[English] 日本語
Yorodumi
- PDB-9m6c: Crystal structure of xanthine/guanine RNA aptamer with xanthine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9m6c
TitleCrystal structure of xanthine/guanine RNA aptamer with xanthine
ComponentsRNA (32-MER)
KeywordsRNA / xanthine/guanine RNA aptamer / xanthine
Function / homology: / GUANOSINE-5'-TRIPHOSPHATE / XANTHINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLi, M. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: To Be Published
Title: Crystal structure of xanthine/guanine RNA aptamer
Authors: Li, M. / Huang, L.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (32-MER)
B: RNA (32-MER)
C: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,46014
Polymers30,7473
Non-polymers2,71311
Water905
1
A: RNA (32-MER)
hetero molecules

A: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1238
Polymers20,4982
Non-polymers1,6256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2
B: RNA (32-MER)
hetero molecules

B: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,39810
Polymers20,4982
Non-polymers1,9008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
3
C: RNA (32-MER)
hetero molecules

C: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,39810
Polymers20,4982
Non-polymers1,9008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_446-y-1,-x-1,-z+11
Unit cell
Length a, b, c (Å)107.730, 107.730, 47.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GTPGTPGTPGTPAD101
d_12GGCCAA2 - 32 - 3
d_13XANXANXANXANAE102
d_21GTPGTPGTPGTPBG101
d_22GGCCBB2 - 32 - 3
d_23XANXANXANXANBH102
d_31GTPGTPGTPGTPCK101
d_32GGCCCC2 - 32 - 3
d_33XANXANXANXANCL102

NCS oper:
IDCodeMatrixVector
1given(0.943183812526, 0.0412088328955, -0.32970612351), (-0.0987099181259, 0.98223238867, -0.159611674732), (0.317270622422, 0.183088412355, 0.930493409654)-17.5616171978, -20.3635883811, 11.9072868141
2given(0.0200083492135, 0.976665880431, 0.213830362585), (-0.999776851669, 0.020994409394, -0.00234129028775), (-0.0067759005132, -0.213735801343, 0.976868002545)-37.6169174356, -69.3700856221, 17.9589406971

-
Components

#1: RNA chain RNA (32-MER)


