[English] 日本語
Yorodumi
- PDB-6hmj: Structure of an RNA-binding Light-Oxygen-Voltage Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hmj
TitleStructure of an RNA-binding Light-Oxygen-Voltage Receptor
ComponentsPutative PAS/PAC sensor protein
KeywordsSIGNALING PROTEIN / sensory photoreceptor / light-oxygen-voltage / RNA binding
Function / homology
Function and homology information


nucleotide binding / RNA binding
Similarity search - Function
ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / CheY-like superfamily ...ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / CheY-like superfamily / PAS repeat profile. / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / IMIDAZOLE / Putative PAS/PAC sensor protein
Similarity search - Component
Biological speciesNakamurella multipartita DSM 44233 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsZiegler, T. / Moniot, S. / Moeglich, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMO2192/6-1 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A blue light receptor that mediates RNA binding and translational regulation.
Authors: Weber, A.M. / Kaiser, J. / Ziegler, T. / Pilsl, S. / Renzl, C. / Sixt, L. / Pietruschka, G. / Moniot, S. / Kakoti, A. / Juraschitz, M. / Schrottke, S. / Lledo Bryant, L. / Steegborn, C. / ...Authors: Weber, A.M. / Kaiser, J. / Ziegler, T. / Pilsl, S. / Renzl, C. / Sixt, L. / Pietruschka, G. / Moniot, S. / Kakoti, A. / Juraschitz, M. / Schrottke, S. / Lledo Bryant, L. / Steegborn, C. / Bittl, R. / Mayer, G. / Moglich, A.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative PAS/PAC sensor protein
B: Putative PAS/PAC sensor protein
C: Putative PAS/PAC sensor protein
D: Putative PAS/PAC sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,98114
Polymers161,6874
Non-polymers2,29510
Water2,846158
1
A: Putative PAS/PAC sensor protein
B: Putative PAS/PAC sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9176
Polymers80,8432
Non-polymers1,0744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-67 kcal/mol
Surface area34350 Å2
MethodPISA
2
C: Putative PAS/PAC sensor protein
D: Putative PAS/PAC sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0648
Polymers80,8432
Non-polymers1,2216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-60 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.013, 150.345, 219.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative PAS/PAC sensor protein


Mass: 40421.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nakamurella multipartita DSM 44233 (bacteria)
Strain: ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 / Y-104
Gene: Namu_4361 / Production host: Escherichia coli (E. coli) / References: UniProt: C8XJT7

-
Non-polymers , 5 types, 168 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 277.3 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bicine, pH 9.2, 15% (w/v) PEG 20,000, 2% dioxane, 0.8 M imidazole acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91814 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91814 Å / Relative weight: 1
ReflectionResolution: 2.51→71.127 Å / Num. obs: 75981 / % possible obs: 98.69 % / Redundancy: 4.3 % / Rpim(I) all: 0.1082 / Rrim(I) all: 0.2283 / Net I/σ(I): 8
Reflection shellResolution: 2.51→2.6 Å / Rpim(I) all: 1.074 / Rrim(I) all: 2.321

