[English] 日本語
Yorodumi
- PDB-5zzw: Proteobacterial origin of protein arginine methylation and regula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zzw
TitleProteobacterial origin of protein arginine methylation and regulation of Complex I assembly by MidA
ComponentsProtein arginine methyltransferase NDUFAF7 homolog, mitochondrial
KeywordsTRANSFERASE / Mitochondria Complex I / Methyl Transferase / MidA/NDUFAF7 / SAM / SAH / NDUFS2
Function / homology
Function and homology information


Complex I biogenesis / pinocytosis / phototaxis / culmination involved in sorocarp development / type II protein arginine methyltransferase / glutamate metabolic process / protein-arginine omega-N symmetric methyltransferase activity / thermotaxis / sporulation resulting in formation of a cellular spore / glycogen metabolic process ...Complex I biogenesis / pinocytosis / phototaxis / culmination involved in sorocarp development / type II protein arginine methyltransferase / glutamate metabolic process / protein-arginine omega-N symmetric methyltransferase activity / thermotaxis / sporulation resulting in formation of a cellular spore / glycogen metabolic process / positive regulation of mitochondrial fission / mitochondrial respiratory chain complex I assembly / phagocytosis / ATP metabolic process / negative regulation of autophagy / methylation / mitochondrion
Similarity search - Function
Protein arginine methyltransferase NDUFAF7 / Protein arginine methyltransferase NDUFAF7 superfamily / Putative S-adenosyl-L-methionine-dependent methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArold, S.T. / Swaminathan, K. / Hameed, U.F.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: Cell Rep / Year: 2018
Title: Proteobacterial Origin of Protein Arginine Methylation and Regulation of Complex I Assembly by MidA.
Authors: Shahul Hameed, U.F.S. / Sanislav, O. / Lay, S.T. / Annesley, S.J. / Jobichen, C. / Fisher, P.R. / Swaminathan, K. / Arold, S.T.
History
DepositionJun 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
A: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
C: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9436
Polymers140,7903
Non-polymers1,1533
Water72140
1
B: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3142
Polymers46,9301
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3142
Polymers46,9301
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3142
Polymers46,9301
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.950, 103.540, 192.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SAH / End label comp-ID: SAH / Refine code: _ / Auth seq-ID: 83 - 501 / Label seq-ID: 13

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BA - D
21AB - E
12BA - D
22CC - F
13AB - E
23CC - F

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial / Mitochondrial dysfunction gene A / NADH dehydrogenase [ubiquinone] complex I / assembly factor 7 homolog


Mass: 46930.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: midA, DDB_G0282615 / Production host: Escherichia coli (E. coli)
References: UniProt: Q54S83, type II protein arginine methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M BIS-TRIS pH 6.5, 10% w/v polyethylene glycol 10000

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.59→54.54 Å / Num. obs: 43310 / % possible obs: 97.7 % / Redundancy: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.186 / Net I/σ(I): 4.9
Reflection shellResolution: 2.59→2.693 Å / Num. unique obs: 4454

-
Processing

Software
NameVersionClassification
REFMAC5.8.0216refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZTZ

5ztz


Resolution: 2.6→54.54 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.901 / SU B: 42.695 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R: 0.963 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27989 2280 5 %RANDOM
Rwork0.24847 ---
obs0.25001 43310 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.264 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---0.31 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.6→54.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9579 0 78 40 9697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199870
X-RAY DIFFRACTIONr_bond_other_d0.0020.029366
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.97813326
X-RAY DIFFRACTIONr_angle_other_deg0.825321828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22551197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72425.07426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.542151821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0131533
X-RAY DIFFRACTIONr_chiral_restr0.0950.21485
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021920
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7914.7824806
X-RAY DIFFRACTIONr_mcbond_other0.7914.7814805
X-RAY DIFFRACTIONr_mcangle_it1.4537.1685997
X-RAY DIFFRACTIONr_mcangle_other1.4537.1695998
X-RAY DIFFRACTIONr_scbond_it0.4484.855064
X-RAY DIFFRACTIONr_scbond_other0.4484.855064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8687.2577329
X-RAY DIFFRACTIONr_long_range_B_refined3.6956.2211113
X-RAY DIFFRACTIONr_long_range_B_other3.6956.22611113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B122190.14
12A122190.14
21B122190.13
22C122190.13
31A123340.13
32C123340.13
LS refinement shellResolution: 2.599→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 164 -
Rwork0.373 3113 -
obs--99.24 %
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)
13.9628-1.0046-0.17221.82750.81861.90680.15560.29180.3357-0.2957-0.0085-0.1926-0.14540.1085-0.14710.3125-0.02780.02630.03360.0030.174-15.75826.409-9.293
23.1381-0.8431-0.85973.93271.13892.6224-0.1935-0.2069-0.06860.35280.03160.20380.2478-0.02570.16190.4697-0.06110.01110.15080.02630.02040.14463.917-27.024
32.0981-0.03640.30942.1568-0.3772.0844-0.09120.02830.1686-0.0992-0.04760.14-0.2581-0.21210.13880.54130.0759-0.00430.1774-0.07040.0567.47359.37132.786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B83 - 501
2X-RAY DIFFRACTION2A83 - 501
3X-RAY DIFFRACTION3C83 - 501

+
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