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

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Basic information

Entry
Database: PDB / ID: 8vev
TitleStructure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, m6A nucleoside ligand
Components(N6-methyladenosine (m6A) binding IgG Fab, ...) x 2
KeywordsIMMUNE SYSTEM / IgG Fab / N6-methyladenosine (m6A) / RNA binding protein (RBP) / modified RNA / small molecule ligand
Function / homologyN-methyladenosine / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsAoki, S.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, m6A nucleoside ligand
Authors: Aoki, S.T.
History
DepositionDec 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N6-methyladenosine (m6A) binding IgG Fab, heavy chain
B: N6-methyladenosine (m6A) binding IgG Fab, light chain
C: N6-methyladenosine (m6A) binding IgG Fab, heavy chain
D: N6-methyladenosine (m6A) binding IgG Fab, light chain
H: N6-methyladenosine (m6A) binding IgG Fab, heavy chain
L: N6-methyladenosine (m6A) binding IgG Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,05322
Polymers141,1976
Non-polymers1,85716
Water90150
1
A: N6-methyladenosine (m6A) binding IgG Fab, heavy chain
B: N6-methyladenosine (m6A) binding IgG Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3645
Polymers47,0662
Non-polymers2983
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-55 kcal/mol
Surface area20150 Å2
MethodPISA
2
C: N6-methyladenosine (m6A) binding IgG Fab, heavy chain
D: N6-methyladenosine (m6A) binding IgG Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7317
Polymers47,0662
Non-polymers6665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-65 kcal/mol
Surface area19400 Å2
MethodPISA
3
H: N6-methyladenosine (m6A) binding IgG Fab, heavy chain
L: N6-methyladenosine (m6A) binding IgG Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,95910
Polymers47,0662
Non-polymers8938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-105 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.640, 128.377, 150.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 6 molecules ACHBDL

#1: Antibody N6-methyladenosine (m6A) binding IgG Fab, heavy chain


Mass: 24023.018 Da / Num. of mol.: 3
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 N6-methyladenosine (m6A) binding IgG Fab, light chain


Mass: 23042.525 Da / Num. of mol.: 3
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)

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Non-polymers , 5 types, 66 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6MD / N-methyladenosine / N6-Methyladenosine


Mass: 281.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.17 M Ammonium sulfate; 25,5 %(w/v) PEG 4000; 15 %(v/v) Glycerol, 0.2 mM m6A nucleoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 3.06→48.23 Å / Num. obs: 31244 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 70.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.06-3.186.80.416433990.9630.1720.451100
3.18-3.336.60.2835.634280.9760.1190.308100
3.33-3.56.40.1928.134270.9880.0820.20999.9
3.5-3.726.90.14211.334220.9940.0580.154100
3.72-4.016.80.11214.634570.9950.0460.121100
4.01-4.416.70.07920.834630.9970.0330.086100
4.41-5.056.40.06125.234690.9970.0260.067100
5.05-6.3660.05925.335170.9970.0260.06599.9
6.36-43.236.10.0434.836620.9980.0170.04499.7

