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- PDB-8tca: Structure of a mouse IgG antibody antigen-binding fragment (Fab) ... -

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Basic information

Entry
Database: PDB / ID: 8tca
TitleStructure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, no ligand
Components
  • m6A binding IgG Fab, heavy chain
  • m6A binding IgG Fab, light chain
KeywordsIMMUNE SYSTEM / IgG / Fab / m6A / RNA
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsAngelo, M.C. / Aoki, S.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM142691 United States
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
DepositionJun 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: m6A binding IgG Fab, heavy chain
L: m6A binding IgG Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,62411
Polymers47,0662
Non-polymers5599
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-4 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.906, 79.906, 145.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Antibody m6A binding IgG Fab, heavy chain


Mass: 24023.018 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 m6A binding IgG Fab, light chain


Mass: 23042.525 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 2K [20% (v/v)], MgCl2 [0.2 M], Tris pH 8.0 [0.1 M], glycerol [5-15% (v/v)]

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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: 2.02→70 Å / Num. obs: 31198 / % possible obs: 98.24 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 0.996 / CC star: 0.84 / Rmerge(I) obs: 0.2183 / Rpim(I) all: 0.08188 / Rrim(I) all: 0.2341 / Net I/σ(I): 9.71
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 7.3 % / Rmerge(I) obs: 2.29 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2999 / CC1/2: 0.546 / CC star: 0.84 / Rpim(I) all: 0.8885 / Rrim(I) all: 2.466 / % possible all: 96.71

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
autoPROCdata processing
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→70 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1547 4.95 %RANDOM
Rwork0.1814 29676 --
obs0.1835 31042 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 2.02→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 36 287 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943349
X-RAY DIFFRACTIONf_angle_d1.18274557
X-RAY DIFFRACTIONf_chiral_restr0.071523
X-RAY DIFFRACTIONf_plane_restr0.0185570
X-RAY DIFFRACTIONf_dihedral_angle_d13.91041173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.080.31981300.31032593X-RAY DIFFRACTION96.66
2.08-2.160.33231360.28622592X-RAY DIFFRACTION95.99
2.16-2.240.29521200.24752694X-RAY DIFFRACTION99.43
2.24-2.340.27881430.24182685X-RAY DIFFRACTION99.61
2.34-2.470.26521310.22292704X-RAY DIFFRACTION99.58
2.47-2.620.27751370.20282715X-RAY DIFFRACTION99.44
2.62-2.820.24521350.18132674X-RAY DIFFRACTION98.18
2.83-3.110.21961530.16552715X-RAY DIFFRACTION99.1
3.11-3.560.20331570.15442713X-RAY DIFFRACTION98.93
3.56-4.480.20021560.14072732X-RAY DIFFRACTION97.4
4.48-700.16891490.15082859X-RAY DIFFRACTION96.44
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)
12.57114191424-0.32570368807-2.033634302820.9088296816170.4965194590613.01881316559-0.299084368006-0.436254362058-0.09492842046230.5146729996960.2111162885810.09839022472960.3273644634150.351761022690.1466316647490.260690762084-0.0462905592893-0.03742881419660.291799464106-0.02292909788530.17810893932843.74358397962.802610470769.2458016193
21.733034192930.0376805413298-1.660535274832.268648059320.08466502214532.65628175896-0.087105756575-0.110785632301-0.005880498258650.067013538715-0.02071218215750.09348886706590.216870822306-0.05923865019490.1055911007810.215376878861-0.0382941918209-0.006813302222220.255674587823-0.02075840911970.21770358167947.154515656561.415785078759.8144035742
31.21420837642-0.120117960386-1.220895324931.232483506970.243449377062.329153641630.0832239400805-0.0663508731670.0204970167843-0.0139306807716-0.040239473279-0.080343665772-0.1438095057350.185193804115-0.0816513912470.207930622237-0.0341324876553-0.01075389561350.233357141556-0.03427954372310.20136581631146.272138460566.10593081859.349691798
41.150366779650.222865284135-0.06352771788511.79337948189-0.03070546268481.92685359653-0.009516486983020.0632170954284-0.1889399788060.1272191922630.2080466645-0.148378031020.372578555690.08663257553980.01191103993840.2535653871840.0365362586782-0.03073948752860.19331810913-0.04822724241540.2590983111626.648835970951.252813330179.9361876186
51.84065468840.406372489209-0.02271611392272.204761525250.4522784357082.294921066030.1129525968560.316715227621-0.423481339628-0.09098515749030.134389776077-0.1689807674510.3588821172460.455372605532-0.2396996745120.3396757486290.0481633545695-0.02329855173090.249890640439-0.1005362216710.32196787091525.828696643347.509331801275.0491158091
61.559815204171.1800913606-0.6928012587354.742870020630.2631047679640.7382182383940.154224437025-0.22399373224-0.4708742450630.9404754167080.130159635317-0.5651149444580.7423042743150.346794309315-0.1387281264030.6351232968580.0757886187911-0.1578139532730.279654936419-0.01901364606410.47199088831227.970753804343.188839311286.27500178
71.725714053190.681225455329-0.3236803021592.96549347078-0.05278518808881.579169768830.0455682847694-0.009660060095350.02093246554710.0318979300471-0.0574545745987-0.0151472213749-0.00685744726446-0.02365655870790.01347548313380.201568589824-0.00428597966766-0.01411189488040.201126893362-0.01535578780890.14905730265936.676428973153.319800133844.7073862559
80.89484408720.33738309444-1.179019786620.287080186305-0.6063572774281.68139445287-0.08916050142430.00618081781455-0.001744083212350.00942775329870.05801798694640.07873257720040.243445962728-0.1064290361140.04465035135280.262233150844-0.0130697926609-0.0005939902272410.21090004505-0.00787085216790.21249646999324.739261348848.463176937760.5396914704
93.088383004750.357224158933-1.514119040011.26210469473-0.0141725838473.775783614470.03919209879190.09496085731720.149864039346-0.0204960470559-0.01033124902460.1304195750910.126508044744-0.193688977646-0.03821055387740.265756074841-0.03456219854430.01617333527090.2726013954920.01631808464980.26366556246411.627676492646.201104136771.4030406712
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 43 )HA18 - 4318 - 43
33chain 'H' and (resid 44 through 114 )HA44 - 11444 - 114
44chain 'H' and (resid 115 through 162 )HA115 - 162115 - 156
55chain 'H' and (resid 163 through 189 )HA163 - 189157 - 183
66chain 'H' and (resid 190 through 218 )HA190 - 218184 - 212
77chain 'L' and (resid 1 through 71 )LB1 - 711 - 71
88chain 'L' and (resid 72 through 153 )LB72 - 15372 - 153
99chain 'L' and (resid 154 through 213 )LB154 - 213154 - 213

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