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- PDB-7tqb: Crystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid -

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Basic information

Entry
Database: PDB / ID: 7tqb
TitleCrystal structure of monoclonal S9.6 Fab bound to DNA-RNA hybrid
Components
  • DNA
  • FAB S9.6 Heavy Chain
  • FAB S9.6 Light Chain
  • RNA
KeywordsIMMUNE SYSTEM/DNA-RNA HYBRID / Antibody Fab DNA:RNA hybrid Nucleic Acid DNA:RNA hybrid binding protein / DNA-RNA HYBRID / IMMUNE SYSTEM-DNA-RNA HYBRID complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBou-Nader, C. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of R-loop recognition by the S9.6 monoclonal antibody.
Authors: Bou-Nader, C. / Bothra, A. / Garboczi, D.N. / Leppla, S.H. / Zhang, J.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Apr 27, 2022Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.type
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAB S9.6 Heavy Chain
L: FAB S9.6 Light Chain
A: RNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2855
Polymers57,1934
Non-polymers921
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-31 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.426, 158.884, 43.142
Angle α, β, γ (deg.)90.000, 105.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody FAB S9.6 Heavy Chain


Mass: 24972.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody FAB S9.6 Light Chain


Mass: 24124.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)

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RNA chain / DNA chain , 2 types, 2 molecules AB

#3: RNA chain RNA


Mass: 4094.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA


Mass: 4000.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 37 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1000 0.2 M sodium narrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→40.5 Å / Num. obs: 9509 / % possible obs: 98.7 % / Redundancy: 12.1 % / CC1/2: 0.841 / CC star: 0.956 / Net I/σ(I): 3.78
Reflection shellResolution: 3.02→3.13 Å / Mean I/σ(I) obs: 1.55 / Num. unique obs: 925 / CC1/2: 0.393

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TT1

3tt1


Resolution: 3.1→37.091 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 463 5.33 %
Rwork0.2294 8218 -
obs0.2317 8681 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.3 Å2 / Biso mean: 30.6873 Å2 / Biso min: 12.31 Å2
Refinement stepCycle: final / Resolution: 3.1→37.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 542 14 36 3849
Biso mean--33.23 19.69 -
Num. residues----450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.54820.2731450.2454274596
3.5482-4.46920.26611650.2208272196
4.4692-37.09010.27751530.227275295
Refinement TLS params.Method: refined / Origin x: 12.6181 Å / Origin y: -28.8717 Å / Origin z: 12.3193 Å
111213212223313233
T-0.1568 Å20.0422 Å20.0111 Å2-0.3924 Å2-0.0292 Å2--0.0806 Å2
L0.7416 °20.0978 °2-0.2586 °2-0.5441 °2-0.2777 °2--1.0953 °2
S0.0278 Å °-0.0433 Å °0.0263 Å °-0.2024 Å °0.0243 Å °-0.0369 Å °-0.0391 Å °0.0683 Å °-0.0139 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 215
2X-RAY DIFFRACTION1allH216 - 235
3X-RAY DIFFRACTION1allL1 - 301
4X-RAY DIFFRACTION1allL302 - 315
5X-RAY DIFFRACTION1allA1 - 13
6X-RAY DIFFRACTION1allA14
7X-RAY DIFFRACTION1allB1 - 13
8X-RAY DIFFRACTION1allB14

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