[English] 日本語
Yorodumi
- PDB-8twd: Structure of IraM-bound RssB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8twd
TitleStructure of IraM-bound RssB
Components
  • Anti-adapter protein IraM
  • Regulator of RpoS
KeywordsSIGNALING PROTEIN / response regulator / ClpXP anti-adaptor
Function / homology
Function and homology information


sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / positive regulation of proteolysis / cellular response to starvation / protein-DNA complex / protein destabilization / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription ...sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / positive regulation of proteolysis / cellular response to starvation / protein-DNA complex / protein destabilization / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytoplasm / cytosol
Similarity search - Function
Anti-adapter protein IraM / Signal transduction protein PmrD superfamily / Regulator of RpoS / : / PPM-type phosphatase-like domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
ACETATE ION / Regulator of RpoS / Anti-adapter protein IraM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBrugger, C. / Deaconescu, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121975 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144124 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: IraM remodels the RssB segmented helical linker to stabilize sigma s against degradation by ClpXP.
Authors: Brugger, C. / Srirangam, S. / Deaconescu, A.M.
History
DepositionAug 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-adapter protein IraM
B: Anti-adapter protein IraM
C: Regulator of RpoS
D: Regulator of RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2035
Polymers93,1444
Non-polymers591
Water00
1
A: Anti-adapter protein IraM
C: Regulator of RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6313
Polymers46,5722
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area19180 Å2
MethodPISA
2
B: Anti-adapter protein IraM
D: Regulator of RpoS


Theoretical massNumber of molelcules
Total (without water)46,5722
Polymers46,5722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-29 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.664, 191.229, 96.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Anti-adapter protein IraM


Mass: 9233.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iraM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8SRD3
#2: Protein Regulator of RpoS


Mass: 37338.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rssB, hnr, sprE, ychL, b1235, JW1223 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEV1
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.5 120mM magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 2, 2018
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.3→49.33 Å / Num. obs: 18674 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 119.84 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 17.3
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 3782 / CC1/2: 0.79

