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- PDB-6pmo: Co-crystal structure of the Geobacillus kaustophilus glyQ T-box r... -

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Basic information

Entry
Database: PDB / ID: 6pmo
TitleCo-crystal structure of the Geobacillus kaustophilus glyQ T-box riboswitch discriminator domain in complex with tRNA-Gly
Components
  • T-box riboswitch discriminator
  • tRNA-Gly
KeywordsRNA / Riboswitch / tRNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65703362888 Å
AuthorsLi, S. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA-DK075136 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions.
Authors: Shuang Li / Zhaoming Su / Jean Lehmann / Vassiliki Stamatopoulou / Nikoleta Giarimoglou / Frances E Henderson / Lixin Fan / Grigore D Pintilie / Kaiming Zhang / Muyuan Chen / Steven J Ludtke ...Authors: Shuang Li / Zhaoming Su / Jean Lehmann / Vassiliki Stamatopoulou / Nikoleta Giarimoglou / Frances E Henderson / Lixin Fan / Grigore D Pintilie / Kaiming Zhang / Muyuan Chen / Steven J Ludtke / Yun-Xing Wang / Constantinos Stathopoulos / Wah Chiu / Jinwei Zhang /
Abstract: Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of ...Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: tRNA-Gly
A: T-box riboswitch discriminator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,12619
Polymers45,5302
Non-polymers2,59617
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.851, 139.913, 136.023
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

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Components

#1: RNA chain tRNA-Gly


Mass: 24156.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus kaustophilus (bacteria)
#2: RNA chain T-box riboswitch discriminator


Mass: 21373.713 Da / Num. of mol.: 1 / Mutation: A156C, U189G / Source method: obtained synthetically / Details: In vitro transcribed, unmodified RNA / Source: (synth.) Geobacillus kaustophilus (bacteria)
#3: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ir
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.18 %
Description: Rectangular prism-shaped crystals grew in 2-7 days to maximum dimensions of 300 x 300 x 50 micrometer3.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Morpheus Buffer System 2 pH 7.5 (Sodium HEPES; MOPS (acid)), 0.09 M Halogens (NaF; NaBr; NaI), 10% w/v PEG 20000, and 20% v/v PEG 500 monomethyl ether (MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 21, 2017
RadiationMonochromator: MD2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.657→34.98 Å / Num. obs: 12731 / % possible obs: 99.52 % / Redundancy: 6 % / Biso Wilson estimate: 78.2675366044 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06249 / Rpim(I) all: 0.02815 / Rrim(I) all: 0.06872 / Net I/σ(I): 16.89
Reflection shellResolution: 2.657→2.752 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.152 / Num. unique obs: 1219 / CC1/2: 0.698 / Rpim(I) all: 0.5132 / Rrim(I) all: 1.263 / % possible all: 97.59