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5109refinement
autoPROCdata processing
Aimlessdata scaling
autoPROCdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→48.23 Å / SU ML: 0.3566 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Data anisotropic, eventually chose cut refinement cut off based on the "estimates of resolution limits in reciprocal lattice direction" by aimless where CC(1/2) > 0.3 in the anisotropic direction
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1307 4.19 %0.2744
Rwork0.2238 29901 --
obs0.225 31208 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.07 Å2
Refinement stepCycle: LAST / Resolution: 3.06→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9649 0 108 50 9807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329989
X-RAY DIFFRACTIONf_angle_d0.559513653
X-RAY DIFFRACTIONf_chiral_restr0.04421567
X-RAY DIFFRACTIONf_plane_restr0.00381699
X-RAY DIFFRACTIONf_dihedral_angle_d14.08833458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.180.311420.31563249X-RAY DIFFRACTION99.76
3.18-3.330.31691430.27833279X-RAY DIFFRACTION99.77
3.33-3.50.30781440.25053277X-RAY DIFFRACTION99.74
3.5-3.720.28291420.24563272X-RAY DIFFRACTION99.77
3.72-4.010.32331460.24143306X-RAY DIFFRACTION99.88
4.01-4.410.21561440.19793318X-RAY DIFFRACTION99.97
4.41-5.050.17841450.1843325X-RAY DIFFRACTION100
5.05-6.360.23241470.21363372X-RAY DIFFRACTION99.91
6.36-48.230.26071540.2213503X-RAY DIFFRACTION99.59
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)
10.8444296661990.451027437220.2132151482151.269845110310.986431943541.821170216240.2312126584380.0993379209159-0.28859402365-0.54955551469-0.1404015166030.02025188509340.09003455404850.16020582165-1.42057475725E-81.196907506140.07376806880360.251738502950.889984747876-0.05274768479660.82962097445618.1395012405-38.61903534540.0829437505274
20.2232158558520.701998527882-0.5069260925971.370341749730.07240721470981.41441164264-0.10856123623-0.302127059156-0.108079383463-0.15370469759-0.056245715437-0.2923139091560.06440456897690.0574837267177-1.59283901546E-80.8805737454270.06936447292590.1199973040420.7601572712160.01664197098920.77502218962717.5357653701-2.023831069579.53313408837
31.324283156040.754811770007-0.7451778489661.374201089960.1586803140532.23274861897-0.1988415041870.01430121345230.0996311011964-0.171094510446-0.05930907602850.01165359419370.09244513772240.0956408998262-3.15982774307E-90.724190483601-0.03207002987520.08443541918360.658707144767-0.02824227140910.5862321198196.72685012562-38.348657753518.2075915028
41.267135273920.013642925964-0.4346247605031.05884140962-0.08278734448210.96306196143-0.1037116968170.0288617514870.0226561734656-0.13612043024-0.02168101345060.2110438725390.119187520782-0.193427351977-3.67278325159E-90.827763352975-0.03475714459820.05603178765910.783197094470.01352213980560.7302717473112.87528281665-4.9771296181813.9784371421
51.53556714302-0.60784411914-0.1118791692931.3999623834-0.685778890151.61599829465-0.170603169142-0.217214609296-0.06284168716440.3647191236450.1944712629040.510979336947-0.118199884769-0.0231977086219-7.5867412391E-100.7266307960040.03767433660490.1003905141680.7197118550290.0360213187560.71825715426419.444437467641.2695570344-9.56365432219
60.7990690670610.0695736569437-0.1402214179130.37405016320.4143960169981.62111406552-0.1621487709110.3503459321170.6980432024070.09472810814070.0338831073126-0.398957769480.393559173270.01404512448274.02867730366E-90.957760255039-0.0441488830370.2211851557540.7608317513390.08445627223590.98464663756729.35671218845.63792328255-8.06628870659
72.14484503729-1.11066476832-1.67600427151.059885699990.1440489190041.160682399490.1103174301950.0505322468140.00993365651537-0.08897571222630.04987433244810.0664931326438-0.08370454388650.007644516600996.59603730837E-90.605793573426-0.0537526206966-0.02910725329540.6211767646650.001189698507350.65973035628229.116183330139.2556518466-28.6977466977
80.235196713337-0.2261836571640.6192485620050.488915629510.135050006720.8168047943950.29017778448-0.4813342214790.141426695015-0.537748523513-0.3848010311370.0006162271633520.259450865887-0.242494556984-2.13287876445E-81.24231280826-0.1210593357540.144777700881.16506497879-0.02593043793771.0356047741727.51370303325.75080066833-24.5662401669
92.430446939950.6353273663141.753338122331.39930000718-0.9132824708481.150331743610.116874197417-0.0921560523256-0.200394314478-0.009314972918130.1327683395290.2229649929940.0132768510734-0.103377038346-3.56618635193E-90.6003214012380.03407837580760.05836236410380.7816333663870.002690363770310.8791713899525.72842759782-21.0607684594-37.6412531456
101.51749392177-0.2305929305650.07030756948760.9091091834240.4552625141680.567174005864-0.502801556762-0.238928107450.1575410762570.3252732107020.178326638330.4173143612470.0457835855817-0.04626811854282.68779520505E-90.9831232429880.115128951991-0.005201735655050.8348311204880.03001007184220.8834246131844.01342250804-50.5395021471-25.5979578649
112.36189178719-0.3807831451340.9230159439080.623382184985-0.7589316396771.281675642130.08109743041030.0208383904203-0.08979552802580.030664430606-0.06240416382650.02276934971140.07312043830170.1571534447787.20223155369E-90.5919345089930.02686103604370.02959844329410.652870304412-0.02872033139750.64992468763527.3452780597-23.7735352403-37.3006795418
121.250685081090.0782616398958-0.02874067441691.19847041877-0.2976939620530.905842640389-0.02018281275690.164059881564-0.2158235838890.218911665244-0.159223719851-0.257023425325-0.2179503046760.1219378098571.32816840618E-80.848951778583-0.01895281720670.01222186729140.807025279080.09778531558360.85227374474816.1178659369-59.1876906167-31.5656112414
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 116 )AA1 - 1161 - 116
22chain 'A' and (resid 117 through 218 )AA117 - 218117 - 218
33chain 'B' and (resid 1 through 109 )BD1 - 1091 - 109
44chain 'B' and (resid 110 through 213 )BD110 - 213110 - 213
55chain 'C' and (resid 1 through 116 )CH1 - 1161 - 116
66chain 'C' and (resid 117 through 218 )CH117 - 218117 - 211
77chain 'D' and (resid 1 through 109 )DL1 - 1091 - 109
88chain 'D' and (resid 110 through 210 )DL110 - 210110 - 200
99chain 'H' and (resid 1 through 116 )HQ1 - 1161 - 116
1010chain 'H' and (resid 117 through 217 )HQ117 - 217117 - 214
1111chain 'L' and (resid 2 through 109 )LX2 - 1091 - 108
1212chain 'L' and (resid 110 through 212 )LX110 - 212109 - 211

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