[English] 日本語
Yorodumi
- PDB-7o9v: hypothetical protein OMM_04225 residues 244-274 from Candidatus M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o9v
Titlehypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors
ComponentsGeneral control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4
KeywordsPROTEIN FIBRIL / Coiled Coil / beta layer / hexad repeat
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
FG-GAP-like repeat / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / FG-GAP repeat / Integrin alpha, N-terminal ...FG-GAP-like repeat / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / FG-GAP repeat / Integrin alpha, N-terminal / Fibronectin type 3 domain / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin type-III domain-containing protein / General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Candidatus Magnetoglobus multicellularis str. Araruama (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsAdlakha, J. / Albrecht, R. / Hartmann, M.D.
CitationJournal: To Be Published
Title: hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors
Authors: Adlakha, J.
History
DepositionApr 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4
B: General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4
C: General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4


Theoretical massNumber of molelcules
Total (without water)32,4593
Polymers32,4593
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-111 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.827, 34.649, 82.547
Angle α, β, γ (deg.)90.000, 93.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA216 - 2956 - 85
21GLUGLUBB216 - 2956 - 85
12ILEILEAA216 - 2966 - 86
22ILEILECC216 - 2966 - 86
13GLUGLUBB216 - 2956 - 85
23GLUGLUCC216 - 2956 - 85

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein General control transcription factor GCN4,hypothetical protein OMM_04225 residues 244-274 from Candidatus Magnetoglobus multicellularis fused to GCN4 adaptors,General control transcription factor GCN4 / Amino acid biosynthesis regulatory protein / General control protein GCN4


Mass: 10819.589 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Candidatus Magnetoglobus multicellularis str. Araruama (bacteria)
Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, OMM_04225 / Production host: Escherichia coli (E. coli) / References: UniProt: P03069, UniProt: A0A1V1P2N3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2M KSCN, 0.1M bis tris propane pH 8.5, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→37.04 Å / Num. obs: 11390 / % possible obs: 89.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.5
Reflection shellResolution: 1.99→2.12 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 570 / CC1/2: 0.657 / % possible all: 81.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YNY

2yny


Resolution: 1.99→37.04 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 19.611 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3149 779 6.8 %RANDOM
Rwork0.2618 ---
obs0.2656 10611 67.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 44.231 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å21.18 Å2
2--1.16 Å2-0 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 1.99→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 26 2052
Biso mean---35.05 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192051
X-RAY DIFFRACTIONr_bond_other_d0.0060.022026
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9742755
X-RAY DIFFRACTIONr_angle_other_deg1.40134697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.64126.91594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55615441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.155153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022215
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02396
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A39190.16
12B39190.16
21A38910.16
22C38910.16
31B37900.17
32C37900.17
LS refinement shellResolution: 1.99→2.041 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 13 -
Rwork0.375 187 -
all-200 -
obs--15.63 %
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)
12.48081.1208-3.96192.574-2.92614.538-0.04530.0311-0.01830.03320.0081-0.0993-0.29810.0010.03720.03970.0268-0.03970.0518-0.01840.181720.915-1.4191.966
22.5942-1.4649-4.3941.81072.078814.9035-0.06970.0118-0.0882-0.0460.0104-0.01410.14850.14550.05930.0441-0.0298-0.05660.04740.00480.216912.371-3.119-1.308
31.71680.01241.41941.26130.642515.5186-0.03060.0189-0.0143-0.0025-0.00950.08030.0478-0.00860.040.0585-0.0093-0.00230.00340.01830.214615.065.8760.525
44.06760.2462-9.55640.6237-1.273623.96540.87210.44650.5661-0.02130.11180.0844-1.7349-1.3776-0.9840.40180.03050.13290.37010.00540.42195.5482.28940.558
54.47261.1899-7.56561.4029-5.579924.51520.41960.36560.2514-0.0753-0.2073-0.0058-0.11360.3907-0.21230.39460.06330.05230.33560.00130.17225.8350.46240.52
65.5281.7988-7.63580.7293-1.588117.13980.23950.51670.08260.05250.10230.0586-0.2804-1.2225-0.34190.39220.10530.12790.390.08280.32894.4020.90539.824
73.29420.8314-4.87811.93570.125213.4596-0.0128-0.0757-0.04440.08180.10530.04950.0040.1721-0.09250.0570.0428-0.06850.0640.00490.2088-2.977-2.40476.042
83.4304-0.7093-7.12411.58961.801917.257-0.06360.0510.0539-0.10510.00410.0336-0.1510.07850.05960.0505-0.0183-0.07150.12770.01330.2174-12.848-1.57573.475
91.91710.1316-2.01920.82280.43279.4450.07210.13810.0986-0.1278-0.0072-0.0858-0.1465-0.0247-0.06490.17370.0192-0.01580.0199-0.01120.2693-7.8076.03375.169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A216 - 245
2X-RAY DIFFRACTION2B215 - 245
3X-RAY DIFFRACTION3C216 - 245
4X-RAY DIFFRACTION4A246 - 270
5X-RAY DIFFRACTION5B246 - 270
6X-RAY DIFFRACTION6C246 - 270
7X-RAY DIFFRACTION7A271 - 296
8X-RAY DIFFRACTION8B271 - 298
9X-RAY DIFFRACTION9C271 - 296

+
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