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→71.127 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 3748 4.94 %
Rwork0.2431 --
obs0.2437 75886 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→71.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10733 0 155 158 11046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211101
X-RAY DIFFRACTIONf_angle_d0.63415148
X-RAY DIFFRACTIONf_dihedral_angle_d12.1556608
X-RAY DIFFRACTIONf_chiral_restr0.0411764
X-RAY DIFFRACTIONf_plane_restr0.0041976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.54180.46961390.46692619X-RAY DIFFRACTION99
2.5418-2.57530.44551330.43972675X-RAY DIFFRACTION99
2.5753-2.61050.431380.4232655X-RAY DIFFRACTION99
2.6105-2.64780.36451290.38572662X-RAY DIFFRACTION100
2.6478-2.68740.37041480.37622649X-RAY DIFFRACTION99
2.6874-2.72940.32151190.33962645X-RAY DIFFRACTION100
2.7294-2.77410.34021400.33922661X-RAY DIFFRACTION99
2.7741-2.82190.39721350.32112656X-RAY DIFFRACTION99
2.8219-2.87330.35351550.31092623X-RAY DIFFRACTION99
2.8733-2.92850.32651730.30752641X-RAY DIFFRACTION99
2.9285-2.98830.31021200.30412652X-RAY DIFFRACTION100
2.9883-3.05330.37071250.30232690X-RAY DIFFRACTION98
3.0533-3.12430.33931480.31372628X-RAY DIFFRACTION100
3.1243-3.20240.3051350.30372693X-RAY DIFFRACTION98
3.2024-3.2890.3051390.27812648X-RAY DIFFRACTION100
3.289-3.38580.28211330.25292669X-RAY DIFFRACTION98
3.3858-3.49510.26671390.24992657X-RAY DIFFRACTION99
3.4951-3.620.24251300.24622637X-RAY DIFFRACTION98
3.62-3.76490.26011400.24292687X-RAY DIFFRACTION99
3.7649-3.93630.27151380.23862687X-RAY DIFFRACTION99
3.9363-4.14380.21851440.21072673X-RAY DIFFRACTION100
4.1438-4.40330.24071400.18892705X-RAY DIFFRACTION99
4.4033-4.74330.20281370.17522681X-RAY DIFFRACTION98
4.7433-5.22050.17471430.18712688X-RAY DIFFRACTION98
5.2205-5.97560.22741350.21062711X-RAY DIFFRACTION98
5.9756-7.52720.22121580.23452714X-RAY DIFFRACTION97
7.5272-71.15570.18231350.19132832X-RAY DIFFRACTION96
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)
18.51482.08142.73486.61170.72132.8652-0.11450.6690.1145-0.8924-0.0498-0.1228-0.44620.14280.15030.86650.1826-0.01680.67220.00890.3925.877178.710786.5689
21.051-1.0749-2.11960.56281.49665.07860.07320.02840.0154-0.20470.0598-0.0786-0.05140.441-0.17570.5859-0.04360.03250.6403-0.07250.5237-12.760393.0474138.5437
31.99761.0172-2.53995.0116-2.52537.3944-0.0325-0.14280.13290.31520.03740.2245-0.04530.2846-0.01130.33260.0706-0.03770.5114-0.07030.4915-21.2886102.1696180.0543
4-0.29170.11010.57392.4641.99724.76140.0010.1837-0.0526-0.1663-0.1190.3576-0.1866-0.65250.16320.35210.0985-0.02710.51040.020.5794-27.6219102.75163.9345
57.81193.4152-4.38787.0611-1.73062.6526-0.1143-0.07831.29560.218-0.1484-0.9635-0.93740.66260.27540.8920.0639-0.24930.79550.07481.245121.384192.5374100.3312
68.18070.4111-3.25031.2321-0.3764.9189-0.1116-0.04720.60720.0203-0.04160.02990.0257-0.22260.13960.69390.132-0.08210.538-0.04530.495110.239182.6974104.5981
75.71990.96770.27758.77732.03255.9611-0.18040.0108-0.65320.55140.2222-0.17671.61960.6966-0.02911.08060.17550.02460.6149-0.09840.5829-11.162976.0119147.4897
82.9339-0.3994-2.32681.66880.25744.0946-0.3738-0.4486-0.541-0.01830.082-0.03511.15710.85460.21050.88060.260.02080.68290.10140.5735-16.430980.2594178.5826
94.9145-0.66671.57055.9544-0.01824.1097-0.2555-0.60661.07780.29210.1629-0.2138-0.3537-0.06230.12790.8313-0.16480.15850.6531-0.3691.20537.2334128.9498167.3933
101.7541-1.8037-1.4357.08233.30313.5790.07930.02880.05980.0152-0.22570.2307-0.0026-0.02560.20840.2656-0.0050.00040.4247-0.00090.453627.712280.0111128.4124
111.3687-0.6385-0.10532.86440.5552.48230.27640.2664-0.009-0.6862-0.2291-0.12130.02420.1794-0.0820.60080.10160.140.53780.01980.462737.146666.6228108.3931
126.3721-3.0212-0.63354.37110.58311.5767-0.06690.42950.5342-0.69830.2302-0.1837-0.10230.0477-0.22840.7817-0.2080.08970.4849-0.06560.6327-1.3697117.7724153.4323
131.3144-0.5650.02195.3507-0.28481.88030.0274-0.1605-0.13350.3759-0.02650.23830.1828-0.10760.0380.37-0.10550.00810.48510.01480.440728.032854.5697131.6349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 293 )
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 373 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 134 )
7X-RAY DIFFRACTION7chain 'B' and (resid 135 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 367 )
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 113 )
10X-RAY DIFFRACTION10chain 'C' and (resid 114 through 244 )
11X-RAY DIFFRACTION11chain 'C' and (resid 245 through 373 )
12X-RAY DIFFRACTION12chain 'D' and (resid 11 through 134 )
13X-RAY DIFFRACTION13chain 'D' and (resid 135 through 366 )

+
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