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- PDB-4wb2: Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20... -

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Basic information

Entry
Database: PDB / ID: 4wb2
TitleCrystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin
Components
  • Complement C5Complement component 5
  • mixed L-RNA/L-DNA mirror-image aptamer NOX-D20 (40-MER)
KeywordsDNA-RNA HYBRID / protein-RNA complex / mirror-image aptamer / G-quadruplex / complement anaphylatoxin
Function / homology
Function and homology information


Terminal pathway of complement / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / membrane attack complex / G alpha (i) signalling events / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production ...Terminal pathway of complement / Activation of C3 and C5 / Peptide ligand-binding receptors / Regulation of Complement cascade / membrane attack complex / G alpha (i) signalling events / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / positive regulation of angiogenesis / killing of cells of another organism / in utero embryonic development / inflammatory response / extracellular space
Similarity search - Function
Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain ...Anaphylotoxins (complement system) / Influenza Virus Matrix Protein; Chain A, domain 1 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Complement C5
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsYatime, L. / Maasch, C. / Hoehlig, K. / Klussmann, S. / Vater, A. / Andersen, G.R.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer.
Authors: Yatime, L. / Maasch, C. / Hoehlig, K. / Klussmann, S. / Andersen, G.R. / Vater, A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 26, 2023Group: Database references / Derived calculations / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C5
B: Complement C5
C: Complement C5
D: mixed L-RNA/L-DNA mirror-image aptamer NOX-D20 (40-MER)
E: mixed L-RNA/L-DNA mirror-image aptamer NOX-D20 (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,70019
Polymers53,0565
Non-polymers64314
Water9,152508
1
A: Complement C5
D: mixed L-RNA/L-DNA mirror-image aptamer NOX-D20 (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2678
Polymers22,0042
Non-polymers2636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1663
Polymers9,0481
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C5
E: mixed L-RNA/L-DNA mirror-image aptamer NOX-D20 (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2678
Polymers22,0042
Non-polymers2636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.470, 282.254, 45.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-918-

HOH

21B-924-

HOH

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Components

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Protein / DNA/RNA hybrid , 2 types, 5 molecules ABCDE

#1: Protein Complement C5 / Complement component 5 / Hemolytic complement


Mass: 9047.569 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C5, Hc / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7 Express / References: UniProt: P06684
#2: DNA/RNA hybrid mixed L-RNA/L-DNA mirror-image aptamer NOX-D20 (40-MER)


Mass: 12956.734 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: All DNA and RNA nucleotides of the entity are in the L-conformation
Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 522 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMAX II I911-310.91
SYNCHROTRONMAX II I911-321.1403
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDMar 24, 2013
MARMOSAIC 225 mm CCD2CCDJun 16, 2013Dataset for SAD phasing
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.911
21.14031
ReflectionResolution: 1.8→50 Å / Num. obs: 57409 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rsym value: 0.065 / Net I/σ(I): 21.62
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2.98 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.877 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 2853 5.09 %random selection
Rwork0.167 ---
obs0.1683 56027 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 1716 32 508 3941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063742
X-RAY DIFFRACTIONf_angle_d1.3665434
X-RAY DIFFRACTIONf_dihedral_angle_d43.3031658
X-RAY DIFFRACTIONf_chiral_restr0.062568
X-RAY DIFFRACTIONf_plane_restr0.006406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83110.28451250.25122546X-RAY DIFFRACTION95
1.8311-1.86430.24371400.22952560X-RAY DIFFRACTION95
1.8643-1.90020.24631490.21082527X-RAY DIFFRACTION96
1.9002-1.9390.23251450.21232584X-RAY DIFFRACTION95
1.939-1.98110.24511390.20562611X-RAY DIFFRACTION97
1.9811-2.02720.22231320.20022581X-RAY DIFFRACTION96
2.0272-2.07790.23771180.19542624X-RAY DIFFRACTION97
2.0779-2.13410.19481420.18532604X-RAY DIFFRACTION97
2.1341-2.19690.20831350.17932647X-RAY DIFFRACTION97
2.1969-2.26780.21811510.17682581X-RAY DIFFRACTION97
2.2678-2.34880.21071430.17742661X-RAY DIFFRACTION98
2.3488-2.44280.21511670.17892652X-RAY DIFFRACTION98
2.4428-2.5540.23191340.18462665X-RAY DIFFRACTION98
2.554-2.68860.22371270.18132689X-RAY DIFFRACTION98
2.6886-2.8570.19491470.18262697X-RAY DIFFRACTION98
2.857-3.07750.19651570.16442681X-RAY DIFFRACTION98
3.0775-3.38690.17931380.15412721X-RAY DIFFRACTION99
3.3869-3.87650.16561500.13842798X-RAY DIFFRACTION100
3.8765-4.88210.15571560.13782780X-RAY DIFFRACTION100
4.8821-35.88460.16221580.15272965X-RAY DIFFRACTION99
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)
14.1331-1.08710.12162.86680.49732.3071-0.0036-0.43680.15710.49350.01210.02990.03180.0631-0.00590.2488-0.08590.03060.2226-0.04580.1579-3.98322.794339.3982
23.64220.30060.92315.06340.87872.4533-0.0523-0.15830.2320.1460.1445-0.4817-0.32330.3118-0.08070.1936-0.08240.00970.251-0.02140.199213.03846.852533.7525
33.4681-1.18090.94154.6762-1.69161.77730.12020.06360.1372-0.53260.21190.7107-0.3892-0.5727-0.29770.43450.09050.01210.31470.08710.3937-22.948557.92921.5107
42.12631.01620.03722.70870.44661.84180.0250.14060.3081-0.0581-0.01680.3368-0.0695-0.1887-0.00030.1255-0.0259-0.00330.1750.03870.1948-11.764121.124424.766
52.6480.6862-0.19393.4548-0.4352.68720.0314-0.0930.00950.145-0.0294-0.3017-0.42910.1089-0.03420.3286-0.02880.00760.19320.06080.2595-6.382553.8226.7539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D and resid 1:40
5X-RAY DIFFRACTION5chain E and resid 1:40

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