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- PDB-9o70: Motif1-Motif2, two domain left-handed parallel G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 9o70
TitleMotif1-Motif2, two domain left-handed parallel G-quadruplex
ComponentsDNA (26-MER)
KeywordsDNA / G-quadruplex / left-handed G-quadruplex / parallel
Function / homology: / COBALT HEXAMMINE(III) / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsXing, E.R. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: To be Published
Title: Structure of a left-right-handed G-quadruplex from the promoter of the NSD1 gene
Authors: Xing, E.R. / Yatsunyk, L.A.
History
DepositionApr 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (26-MER)
B: DNA (26-MER)
C: DNA (26-MER)
D: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,42438
Polymers41,3215
Non-polymers3,10333
Water55831
1
A: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,37711
Polymers8,2641
Non-polymers1,11310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5435
Polymers8,2641
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7557
Polymers8,2641
Non-polymers4916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7997
Polymers8,2641
Non-polymers5356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9508
Polymers8,2641
Non-polymers6867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.944, 122.741, 103.138
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 1 through 12 or resid 15 through 24 or resid 26 through 103))
d_2ens_1(chain "B" and (resid 1 through 12 or resid 15 through 24 or resid 26 through 103))
d_3ens_1(chain "C" and (resid 1 through 12 or resid 15 through 24 or resid 26 through 103))
d_4ens_1(chain "D" and (resid 1 through 12 or resid 15 through 24 or resid 26 through 103))
d_5ens_1(chain "E" and (resid 1 through 12 or resid 15 through 24 or resid 26 through 103))

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_11DGDGDGDGAA11
d_12KKKKAF101
d_13KKKKAG102
d_21DGDGDGDGBB11
d_22KKKKBP101
d_23KKKKBQ102
d_31DGDGDGDGCC11
d_32KKKKCT101
d_33KKKKCU102
d_41DGDGDGDGDD11
d_42KKKKDZ101
d_43KKKKDAA102
d_51DGDGDGDGEE11
d_52KKKKEFA101
d_53KKKKEGA102

NCS oper:
IDCodeMatrixVector
1given(-0.168812898087, 0.525994857067, -0.833565603764), (-0.482147571817, -0.781681349819, -0.395610902701), (-0.859671986533, 0.335117408806, 0.385565037166)13.5359880128, -23.7872125918, 9.70726068324
2given(0.999735252437, -0.0169376732105, 0.0155737041292), (-0.0215051643006, -0.447125671297, 0.894212593277), (-0.00818247777226, -0.894310767739, -0.44737154331)-0.0648632359818, -45.2721646034, 24.3304202635
3given(-0.0698997518582, 0.4695437467, 0.880137883871), (-0.490560566039, -0.78442029545, 0.379519605731), (0.868599076524, -0.405232612238, 0.285170430166)-30.6924973788, -81.2215069249, 37.1908996862
4given(0.0718334886725, -0.488150261472, -0.869798408903), (0.554824604932, -0.705124737378, 0.441552672395), (-0.828860427133, -0.514303827481, 0.220186206134)2.60697062357, -66.1697423952, 12.501571377

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Components

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DNA chain , 1 types, 5 molecules ABCDE

#1: DNA chain
DNA (26-MER)


Mass: 8264.264 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 7 types, 64 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M potassium chloride 5 mM Hexammine cobalt chloride 0.05 M MES pH 6.5 25% PEG 4000

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Data collection

DiffractionMean temperature: 196 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.02→61.37 Å / Num. obs: 23606 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 42.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.1
Reflection shellResolution: 2.02→2.06 Å / Rmerge(I) obs: 2.308 / Num. unique obs: 1169 / CC1/2: 0.409

