50.2925
214.89430.9061-0.24824.53410.17693.72880.0782-0.24390.20270.20280.4335-1.0568-0.67310.9126-0.24190.7778-0.20830.13740.6266-0.22560.650220.227813.1535-47.083
223.89630.7893-0.32432.84690.79122.3732-0.0511-0.3312-0.2724-0.1103-0.0547-0.2207-0.2089-0.3602-0.14920.33040.04240.10440.4781-0.00210.38830.01631.9352-47.248
231.1850.4422-0.88373.70410.05781.47980.2309-0.05420.3324-0.3239-0.31860.3155-0.379-0.7662-0.0690.49350.12140.10340.6334-0.08670.4935-14.786512.7138-40.5367
242.4980.5294-0.44993.1598-0.43512.03670.0785-0.30660.21940.5654-0.25470.1194-0.3441-0.24280.30770.5279-0.05330.0850.7208-0.07360.4401-12.23856.9952-32.4777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 289 )
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 318 )
6X-RAY DIFFRACTION6chain 'A' and (resid 319 through 381 )
7X-RAY DIFFRACTION7chain 'A' and (resid 382 through 462 )
8X-RAY DIFFRACTION8chain 'B' and (resid 132 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 282 )
10X-RAY DIFFRACTION10chain 'B' and (resid 283 through 305 )
11X-RAY DIFFRACTION11chain 'B' and (resid 306 through 439 )
12X-RAY DIFFRACTION12chain 'B' and (resid 440 through 462 )
13X-RAY DIFFRACTION13chain 'C' and (resid 131 through 150 )
14X-RAY DIFFRACTION14chain 'C' and (resid 151 through 235 )
15X-RAY DIFFRACTION15chain 'C' and (resid 236 through 271 )
16X-RAY DIFFRACTION16chain 'C' and (resid 272 through 333 )
17X-RAY DIFFRACTION17chain 'C' and (resid 334 through 420 )
18X-RAY DIFFRACTION18chain 'C' and (resid 421 through 462 )
19X-RAY DIFFRACTION19chain 'D' and (resid 132 through 230 )
20X-RAY DIFFRACTION20chain 'D' and (resid 231 through 269 )
21X-RAY DIFFRACTION21chain 'D' and (resid 270 through 305 )
22X-RAY DIFFRACTION22chain 'D' and (resid 306 through 359 )
23X-RAY DIFFRACTION23chain 'D' and (resid 360 through 421 )
24X-RAY DIFFRACTION24chain 'D' and (resid 422 through 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