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- PDB-7jtn: Human Complement Factor B Inhibited by a Slow Off-Rate Modified A... -

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Basic information

Entry
Database: PDB / ID: 7jtn
TitleHuman Complement Factor B Inhibited by a Slow Off-Rate Modified Aptamer of 29 Bases
Components
  • Complement factor B
  • DNA (30-MER)
KeywordsIMMUNE SYSTEM/DNA / Complement / Protease / Convertase / Inhibitor / Aptamer / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan
Similarity search - Domain/homology
DNA / DNA (> 10) / Complement factor B
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsXu, X. / Geisbrecht, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI113552 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS104767 United States
CitationJournal: J Immunol. / Year: 2021
Title: Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B.
Authors: Xu, X. / Zhang, C. / Denton, D.T. / O'Connell, D. / Drolet, D.W. / Geisbrecht, B.V.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor B
B: DNA (30-MER)
C: Complement factor B
D: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)192,8074
Polymers192,8074
Non-polymers00
Water00
1
A: Complement factor B
B: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)96,4032
Polymers96,4032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Complement factor B
D: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)96,4032
Polymers96,4032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.126, 144.407, 87.185
Angle α, β, γ (deg.)90.000, 109.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Complement factor B / C3/C5 convertase / Glycine-rich beta glycoprotein / GBG / PBF2 / Properdin factor B


Mass: 85641.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#2: DNA chain DNA (30-MER)


Mass: 10761.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SL1103 / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M bis-tris, 0.2 M ammonium acetate, 25% peg-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 36509 / % possible obs: 99.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.101 / Rrim(I) all: 0.248 / Χ2: 0.923 / Net I/σ(I): 4.7 / Num. measured all: 209444
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.214.10.86435250.5730.4610.9850.61996
3.21-3.344.70.72536300.6790.3670.8160.73899.3
3.34-3.495.20.56336210.8210.2710.6270.70499.7
3.49-3.685.50.4236630.9060.1940.4640.85399.8
3.68-3.915.70.33436480.9180.1520.3680.99799.7
3.91-4.215.20.25436390.9540.120.2820.97899.5
4.21-4.636.50.19736790.9760.0840.2140.9799.9
4.63-5.37.10.17236730.9780.070.1861.03599.9
5.3-6.676.90.15237070.9860.0620.1651.01999.9
6.67-506.40.12737240.9560.0540.1391.04899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.17refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OK5

2ok5


Resolution: 3.1→42.9 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 1993 5.47 %
Rwork0.2079 34462 -
obs0.2098 36455 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.84 Å2 / Biso mean: 60.891 Å2 / Biso min: 16.86 Å2
Refinement stepCycle: final / Resolution: 3.1→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11080 1422 40 0 12542
Biso mean--136.15 --
Num. residues----1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312972
X-RAY DIFFRACTIONf_angle_d1.62117836
X-RAY DIFFRACTIONf_dihedral_angle_d25.8542096
X-RAY DIFFRACTIONf_chiral_restr0.0751878
X-RAY DIFFRACTIONf_plane_restr0.0072078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.180.33291230.28772132225587
3.18-3.260.34961390.29052424256398
3.26-3.360.27891480.268825502698100
3.36-3.470.25651410.251524332574100
3.47-3.590.31731450.23725162661100
3.59-3.730.24121400.221324472587100
3.73-3.90.27811430.209124852628100
3.9-4.110.2271440.190324722616100
4.11-4.370.211410.186924932634100
4.37-4.70.21811450.17124652610100
4.7-5.180.23251410.173225042645100
5.18-5.920.18341480.193425102658100
5.92-7.460.21521450.202224892634100
7.46-42.90.23111500.1992542269299

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