[English] 日本語
Yorodumi
- PDB-3r2c: Crystal Structure of Antitermination Factors NusB and NusE in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r2c
TitleCrystal Structure of Antitermination Factors NusB and NusE in complex with BoxA RNA
Components
  • 30S ribosomal protein S10
  • 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
  • N utilization substance protein B
KeywordsTRANSCRIPTION/RNA / cross species NusB-NusE-RNA interaction / transcription elongation / gene regulation / protein-RNA interaction / TRANSCRIPTION-RNA complex
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / small ribosomal subunit / tRNA binding / structural constituent of ribosome / translation / RNA binding / cytosol
Similarity search - Function
N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Ribosomal protein S10 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 ...N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Ribosomal protein S10 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / RNA / RNA (> 10) / Small ribosomal subunit protein uS10 / Transcription antitermination protein NusB
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.902 Å
AuthorsStagno, J.R. / Ji, X.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination.
Authors: Stagno, J.R. / Altieri, A.S. / Bubunenko, M. / Tarasov, S.G. / Li, J. / Court, D.L. / Byrd, R.A. / Ji, X.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N utilization substance protein B
B: N utilization substance protein B
J: 30S ribosomal protein S10
K: 30S ribosomal protein S10
R: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
S: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,07618
Polymers60,8976
Non-polymers1,17912
Water4,306239
1
A: N utilization substance protein B
J: 30S ribosomal protein S10
R: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,14410
Polymers30,4483
Non-polymers6967
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N utilization substance protein B
K: 30S ribosomal protein S10
S: 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9328
Polymers30,4483
Non-polymers4845
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.530, 113.008, 65.763
Angle α, β, γ (deg.)90.000, 102.870, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ABJK

#1: Protein N utilization substance protein B / protein nusB


Mass: 17142.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_133, nusB / Plasmid: pDest42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66530
#2: Protein 30S ribosomal protein S10 / protein nusE


Mass: 9501.236 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_008, NUSE, rpsJ / Plasmid: pDest42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66430

-
RNA chain , 1 types, 2 molecules RS

#3: RNA chain 5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'


Mass: 3804.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: BoxA RNA / Source: (synth.) Aquifex aeolicus (bacteria)

-
Non-polymers , 3 types, 251 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE RIBOSOME BINDING LOOP (UNP RESIDUES 47-68) OF CHAINS J AND K (NUSE) HAS BEEN REPLACED WITH A ...THE RIBOSOME BINDING LOOP (UNP RESIDUES 47-68) OF CHAINS J AND K (NUSE) HAS BEEN REPLACED WITH A SERINE (SER47)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 25% PEG8000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 310K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MAR 225 / Detector: CCD / Date: Feb 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 42602 / % possible obs: 94.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.102 / Χ2: 1.6 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.80.5233541.25174.5
1.97-2.053.40.53738381.231185.1
2.05-2.1440.44741631.28192.2
2.14-2.254.70.35543611.422196.5
2.25-2.395.50.28844011.406197.9
2.39-2.585.90.22344181.299198.6
2.58-2.8460.16244991.43199.1
2.84-3.255.90.11144681.703199.1
3.25-4.095.80.06445282.109199.3
4.09-405.60.04745722.229199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.56 Å
Translation2.5 Å37.56 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R2D

3r2d


Resolution: 1.902→35.663 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8686 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 2160 5.08 %
Rwork0.1693 --
obs0.171 42498 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.845 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 122.21 Å2 / Biso mean: 37.7366 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.9657 Å20 Å2-6.5546 Å2
2---1.126 Å20 Å2
3----2.8397 Å2
Refinement stepCycle: LAST / Resolution: 1.902→35.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 376 78 239 4218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074126
X-RAY DIFFRACTIONf_angle_d1.0285605
X-RAY DIFFRACTIONf_chiral_restr0.061639
X-RAY DIFFRACTIONf_plane_restr0.005638
X-RAY DIFFRACTIONf_dihedral_angle_d15.5161680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9022-1.94640.292980.2582052215071
1.9464-1.99510.26551240.23122259238379
1.9951-2.04910.25231320.23052466259886
2.0491-2.10930.26041420.21542588273091
2.1093-2.17740.25511380.18872700283895
2.1774-2.25520.20571380.16692791292997
2.2552-2.34550.20981400.15142788292898
2.3455-2.45220.20581510.15752784293598
2.4522-2.58150.19811620.1612796295898
2.5815-2.74320.20861690.1612831300099
2.7432-2.95490.19861380.15432835297399
2.9549-3.25210.22171600.17352829298999
3.2521-3.72220.20161670.16252851301899
3.7222-4.68790.16131650.13992850301599
4.6879-35.66940.18011360.18252918305499
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)
10.4572-0.1150.28230.34220.01340.56440.0253-0.0127-0.0171-0.02560.010.01410.0293-0.018300.00850.00470.0220.04760.00110.04772.0473-24.693220.0385
20.4437-0.17790.22890.4380.11080.7587-0.0854-0.0360.008-0.0610.02710.0242-0.0757-0.021600.05990.0075-0.0150.04860.00290.050214.1246-18.288551.6574
30.2007-0.0921-0.03270.3114-0.10860.2087-0.08470.06340.04070.0628-0.0063-0.0793-0.22370.009400.1538-0.0204-0.02220.07160.0220.10028.8483-3.337524.5805
40.13370.1106-0.06330.1151-0.16650.23960.10180.0391-0.09080.00050.035-0.00720.30820.18700.19740.0765-0.06220.0872-0.03280.127418.3832-38.903942.1543
50.034-0.0731-0.02440.083-0.09290.17660.17510.0951-0.1039-0.5796-0.06250.23480.05110.060400.08670.00520.06320.1181-0.0190.00982.4505-27.26045.951
60.1365-0.00650.22380.2307-0.19820.1403-0.1428-0.0332-0.00740.080.0114-0.13880.05520.1309-00.1109-0.0033-0.00390.1507-0.01070.134127.0264-15.854557.5873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:137)A1 - 137
2X-RAY DIFFRACTION2(chain B and resid 1:140)B1 - 140
3X-RAY DIFFRACTION3(chain J and resid 3:82)J3 - 82
4X-RAY DIFFRACTION4(chain K and resid 3:81)K3 - 81
5X-RAY DIFFRACTION5(chain R and resid 1:9)R1 - 9
6X-RAY DIFFRACTION6(chain S and resid 1:10)S1 - 10

+
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