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→49.33 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 33.0358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 1722 10.07 %
Rwork0.2446 15381 -
obs0.2474 17103 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 158.02 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 4 0 6405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326527
X-RAY DIFFRACTIONf_angle_d0.64278857
X-RAY DIFFRACTIONf_chiral_restr0.04351032
X-RAY DIFFRACTIONf_plane_restr0.00421127
X-RAY DIFFRACTIONf_dihedral_angle_d11.91352409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.40.4311200.39551021X-RAY DIFFRACTION74.62
3.4-3.510.41681250.34271099X-RAY DIFFRACTION79.48
3.51-3.630.36281260.30411167X-RAY DIFFRACTION84.73
3.63-3.780.30041350.30451214X-RAY DIFFRACTION87.65
3.78-3.950.32951380.29171222X-RAY DIFFRACTION89.65
3.95-4.160.27811490.29461293X-RAY DIFFRACTION93.27
4.16-4.420.311490.24321348X-RAY DIFFRACTION96.39
4.42-4.760.23081490.21621352X-RAY DIFFRACTION97.47
4.76-5.240.2961540.24111381X-RAY DIFFRACTION98.33
5.24-5.990.29861550.27651390X-RAY DIFFRACTION98.72
6-7.540.31681550.27711415X-RAY DIFFRACTION98.74
7.55-49.330.20131670.18291479X-RAY DIFFRACTION99.46
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)
13.99985627702-2.415004158911.224770782932.9585310212-1.589414415088.64148384563-0.478954829352.844046090880.786133963585-0.8451593794630.0248895124447-0.107701167748-0.5011528798770.4739784456740.6146905671961.86104355456-0.4275210791910.1279964614260.7461454072890.1210385828161.2306779388629.75990020313.0942966013-1.08277693461
26.4048493286-4.04577200245-4.816010918357.504264103386.993224935086.74692409866-1.70794794363-2.00775927854-0.9143953000421.635971120872.783411758430.8369067033081.37054744622.050429147460.9584971218530.700835187009-0.5422873867840.5333389735970.344227492928-0.0914236692451.4050364737635.23654882168.768719876136.45372432063
36.541837025234.651076801441.853274223172.991477683161.144287647985.202242682460.3439368643910.0618054867801-0.09440407074460.118201733558-0.02192127366630.319215227886-0.0430659143720.15809370942-0.1799762263751.35695844650.09471991223010.1790775287130.541455765675-0.009221720658831.3633061233430.715326293310.90730422352.10558899261
42.03040714922-6.77845212547-4.049708860514.72271604364.802876326012.012711722-1.63905112036-0.571209787696-2.0792676491.9323404138-1.079581628710.93623067751-0.137811954201-2.726331026852.683465422390.7642266942290.06505168749630.005766111399150.725531794695-0.116846931981.4894917367220.1319622519.405902292920.160912722915
57.37346987252-1.17433796424-1.164068873750.5211524553840.2021405041254.02286816758-0.07099665235460.3678220241621.074756780180.5327088497570.2285468772331.02764428576-0.2604453254331.36695671109-0.2233143943891.20167186642-0.144562621651-0.02093562510530.552675110313-0.03462735349541.1024088142132.887433004811.17391355355.72195047886
67.470702755891.84306194486-0.8474756292244.50321949851.5501928678.41107632682-0.227313370076-0.2347201898820.8447962894070.3101808364160.160996220585-0.119151460872-0.8115824512050.118834741664-0.05704992000171.10377319515-0.00276481826308-0.05731362775420.691489406399-0.02668376008171.096904189819.2497636872222.411008488418.0435776056
76.179396657363.339775658830.29454007434.41332393788-2.35636985095.646214134461.25893053012-1.10190297298-2.01459373582-1.56903217822-2.47429510315-0.932580489911-0.579942212572-0.716139107087-0.0918844758361.36625799081-0.0215752621039-0.5132480951280.976254285185-0.2465431297121.290844589156.3375424365819.803143023115.4076279497
89.89890318661-3.22265119491-6.537951339952.848262473054.565751614889.61866775004-0.383478437605-2.092927108460.791877672939-1.878111187620.193989217604-1.282033875483.3657621938-0.611554984891-0.03329999455581.21030261691-0.223650455895-0.03879698318721.15591030465-0.0724847161421.1824771869812.179456839316.890428409122.5682026858
92.32240774137-0.2227163869920.549010906942.404013063391.494821121921.18764636864-1.3076431493-2.11576530163-1.341295154772.3163125314-1.673351553340.5606193114664.58781241968-0.948220876392.779872549711.95716111524-0.3221460839410.6012374380241.376975812940.01951013412081.3541308019810.04511138759.9292903871222.4435712015
103.51308072762-5.79509591355-2.390956908569.14467165574.347211952656.442890298871.321720350740.8175909963211.394316265370.0143813984045-0.755276468099-1.1036935935-1.57659055427-0.297181953018-0.4648677276521.7278684171-0.218504315849-0.03605664476210.7056787881970.01537723579731.103023014976.5606365830528.118056751711.0814878603
115.763934779964.62762713613-4.061275359888.8263462927-5.069840306916.97669956844-0.03346775100080.3228494120790.482203381104-0.931159607153-0.138719303676-0.3163093977070.09785507927340.2220929172630.3257358622291.53825850985-0.118339914490.08842502437310.724553009294-0.02022805517021.3755722794336.615154652232.5046285526-4.71686520553
128.29507486249-0.6673439868982.533870536234.60441781051-1.627575010483.140607042780.341153228253-0.766033349772-1.001246171080.185260443312-0.0215697391191-0.1622755785170.1708684314940.235527636857-0.2989746612451.14994600988-0.0222824602939-0.005556483926651.124892583850.03617778577541.0221148172844.24063553764.972281187527.7488655988
136.029803115120.879531560064-0.8045459699795.445686529384.08447251168.04100020883-0.199074157981-0.09095938242280.00183225675132-0.0867706716433-0.1227851411770.5213171419090.0209892222957-0.1520606340720.3706805392681.48606212479-0.15274210658-0.08374289899170.649845484893-0.1961522037651.2245444601419.475025774142.477274766825.9470406743
144.65276924121-2.23119533089-0.125641563656.4922829771-1.911364901391.77640849050.3269696803841.43103252624-0.0947869658986-0.6907263629150.05819252771410.4841060020370.355795261166-0.514110849895-0.4152426026591.209225633410.0457243148482-0.09480015015571.18835548027-0.0215215139290.814975794211-2.8988380812228.8042796553-6.46346553045
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 11 )AA-1 - 111 - 13
22chain 'A' and (resid 12 through 22 )AA12 - 2214 - 24
33chain 'A' and (resid 23 through 43 )AA23 - 4325 - 45
44chain 'A' and (resid 44 through 52 )AA44 - 5246 - 54
55chain 'A' and (resid 53 through 78 )AA53 - 7855 - 80
66chain 'B' and (resid -1 through 25 )BB-1 - 251 - 27
77chain 'B' and (resid 26 through 37 )BB26 - 3728 - 39
88chain 'B' and (resid 38 through 47 )BB38 - 4740 - 49
99chain 'B' and (resid 48 through 59 )BB48 - 5950 - 61
1010chain 'B' and (resid 60 through 78 )BB60 - 7862 - 80
1111chain 'C' and (resid 2 through 146 )CC2 - 1461 - 145
1212chain 'C' and (resid 147 through 335 )CC147 - 335146 - 328
1313chain 'D' and (resid 2 through 134 )DD2 - 1341 - 133
1414chain 'D' and (resid 135 through 335 )DD135 - 335134 - 329

+
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://pdbjlvh1.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