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Coot0.9.5model building
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→61.37 Å / SU ML: 0.3104 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 1200 5.09 %
Rwork0.2264 22374 -
obs0.2282 23574 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.09 Å2
Refinement stepCycle: LAST / Resolution: 2.02→61.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2727 155 31 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983183
X-RAY DIFFRACTIONf_angle_d1.21654928
X-RAY DIFFRACTIONf_chiral_restr0.0639514
X-RAY DIFFRACTIONf_plane_restr0.0111128
X-RAY DIFFRACTIONf_dihedral_angle_d38.23371339
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.289931552064
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.379232339548
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.300537885694
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.345970679949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.10.36141420.32512429X-RAY DIFFRACTION99.88
2.1-2.20.33381320.30592455X-RAY DIFFRACTION100
2.2-2.320.33461360.28112465X-RAY DIFFRACTION100
2.32-2.460.27151200.26742460X-RAY DIFFRACTION100
2.46-2.650.2651210.25252478X-RAY DIFFRACTION100
2.65-2.920.27441450.24452475X-RAY DIFFRACTION100
2.92-3.340.21521210.21372494X-RAY DIFFRACTION99.47
3.34-4.210.24871410.19172499X-RAY DIFFRACTION99.7
4.21-61.370.25411420.21412619X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.013407143191.834220116656.720691494997.22420326296-0.4594270267697.175152150030.178135331675-0.86401304604-1.895458235620.7001304311951.101583556370.3817026024090.329928870686-0.672357717091-1.315689891070.7367972147470.1052992065740.3975748228980.893214667621-0.124710502061.44480382086-29.3530272687-50.185119120846.1277215794
27.92378818231-0.1120997213210.8268990845234.54267362196-0.09084896715749.37519312426-0.4329924197720.522774487533-0.00456087728395-0.7060695996720.4348928569220.589510598080.371611784673-1.188863007930.08802763937140.447896085386-0.195411556024-0.1266154708080.42520045071-0.02681263252150.32431031171-4.12184499412-49.767128631841.7996046381
38.357041350882.64396367875-7.373609892512.70458370759-1.200982745678.727803622680.1705143298761.732054136762.18644365611-0.2564056112491.263304413180.122486974533-0.668634083646-2.15138920805-1.07658585080.598706382983-0.055679408463-0.1168095903930.981545430930.2257541977920.878990751444-3.92615724966-38.345390983537.6619320486
44.36768036864-2.95985370475-1.307536221559.558908856030.6628328435437.75725381325-0.139109057952-0.0844088346210.473706627557-0.4843462015660.212478531503-0.264579986528-0.3714843440790.0567436383073-0.09145255017730.347985259493-0.0748277222202-0.1140111166760.431657259105-0.01819520327320.3967864912512.77695245692-46.178642122243.8364610044
59.734619406921.42810712827-0.04802087564849.616623438590.06892596302318.899319008740.09997174582550.04683002453060.988405991783-0.3460704040520.02196129017820.587097692105-0.227926196351-0.163664989444-0.1054506333060.243104127419-0.0475210209977-0.03320178823360.189387218202-0.01634895828120.319476513214-15.6148561488-23.368129120819.5467224634
66.493907771234.655431933841.351780044799.81958740314-2.844464203395.88770821339-0.267669695407-0.454387396048-0.587245111468-0.785640807106-0.323273824469-1.47636931108-0.913451035240.8059048557810.4359497478430.396700786571-0.01927577172810.02808153323110.512874764706-0.05813356251660.3932272547-6.81308417519-29.070286187923.6521409182
78.21901031521-0.4650077583971.556950958327.649233076641.077700595927.71878799084-0.09164079240770.409642370588-0.321488911226-0.8069565254190.03487522692160.06812741783270.1867522015620.2296950482760.06124976702950.481127257533-0.130419931277-0.05273124290350.247967055987-0.007802632072730.380376465387-14.9665652919-29.940028298415.490882342
89.766965521530.9987353024740.2681120882679.96287962901-5.42137380587.56720825571-0.199336849524-0.596230924533-0.5598072542990.3175116688650.0368412256486-0.167318357335-0.184229730616-0.1744267510630.2406108164710.5218758667280.03368952416910.01214434427290.2501859061820.07360045033870.355262870719-12.3580297436-5.7202732447322.800490571
97.30679864431-6.24539024975-2.529779961129.34181110406-0.1670438044482.256338353010.9496974233910.424579750997-0.679815197974-2.79748937058-0.4496455466591.226774472040.657396103858-1.39087531844-1.202623428120.940555725932-0.0996226384691-0.2942800782120.5940678510890.3238529368121.02529755325-21.1297728879-6.6285250905114.4403358552
