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- PDB-6q8u: Structure of the standard kink turn HmKt-7 variant A2bm6A bound w... -

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Basic information

Entry
Database: PDB / ID: 6q8u
TitleStructure of the standard kink turn HmKt-7 variant A2bm6A bound with AfL7Ae protein
Components
  • 50S ribosomal protein L7AeRibosome
  • RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3')
KeywordsRNA / Gene regulation / RNA structure / kink-turn / X-ray crystallography / RNA modification
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Haloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: Rna Biol. / Year: 2019
Title: Effect of methylation of adenine N6on kink turn structure depends on location.
Authors: Ashraf, S. / Huang, L. / Lilley, D.M.J.
History
DepositionDec 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3')
B: RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3')
C: 50S ribosomal protein L7Ae
D: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,07214
Polymers40,8424
Non-polymers23010
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-130 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.360, 60.800, 119.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (5'-R(*CP*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*CP*G)-3')


Mass: 6898.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Haloarcula marismortui (Halophile)
#2: Protein 50S ribosomal protein L7Ae / Ribosome / Ribosomal protein L8e


Mass: 13522.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: rpl7ae, AF_0764 / Plasmid: pET-Duet1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O29494
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.001 M Spermine tetrahydrochloride, 0.05 M MES pH6.5, 25 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9197 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.99→33.415 Å / Num. obs: 29389 / % possible obs: 99.56 % / Observed criterion σ(I): 1.5 / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0557 / Rpim(I) all: 0.025 / Net I/σ(I): 12.73
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1459 / CC1/2: 0.75 / Rpim(I) all: 0.44 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bw0