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65703362888→34.97825 Å / SU ML: 0.481115594293 / Cross valid method: FREE R-VALUE / σ(F): 1.33790769823 / Phase error: 33.072431739
RfactorNum. reflection% reflection
Rfree0.272581164281 1263 9.92612386042 %
Rwork0.224671142035 --
obs0.229497931299 12724 99.5773986539 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 89.1436737441 Å2
Refinement stepCycle: LAST / Resolution: 2.65703362888→34.97825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2755 17 18 2790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003968292067973078
X-RAY DIFFRACTIONf_angle_d0.8023187503644790
X-RAY DIFFRACTIONf_chiral_restr0.0345453769941647
X-RAY DIFFRACTIONf_plane_restr0.00477916731104127
X-RAY DIFFRACTIONf_dihedral_angle_d15.38297465041542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.76340.3839935426341270.3714951711451231X-RAY DIFFRACTION97.8386167147
2.7634-2.88910.4615533499491380.3893668985511244X-RAY DIFFRACTION99.7833935018
2.8891-3.04130.3969215555421410.3331744437061269X-RAY DIFFRACTION99.9291282778
3.0413-3.23170.3107308833171410.2437952736381254X-RAY DIFFRACTION99.7140814868
3.2317-3.48110.2937434535161420.2327705532861265X-RAY DIFFRACTION99.5753715499
3.4811-3.8310.245461975081370.2132060159131255X-RAY DIFFRACTION99.7134670487
3.831-4.38440.2525799138191430.1841673448851288X-RAY DIFFRACTION100
4.3844-5.52040.2195569347751430.1871384132871294X-RAY DIFFRACTION99.9304589708
5.5204-34.978250.2689145142871510.2239818279531361X-RAY DIFFRACTION99.6704021094
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)
13.707529797273.57193125113-2.838752424126.74791490105-4.443389267315.416361179260.0607337429933-0.181609891707-1.239232900310.913001014222-0.455418538065-1.58632335935-0.03132797947930.1288464762530.4992869860620.544526462857-0.0213115982069-0.1441609395920.5035123289-0.004952086309281.263388641928.674775289160.427502611855-25.8074924335
23.62726996321-0.609703877847-0.00364607892814.044568333215.218797712097.38435319059-0.5143329825810.172783385007-0.35138780224-0.2497941933050.5809427971030.423948131763-0.2827360597460.545717330654-0.00612171283580.398124267551-0.0606407328510.01790199132990.766299326840.01437094044810.75475120251516.883521640212.5694285956-29.9274670905
31.76560885332-3.45680902878-0.02764995604986.69255972311-1.387097672977.205137736910.61783799391.67781818975-0.283098028807-1.06223879108-0.5887386392240.0386549106819-0.125332450312-1.333394609270.03506525369720.499769234145-0.01969931551210.02614502007541.27831890022-0.1681575083890.77105192636112.563562778610.8534813479-47.0638844923
41.355863205164.11632205791-0.7835714509577.02860349365-2.696084998531.604212276120.1268701054570.079414229718-0.1801727076770.678764564680.282242681430.2285229110170.0350729749332-0.455593044217-0.4488095514910.6297479166520.08678771536650.07143247839650.5860884855390.1897293276590.708966510485.162404963693.47202313761-16.8542581723
58.56668245950.06878861638521.877255437575.126972972732.111882623311.88517734161-1.253248205780.0402189091820.602517251607-0.9245388640110.5648311744440.517092559245-0.01805892431460.5224034682560.6233069362090.823261106866-0.07027545679430.139667588360.8240919101950.4619105418451.02810032138-15.3173948815-18.7445806043-20.1759359198
60.249137652325-0.489060073906-0.06240733069241.923505503731.748580336843.36144476485-0.2164401243140.7146031608190.0486312106601-0.0487771947442-0.641449796131.63000189740.341087793847-0.5974939838141.142615885930.488645249673-0.07538232181430.1895028241350.803323138164-0.07598418683730.802869883302-23.1209874721-32.1394955955-22.3027360291
73.19181862943-1.33717656096-1.305158273544.962230363670.546796430445.085066904450.6850135380570.6904107039680.537705096339-0.46587346946-0.293735786481.04491913289-0.863675121691-1.46415146629-0.3173653565580.9569054956750.2474632244130.0427250733091.433190740530.1117202630761.61041127919-34.670521247-29.7137715363-26.2576072254
84.819695066331.55214571859-0.5357613372886.149595257811.429612031965.11856347675-1.083919404330.225710183189-0.0339397747579-0.08554853329690.3257441455281.72614564697-0.0839395437147-0.5864007861570.4015963443990.8233623752930.01724344775120.09860456266420.5658203861250.02371003340240.667096436543-18.8452953243-38.5789585356-15.0171224277
94.945614673620.4992650714161.379755647814.016527532820.7525458903281.351427690280.170140300541-0.3693177594370.5984744859190.9332796139460.02608148380440.138763324922-0.5082710449370.287913064395-0.2024797972420.826942911289-0.003574469021190.1050834851510.537464821080.01035781220120.510212815098-10.373472667-24.4213348082-11.2980494944
105.05639525233-1.96404267306-4.855007013861.364442180391.016451363316.129865968240.0725254023723-2.420476506951.3873716421.540099272590.00794572040281.041941180650.259804777146-1.49652023920.3595190743591.74307156943-0.3829206706460.6921841101371.44762595125-0.698084431330.482785841295-17.6281681389-24.88959384314.54619571134
114.986908560610.4401678345161.199493659755.64426386278-2.752132515912.33488563215-0.2461449891010.793704426101-0.4853434805110.1091645130750.255949933115-0.3177068154990.143926003743-0.245197339734-0.1460909908640.5236012262190.005471553666540.05782909539040.527095838904-0.04451774328120.491950711706-7.90440007269-31.4266184034-18.8116184713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 11 )
2X-RAY DIFFRACTION2chain 'B' and (resid 12 through 21 )
3X-RAY DIFFRACTION3chain 'B' and (resid 22 through 51 )
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 132 )
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 137 )
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 148 )
8X-RAY DIFFRACTION8chain 'A' and (resid 149 through 154 )
9X-RAY DIFFRACTION9chain 'A' and (resid 155 through 174 )
10X-RAY DIFFRACTION10chain 'A' and (resid 175 through 181 )
11X-RAY DIFFRACTION11chain 'A' and (resid 182 through 191 )

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