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- PDB-4wb3: Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20... -

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Basic information

Entry
Database: PDB / ID: 4wb3
TitleCrystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin
Components
  • Complement C5
  • mixed L-RNA/L-DNA 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 / complement activation, alternative pathway / endopeptidase inhibitor activity / complement activation, classical pathway / positive regulation of angiogenesis ...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 / complement activation, alternative pathway / endopeptidase inhibitor activity / complement activation, classical pathway / positive regulation of angiogenesis / in utero embryonic development / killing of cells of another organism / 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, complement system / Anaphylatoxin/fibulin / 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, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / : / 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 / Netrin domain / NTR domain profile. / 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 / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jan 10, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: Complement C5
B: Complement C5
C: Complement C5
D: mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)
E: mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,05116
Polymers52,5855
Non-polymers46611
Water6,720373
1
A: Complement C5
D: mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0517
Polymers21,8472
Non-polymers2045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0083
Polymers8,8901
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C5
E: mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9926
Polymers21,8472
Non-polymers1454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.840, 282.630, 45.760
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-915-

HOH

21B-920-

HOH

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Components

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

#1: Protein Complement C5 / Hemolytic complement


Mass: 8890.376 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 aptamer NOX-D20 (40-MER)


Mass: 12956.734 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 384 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#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


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 41442 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rsym value: 0.098 / Net I/σ(I): 12.01
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.72 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WB2

4wb2


Resolution: 2→32.852 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 2023 5.02 %random selection
Rwork0.1626 ---
obs0.1645 40265 97.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 1716 20 373 3762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073638
X-RAY DIFFRACTIONf_angle_d1.4695284
X-RAY DIFFRACTIONf_dihedral_angle_d43.9951615
X-RAY DIFFRACTIONf_chiral_restr0.066556
X-RAY DIFFRACTIONf_plane_restr0.006379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24271490.21722599X-RAY DIFFRACTION95
2.05-2.10550.24791300.20772650X-RAY DIFFRACTION95
2.1055-2.16740.25811360.19142673X-RAY DIFFRACTION96
2.1674-2.23730.23081420.18542628X-RAY DIFFRACTION96
2.2373-2.31730.23861330.18192685X-RAY DIFFRACTION96
2.3173-2.410.2231280.18212734X-RAY DIFFRACTION97
2.41-2.51970.21421530.18392637X-RAY DIFFRACTION97
2.5197-2.65250.22781380.1872710X-RAY DIFFRACTION97
2.6525-2.81860.22291450.18462756X-RAY DIFFRACTION98
2.8186-3.03610.2341480.17542758X-RAY DIFFRACTION98
3.0361-3.34130.19071550.15272741X-RAY DIFFRACTION98
3.3413-3.82420.1751440.14212854X-RAY DIFFRACTION99
3.8242-4.81560.14691600.13792803X-RAY DIFFRACTION99
4.8156-32.85630.18491620.14013014X-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)
13.88351.14250.38013.2281-0.62812.706-0.03870.39890.194-0.49940.0566-0.0214-0.0610.0092-0.04020.20430.05920.02410.21150.04170.1491-19.289423.0218-16.3148
22.93580.51290.65893.6054-0.32852.9816-0.16470.0710.3042-0.0520.18490.2735-0.3161-0.1675-0.01190.09830.0339-0.00020.23020.01950.2099-36.02217.0856-10.7311
32.41841.79171.01312.64221.2130.5881-0.03670.05650.31940.25710.1502-0.8264-0.79350.6214-0.14010.6095-0.1265-0.00970.3485-0.04230.5702-0.974457.262320.6915
42.2405-0.48970.09333.2762-0.18081.82580.0251-0.16150.30310.05720.0331-0.266-0.12620.1339-0.06220.13810.0261-0.00060.1766-0.0460.165-11.53721.2456-1.6082
52.9898-0.67880.48913.13040.06211.7745-0.02840.06090.2209-0.2458-0.02830.2628-0.6505-0.18520.05090.54290.05790.02140.2239-0.05210.3253-17.065953.832616.3845
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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