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- PDB-8sip: Structure of a mouse IgG antibody fragment that binds Inosine, an... -

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Basic information

Entry
Database: PDB / ID: 8sip
TitleStructure of a mouse IgG antibody fragment that binds Inosine, an RNA modification
Components
  • Inosine binding IgG Fab, heavy chain
  • Inosine binding IgG Fab, kappa chain
KeywordsIMMUNE SYSTEM / IgG Fab / Inosine / RNA binding protein / modified RNA / small molecule ligand
Function / homologyINOSINE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsAoki, S.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: In silico lambda-dynamics predicts protein binding specificities to modified RNAs.
Authors: Angelo, M. / Zhang, W. / Vilseck, J.Z. / Aoki, S.T.
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Aug 20, 2025Group: Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Inosine binding IgG Fab, heavy chain
L: Inosine binding IgG Fab, kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5063
Polymers48,2382
Non-polymers2681
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-22 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.817, 49.090, 57.385
Angle α, β, γ (deg.)83.840, 88.820, 89.680
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody Inosine binding IgG Fab, heavy chain


Mass: 23942.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#2: Antibody Inosine binding IgG Fab, kappa chain


Mass: 24295.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#3: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 50 mM TRIS PH 8.3, 15% PEG 4000, 0.1 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2023
RadiationMonochromator: Kohzu HLD-15 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.94→57.04 Å / Num. obs: 30888 / % possible obs: 96.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.61 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1901 / Rpim(I) all: 0.06938 / Rrim(I) all: 0.2027 / Net I/σ(I): 6.33
Reflection shellResolution: 1.94→2.009 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.506 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 2931 / CC1/2: 0.586 / CC star: 0.86 / Rpim(I) all: 0.6427 / Rrim(I) all: 1.642 / % possible all: 91.25

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→57.04 Å / SU ML: 0.242 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 1554 5.04 %random selection
Rwork0.2043 29251 --
obs0.2064 30805 96.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.66 Å2
Refinement stepCycle: LAST / Resolution: 1.94→57.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 19 235 3522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843384
X-RAY DIFFRACTIONf_angle_d1.09874616
X-RAY DIFFRACTIONf_chiral_restr0.068522
X-RAY DIFFRACTIONf_plane_restr0.0087577
X-RAY DIFFRACTIONf_dihedral_angle_d16.48931202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-20.28721440.24472534X-RAY DIFFRACTION91.27
2-2.070.3181340.24642546X-RAY DIFFRACTION92.29
2.07-2.160.25291300.2352552X-RAY DIFFRACTION91.79
2.16-2.260.25261410.22382530X-RAY DIFFRACTION91.85
2.26-2.370.30981380.21972698X-RAY DIFFRACTION98.27
2.37-2.520.27471490.23022734X-RAY DIFFRACTION98.5
2.52-2.720.27681440.22722730X-RAY DIFFRACTION98.59
2.72-2.990.31631400.21832707X-RAY DIFFRACTION98.27
2.99-3.420.23531460.20552706X-RAY DIFFRACTION98.18
3.42-4.310.20011420.18642748X-RAY DIFFRACTION99.52
4.31-57.040.21371460.1742766X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: -12.0772151881 Å / Origin y: 23.4036181553 Å / Origin z: -3.77583644921 Å
111213212223313233
T0.0986186695414 Å2-0.010139238944 Å2-0.00808413858644 Å2-0.0858111592758 Å2-0.00758876800764 Å2--0.0959213565362 Å2
L0.292113665109 °2-0.0457304455036 °2-0.208703854658 °2-0.148183155072 °2-0.0190243114343 °2--0.19760623646 °2
S-0.0252270799 Å °0.0563274237013 Å °0.0334171151596 Å °0.0686457221633 Å °-0.0136649727228 Å °0.014421571381 Å °0.0563728743844 Å °-0.0396787434385 Å °-4.38455512405E-11 Å °
Refinement TLS groupSelection details: all

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