Mass: 10249.092 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ba
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.08 M Potassium chloride 0.02 M Barium chloride dehydrate 32% v/v (+/-)-2-Methyl-2,4-pentanediol 0.012 M Spermine tetrahydrochloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.51→35.91 Å / Num. obs: 9962 / % possible obs: 99.9 % / Redundancy: 25.1 % / Biso Wilson estimate: 79.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Net I/σ(I): 22.8
Reflection shellResolution: 2.51→2.58 Å / Rmerge(I) obs: 3.135 / Num. unique obs: 698 / CC1/2: 0.53 / Rpim(I) all: 0.863 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→35.58 Å / SU ML: 0.6352 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.6079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3085 484 4.86 %
Rwork0.2733 9478 -
obs0.2751 9962 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.22 Å2
Refinement stepCycle: LAST / Resolution: 2.51→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1971 134 5 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272334
X-RAY DIFFRACTIONf_angle_d0.86593627
X-RAY DIFFRACTIONf_chiral_restr0.0394477
X-RAY DIFFRACTIONf_plane_restr0.004699
X-RAY DIFFRACTIONf_dihedral_angle_d17.50251149
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DAX-RAY DIFFRACTIONTorsion NCS0.894257800168
ens_1d_3DAX-RAY DIFFRACTIONTorsion NCS1.28681242296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.870.51591570.42613068X-RAY DIFFRACTION99.81
2.87-3.620.29091460.31693135X-RAY DIFFRACTION99.7
3.62-35.580.29561810.24053275X-RAY DIFFRACTION99.88
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)
12.17086157694-3.085405285596.170291741114.24927225996-2.483317486915.663446118581.16014167074.132458683871.49242466733-1.66300866048-2.24120902624-0.04413590805420.7664932622520.4049576656760.8905779404150.8575688390850.307871075114-0.08617780292791.99577838762-0.2641440696220.845136382043-40.6144231512-14.7500909201-5.21757726726
26.013776245884.53565657489-0.8150176728853.82142392196-0.2028389387518.06474494781-0.1630239636181.962722390781.54570119692-0.4641431059130.1107696531322.81715696489-0.79367197139-1.288697484740.1330206611580.9234268515530.3102638880120.2698399157711.516905936340.4681579460371.29514308397-48.4586436205-3.983492588652.67227398399
33.648954425230.977663949006-1.348257673852.215951518070.3109851777885.60344207228-0.1456502566432.22628670968-0.97845982193-0.468563122396-0.513643052566-0.4452320445661.548526912650.00711186735970.5445045622240.9397748381920.1339958329130.2782214064251.37904214727-0.2279039858730.919000692706-35.8490840257-18.7799032441-2.6053181918
44.763759680970.8367978070820.4194019443041.265048774182.419958859764.77387843096-0.00717217287984-0.4697553451182.363254028490.2653153174690.151699072764-2.16908459955-0.3770029718611.36510106223-0.5124537351041.224023141340.2860657659490.3170058216950.8499573747690.2892279925232.46490856319-47.5457210588-32.1431535264-6.70491757186
57.610417075212.361681683452.088786280969.0099777457-3.155534007618.60467174212-0.679815099131-0.4081508124490.308379168169-0.03698743090090.5184959886291.136549321060.0815693577063-0.4341408399350.1531548323621.007082843690.1376136143880.07371419163440.75610423938-0.005489062618220.677668251085-63.6366519671-22.4641401835-4.63340515254
64.85776410809-0.5092818778660.05687464288882.77425380858-0.2051166863324.58174743038-0.599177439023-0.238984008762-1.02081596349-0.9421833747060.127525909165-2.503316640491.053960903061.062565255010.2800142796921.246579078320.2109142893420.3751677370160.6829144676950.156144535891.55801916399-51.2329803171-34.9968471753-5.33557388756
74.184166494651.006279575321.777292174621.45892331219-1.372093545073.62414993022-0.124985103236-0.0332261685361-2.14093095743-0.6161449913330.644386497816-2.092682437751.916619818521.88197960077-0.7217298344591.96661539455-0.2004852791950.5064075995451.31708688259-0.7062814418971.82236062671-55.4442746825-37.351618825116.424459681
87.371263966993.95120865491-1.483472908348.61277881698-4.850328981313.19630706362-0.4986975013191.2472846333-1.045267003450.2470188232090.350577097517-1.2770672515-0.482469500142-0.724269988598-0.2462686001191.15766161813-0.3820097158460.2638977642421.09834438874-0.2848417658940.734529097685-52.5046008956-21.221509769315.9991014727
91.94123920633-0.9566970871982.509703170342.17118593978-0.8184847127714.28595891602-0.1984250153621.148300278721.484612131351.37442335858-0.30837823353-1.23769365526-0.5721358877170.3097471000090.5588427683371.15395385048-0.1636747308710.1555542547460.86452888395-0.04123453614481.11572131968-45.3890134982-20.652106464427.5972600375
106.333902990071.948104191940.629960793678.623844252442.207337447386.198615808380.5221217107051.71040855953-0.2633087076890.732797382647-0.191051339933-0.448423866504-1.447647953961.41293790472-0.3419121505931.36319222305-0.5469106757490.622087321851.33090695744-0.201280524391.49852153894-38.3420096766-20.834576380216.5676528018
118.588534858060.3884974539051.342890434075.17593856528-2.365050762293.138659363990.895218906411-0.584593546869-1.96204507805-0.231898861692-0.918885342070.4386772359620.888728250401-0.4442865928240.367563744731.21012936051-0.2842128194850.3952747305711.08178326069-0.461459302581.36999399547-57.2878917594-33.932425064119.5360682205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 11 )AB2 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )AB12 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 32 )AB22 - 32
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 6 )BE2 - 6
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 21 )BE7 - 21
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 32 )BE22 - 32
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 6 )CH2 - 6
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 11 )CH7 - 11
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 16 )CH12 - 16
10X-RAY DIFFRACTION10chain 'C' and (resid 17 through 21 )CH17 - 21
11X-RAY DIFFRACTION11chain 'C' and (resid 22 through 32 )CH22 - 32

+
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