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- PDB-4zbn: Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High ... -

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Basic information

Entry
Database: PDB / ID: 4zbn
TitleNon-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor
Components
  • Beta-nerve growth factor
  • DNA (28-MER)
KeywordsImmune system/DNA / Complex / Aptamer / Immune system-DNA complex
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway ...NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / NADE modulates death signalling / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of Ras protein signal transduction / PI3K/AKT activation / positive regulation of DNA binding / Frs2-mediated activation / NRAGE signals death through JNK / extrinsic apoptotic signaling pathway via death domain receptors / Signalling to RAS / positive regulation of neuron differentiation / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection morphogenesis / endosome lumen / growth factor activity / modulation of chemical synaptic transmission / Golgi lumen / synaptic vesicle / negative regulation of neuron apoptotic process / axon / negative regulation of cell population proliferation / lipid binding / dendrite / positive regulation of gene expression / extracellular space / extracellular region / cytosol
Similarity search - Function
Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B ...Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor family profile. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Beta-nerve growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.447 Å
AuthorsDavies, D.R. / Edwards, T.E.
CitationJournal: Structure / Year: 2015
Title: Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor.
Authors: Jarvis, T.C. / Davies, D.R. / Hisaminato, A. / Resnicow, D.I. / Gupta, S. / Waugh, S.M. / Nagabukuro, A. / Wadatsu, T. / Hishigaki, H. / Gawande, B. / Zhang, C. / Wolk, S.K. / Mayfield, W.S. ...Authors: Jarvis, T.C. / Davies, D.R. / Hisaminato, A. / Resnicow, D.I. / Gupta, S. / Waugh, S.M. / Nagabukuro, A. / Wadatsu, T. / Hishigaki, H. / Gawande, B. / Zhang, C. / Wolk, S.K. / Mayfield, W.S. / Nakaishi, Y. / Burgin, A.B. / Stewart, L.J. / Edwards, T.E. / Gelinas, A.D. / Schneider, D.J. / Janjic, N.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (28-MER)
E: DNA (28-MER)
A: Beta-nerve growth factor
B: Beta-nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8605
Polymers46,6224
Non-polymers2381
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-33 kcal/mol
Surface area17560 Å2
Unit cell
Length a, b, c (Å)109.201, 60.708, 68.589
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (28-MER)


Mass: 9795.686 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Beta-nerve growth factor / Beta-NGF