4bw0


Resolution: 1.99→33.415 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.76
RfactorNum. reflection% reflection
Rfree0.2272 1408 4.8 %
Rwork0.1888 --
obs0.1906 29324 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→33.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 916 10 5 2783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122904
X-RAY DIFFRACTIONf_angle_d1.3454140
X-RAY DIFFRACTIONf_dihedral_angle_d9.9521658
X-RAY DIFFRACTIONf_chiral_restr0.075503
X-RAY DIFFRACTIONf_plane_restr0.01373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9901-2.06120.32431390.31672748X-RAY DIFFRACTION100
2.0612-2.14370.31361280.28932775X-RAY DIFFRACTION100
2.1437-2.24120.32491340.27232771X-RAY DIFFRACTION100
2.2412-2.35940.29441520.25722752X-RAY DIFFRACTION100
2.3594-2.50710.26141270.23972790X-RAY DIFFRACTION100
2.5071-2.70060.26631500.23752768X-RAY DIFFRACTION100
2.7006-2.97230.27441450.23562768X-RAY DIFFRACTION99
2.9723-3.4020.27791770.21112767X-RAY DIFFRACTION99
3.402-4.28470.20441370.16272816X-RAY DIFFRACTION99
4.2847-33.41940.17041190.15442961X-RAY DIFFRACTION98
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)
16.6043-1.4497-6.51265.86750.18518.3736-0.89582.3075-2.4708-1.14160.25690.60811.44572.70910.52520.80420.337-0.13751.8013-0.39291.215855.936380.4328-13.0032
24.2955-0.76884.39312.719-1.69565.0339-0.10331.0028-1.2817-0.10350.17230.22210.06671.0653-0.05440.54230.07-0.00710.69560.06220.623453.665588.4692-0.7674
35.0941-0.5291-1.70844.48160.18616.31310.26750.8421-0.3697-0.4108-0.29020.91940.433-0.67530.15670.56290.0135-0.15050.62740.03390.584950.220177.642310.8984
44.5176-2.4493-0.2626.0549-2.27998.20420.13231.3984-1.0039-1.1077-0.19121.22710.77-0.60780.03760.5175-0.0626-0.13840.8283-0.12230.709252.174770.68097.5477
56.73613.11754.6224.8768-1.77827.0031-0.02220.7427-0.7115-0.0120.0808-0.57810.08960.8204-0.04740.49090.068-0.09770.68880.03880.607156.623588.08290.7268
68.2592-2.0752-5.60690.7680.32238.2407-0.4631-0.07620.80260.03290.463-0.36771.00550.5548-0.21090.59460.07230.01290.7337-0.08010.675374.86164.455924.1134
73.7315-4.6493.5458.0496-2.0858.9380.4026-0.0725-1.4124-0.0346-0.11960.46441.0982-0.1982-0.20480.7332-0.04520.10940.3986-0.0530.675857.281759.330129.6625
86.5219-2.1734-0.59274.6631-1.19422.4769-0.73040.44730.7813-0.6110.23080.2152-0.2619-0.07010.59550.5873-0.1105-0.01970.3949-0.03810.661257.224975.719624.4727
93.8984-1.8553-0.24813.30520.12075.3286-0.25770.19080.39360.5002-0.02130.0076-0.2207-0.00240.31830.5488-0.06550.02190.3552-0.06260.543563.578670.478424.6429
103.5143-2.446-1.80734.53444.17034.80690.31310.12441.03020.62930.7164-1.5934-1.34271.7807-0.83450.5534-0.1737-0.06640.5910.05090.91669.876975.745924.2415
119.4907-1.4236-1.36676.8732-4.29075.896-0.2679-0.53870.34820.19460.5337-1.2508-1.24690.9388-0.08480.53630.0093-0.02710.3756-0.03110.414366.682768.952529.2927
125.8178-2.34860.61019.4992-1.97597.4554-0.06760.5577-0.5653-0.3343-0.0470.21091.0263-0.0280.01110.5577-0.09090.12220.4155-0.1240.555557.028563.185217.5926
136.75625.722-4.95655.1306-5.11875.59590.2967-0.42180.39961.2551-0.0360.5389-1.0329-0.134-0.32830.64610.09970.14410.4426-0.08720.698854.132768.703232.8606
141.025-0.9559-2.70349.2099-1.41858.088-0.2543-1.45920.79620.93520.0252-0.0651-0.83660.2955-0.0430.8770.0276-0.07990.4722-0.08050.508764.512963.556138.7438
156.8041-0.2491-0.33072.4716-0.95251.29560.0601-0.1962-0.1165-0.5887-0.47970.1799-0.9011-0.60610.52170.81840.2019-0.22060.8653-0.33990.90830.210899.6846-9.9451
162.8742-1.8915-0.72663.27020.77847.36030.21281.33930.6701-1.1266-0.1904-0.2588-1.30870.7610.44691.0551-0.1514-0.22120.98450.22030.819348.4715105.7698-13.3855
172.30081.65120.20199.04954.30869.1734-0.1864-1.66260.23051.5559-0.2787-0.29060.1167-0.05610.70560.92290.0826-0.29430.6031-0.01870.574346.2853100.17682.4146
185.6741.1596-1.56521.84421.53935.1043-0.3950.1731.2510.51030.24260.2254-0.95510.6213-0.12591.08420.0711-0.43740.5683-0.02560.819144.7693105.8678-2.7137
192.9254-2.2286-1.16032.89262.46962.5798-1.1569-0.2999-0.598-0.51470.10941.60150.4195-0.6260.95830.62140.0144-0.0620.6313-0.08720.735636.533491.6885-6.0996
203.81342.46232.66881.83022.29853.6969-0.89420.3331.3831.7710.6356-0.2451-1.01-1.0047-0.2580.93360.2444-0.21010.726-0.12790.67236.1604103.12951.9645
218.30020.38541.01613.08380.25983.7426-1.11970.77950.792-0.4556-0.05150.8578-1.01640.07881.0670.792-0.0186-0.3170.61080.05860.623241.9012101.2857-9.8844
226.39113.1447-2.21394.3212-4.42615.7707-0.18540.92141.11560.8359-0.00290.4341-1.23630.67950.08560.8298-0.2042-0.28980.74160.1690.649450.1804102.6007-8.6312
238.33222.5487-0.51384.14861.45683.3390.05330.87410.9575-0.4894-0.17770.6828-0.8727-0.4252-0.06451.39880.3402-0.240.76760.15241.027338.5395114.69-11.2284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 11 )
3X-RAY DIFFRACTION3chain 'A' and (resid 12 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 21 )
6X-RAY DIFFRACTION6chain 'C' and (resid -3 through 8 )
7X-RAY DIFFRACTION7chain 'C' and (resid 9 through 25 )
8X-RAY DIFFRACTION8chain 'C' and (resid 26 through 40 )
9X-RAY DIFFRACTION9chain 'C' and (resid 41 through 55 )
10X-RAY DIFFRACTION10chain 'C' and (resid 56 through 68 )
11X-RAY DIFFRACTION11chain 'C' and (resid 69 through 78 )
12X-RAY DIFFRACTION12chain 'C' and (resid 79 through 93 )
13X-RAY DIFFRACTION13chain 'C' and (resid 94 through 103 )
14X-RAY DIFFRACTION14chain 'C' and (resid 104 through 118 )
15X-RAY DIFFRACTION15chain 'D' and (resid -3 through 8 )
16X-RAY DIFFRACTION16chain 'D' and (resid 9 through 31 )
17X-RAY DIFFRACTION17chain 'D' and (resid 32 through 40 )
18X-RAY DIFFRACTION18chain 'D' and (resid 41 through 50 )
19X-RAY DIFFRACTION19chain 'D' and (resid 51 through 59 )
20X-RAY DIFFRACTION20chain 'D' and (resid 60 through 68 )
21X-RAY DIFFRACTION21chain 'D' and (resid 69 through 86 )
22X-RAY DIFFRACTION22chain 'D' and (resid 87 through 103 )
23X-RAY DIFFRACTION23chain 'D' and (resid 104 through 118 )

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