107.121217018852.473598092320.278383241188.20266417998-2.877467146928.94202512185-0.350396598016-1.029304825230.3697759271540.0769024089778-0.01254497052290.408048357757-1.54028864225-0.474906442327-0.00854476304850.517959309153-0.0801399267661-0.03488533329290.1061326413950.1292327716250.34912128618-12.67993995030.7193333471918.5437519335
115.40131301243-3.20358228330.6243769075268.011059457181.229269182727.625981652650.01810813249691.61847811438-0.8343301430920.156799038081-0.3744044612510.6671851092540.523077610381-0.7143396792260.2927802506710.321744798145-0.03922005990410.06058971646580.547569655715-0.1307398193330.321920479625-14.97787583-17.043445455636.6019966693
127.1320639096-8.02289696623-5.497946260619.147674188576.034619884254.40582962021-0.505527377021-1.118803422421.367919120491.488520615131.1898236908-1.95590960237-0.3107918810891.77267888711-0.09817016109090.6643146528350.0428391249784-0.1208989175670.9029996435610.08974771658450.556489344952-5.94382636455-10.085365874440.3624301264
137.12475158116-1.86948134017-1.622361459868.194127617720.6869233446748.82359549541-0.3805620135370.0942934811129-0.4676960735460.6804539040820.0456349170525-0.08856392310070.8307805572580.2077659798180.348312100850.440223320082-0.02850757497090.08398405258090.43618510307-0.05916650776320.225318619636-14.3124590245-17.639355817544.3180512654
148.364285935290.3630251094354.761945351627.942261708224.900729059017.920959895760.196345908645-0.831971010693-1.723559317620.304982816380.1990821435290.2028051413981.50803503248-0.21773561651-0.1720487538060.5634338013980.09912959664130.04914756861610.366768245772-0.02799420043450.829761653793-25.7517790968-53.029699119240.7459121074
155.903271919640.2458595029211.715671495444.790623429770.1239742631374.9461717504-0.3875578479861.051749772951.51274038558-0.522678907616-0.391306049761-1.41745858646-0.4051977170490.712768498485-0.7765822905380.293374910340.260808726243-0.1080761693880.5112574980690.1156898725320.616391185008-21.1608611898-42.913622102136.602666249
165.323309266690.2467989001762.385222798587.848393882862.212218246883.59604746131-0.700779818371-2.662737821150.7449971266333.00729850789-0.314057773521-0.251900207479-0.143698449511-0.08824829348430.652730497381.007336968810.3577870128140.01069460569421.077848377630.01330531061830.565757891467-23.00288071-45.726816297849.1331433073
174.838614150381.09962902484.305457021590.3181546719561.173628691125.71120232709-1.23730384007-0.5051066899882.223185629841.175715957960.13579776305-0.653893445768-1.428264055590.1911814625590.2492152270080.6609018389810.218327695739-0.2464167037840.30518349872-0.1221035604790.589032667667-26.6451007424-38.128715124540.6213853037
182.473854208212.33412162396-1.463698401635.7557132427-4.747980000345.879731890110.0371664724729-0.462584446183-0.287373108357-0.2639302909590.8467801522112.25188775511.19855060049-2.1834994464-0.7185120201740.491688831028-0.01189956101820.01236164183640.5583990708180.1003479467350.797639512203-33.2024755482-49.862231944439.9892837895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 26 through 26 )DM26
2X-RAY DIFFRACTION2chain 'E' and (resid 1 through 10 )EQ1 - 10
3X-RAY DIFFRACTION3chain 'E' and (resid 11 through 15 )EQ11 - 15
4X-RAY DIFFRACTION4chain 'E' and (resid 16 through 26 )EQ16 - 26
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 10 )AA1 - 10
6X-RAY DIFFRACTION6chain 'A' and (resid 11 through 15 )AA11 - 15
7X-RAY DIFFRACTION7chain 'A' and (resid 16 through 26 )AA16 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 10 )BE1 - 10
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 15 )BE11 - 15
10X-RAY DIFFRACTION10chain 'B' and (resid 16 through 26 )BE16 - 26
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 10 )CI1 - 10
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 15 )CI11 - 15
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 26 )CI16 - 26
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 5 )DM1 - 5
15X-RAY DIFFRACTION15chain 'D' and (resid 6 through 10 )DM6 - 10
16X-RAY DIFFRACTION16chain 'D' and (resid 11 through 15 )DM11 - 15
17X-RAY DIFFRACTION17chain 'D' and (resid 16 through 20 )DM16 - 20
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 25 )DM21 - 25

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  • 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

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