Mass: 13515.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGF, NGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01138
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 16 % PEG 8000, 100 mM HEPES pH 6.0, 100 mM Magnesium Acetate and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.447→68.2 Å / Num. obs: 15532 / % possible obs: 98.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.3
Reflection shellResolution: 2.447→2.51 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.03 / % possible all: 84.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementResolution: 2.447→68.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.699 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 824 5 %RANDOM
Rwork0.20174 ---
obs0.20447 15532 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å21.15 Å2
2--0.24 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: 1 / Resolution: 2.447→68.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 1320 15 21 2862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0173055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.8574274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2195194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.22522.42466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09715243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.219159
X-RAY DIFFRACTIONr_chiral_restr0.1680.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021974
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5583.26783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9714.855967
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1253.212272
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.42729.4024972
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.447→2.511 Å
Num. reflection% reflection
Rfree55 -
Rwork970 -
obs-84.15 %
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)
12.93131.22310.2152.9978-0.03543.22030.1380.04310.364-0.024-0.19190.3247-0.3619-0.28080.05390.13670.03340.02830.09170.00020.068113.8233-0.540912.3699
210.93513.5472-3.85253.1946-1.12956.42750.06710.46550.0593-0.29780.2450.38270.2517-0.7259-0.31220.1261-0.0411-0.0530.14110.01220.12774.693-12.25273.7944
36.14932.52592.43592.38221.8361.9704-0.39840.29350.8608-0.23090.16850.3637-0.44340.43160.22980.2203-0.10830.05680.23250.00920.209722.08047.991618.706
43.71993.22891.73085.3973.0553.7735-0.01130.34010.0146-0.155-0.06420.0532-0.03860.08420.07550.08120.028400.179-0.0110.027820.9039-2.3789.1516
56.08572.04727.48125.42725.723611.437-0.08460.5423-0.0497-0.4446-0.15630.3562-0.27350.37320.24090.30140.04420.0360.3217-0.07120.127513.4178-13.4620.4902
64.0973.16071.77198.76844.43652.4479-0.13720.14090.36880.0720.08210.1441-0.0250.16150.05510.224-0.0133-0.03220.27110.07910.132126.11034.026815.4967
712.3439-1.5108-3.74669.05140.55241.14140.59080.43260.6331-0.8723-0.37640.1695-0.1829-0.1266-0.21430.25670.0013-0.0460.2899-0.00140.230234.33863.50798.6129
86.72153.9769-0.45776.12931.07132.28610.2727-0.1199-0.68520.4768-0.1595-0.79110.27260.379-0.11320.15510.1022-0.05950.16350.01890.109728.3939-8.386316.4666
95.5628-1.9481-3.48236.2909-0.41947.35780.3317-0.2423-0.6999-0.3612-0.0904-0.18111.0667-0.2519-0.24130.3553-0.1199-0.21920.08360.10760.274111.5889-21.617616.4329
104.81085.44082.16448.5952.9643.34880.6338-0.6638-0.04511.2879-0.5558-0.25280.4870.2938-0.0780.233-0.0408-0.04540.268-0.02530.022428.6577-0.149525.5396
1110.35596.53634.12786.73873.15323.83970.4460.0526-0.45670.6109-0.17050.07430.43940.0046-0.27560.1827-0.00510.0210.1203-0.00510.091913.2156-12.660619.6878
126.98075.7583.686910.02164.56692.53740.4841-0.6782-0.2730.7227-0.3765-0.080.1975-0.1986-0.10760.3154-0.08910.0310.21280.04520.025717.616-5.895222.9973
135.64586.5121-0.328712.4488-0.26241.73140.0619-0.32550.9499-0.7248-0.01011.0043-0.3735-0.6475-0.05190.23440.08620.10280.3154-0.040.3479-3.42374.167126.7682
146.90594.65983.75815.43683.12032.9897-0.4136-0.35191.089-0.23930.03311.0739-0.575-0.53830.38050.45020.06060.16840.4003-0.00410.55497.473612.740523.0958
152.7124-1.2237-0.99332.7432-0.95315.3487-0.11180.05560.1640.0938-0.10120.27430.16670.05060.2130.1416-0.09390.04630.2271-0.0290.1312-0.6488-8.625424.2833
160.3391.19320.43728.211-0.24272.76990.1993-0.1650.11550.4493-0.13910.03430.0551-0.12-0.06020.2532-0.10390.16840.2716-0.16870.186911.47897.575427.1038
170.74762.43361.56219.18837.343110.84880.05750.1399-0.41050.33780.9831-1.12131.00621.1078-1.04050.37490.1698-0.07640.6143-0.15130.459435.6224-19.2776-1.2879
183.53290.2941-0.759211.669411.383411.43390.0336-0.2792-0.19240.91660.7289-0.90650.94750.8733-0.76250.36310.1894-0.14040.79420.16560.675147.6228-9.445615.5038
197.52684.14713.37514.25351.80442.05930.2590.1907-0.53620.15410.1072-0.10370.330.2065-0.36620.31010.11110.00130.2437-0.13240.163629.9599-17.10413.9401
202.32610.88483.04071.33520.87995.0482-0.31870.2868-0.0882-0.30720.1877-0.5073-0.07330.60.1310.25670.07280.06330.4286-0.0550.295135.7473-5.240710.5422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 32
2X-RAY DIFFRACTION2A33 - 52
3X-RAY DIFFRACTION3A53 - 75
4X-RAY DIFFRACTION4A76 - 93
5X-RAY DIFFRACTION5A94 - 103
6X-RAY DIFFRACTION6A104 - 114
7X-RAY DIFFRACTION7B4 - 9
8X-RAY DIFFRACTION8B10 - 25
9X-RAY DIFFRACTION9B26 - 52
10X-RAY DIFFRACTION10B53 - 78
11X-RAY DIFFRACTION11B79 - 99
12X-RAY DIFFRACTION12B100 - 114
13X-RAY DIFFRACTION13D1 - 8
14X-RAY DIFFRACTION14D9 - 14
15X-RAY DIFFRACTION15D15 - 21
16X-RAY DIFFRACTION16D22 - 28
17X-RAY DIFFRACTION17E1 - 5
18X-RAY DIFFRACTION18E6 - 9
19X-RAY DIFFRACTION19E12 - 19
20X-RAY DIFFRACTION20E20 - 28

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