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- PDB-9je3: Structure of #2-911 Fab in complex with MEDI8852 Fab -

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Basic information

Entry
Database: PDB / ID: 9je3
TitleStructure of #2-911 Fab in complex with MEDI8852 Fab
Components
  • #2-911 Fab heavy chain
  • #2-911 Fab light chain
  • (MEDI8852 Fab ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Anti-Idiotypic antibody / Broadly-neutralizing antibody / Complex
Function / homologytrehalose / CITRIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 Å
AuthorsItou, H. / Sano, K. / Ainai, A. / Suzuki, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Finding and mimicking a conserved structural motif hidden in influenza virus haemagglutinins using anti-idiotypic antibodies: A novel approach for universal vaccine antigen design.
Authors: Itou, H. / Sano, K. / Ainai, A. / Otsuki, K. / Inoue, T. / Suzuki, T.
History
DepositionSep 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: #2-911 Fab heavy chain
F: #2-911 Fab light chain
G: MEDI8852 Fab heavy chain
H: MEDI8852 Fab light chain
A: #2-911 Fab heavy chain
B: #2-911 Fab light chain
C: MEDI8852 Fab heavy chain
D: MEDI8852 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,05413
Polymers187,6438
Non-polymers1,4115
Water5,008278
1
E: #2-911 Fab heavy chain
F: #2-911 Fab light chain
G: MEDI8852 Fab heavy chain
H: MEDI8852 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6987
Polymers93,8214
Non-polymers8773
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: #2-911 Fab heavy chain
B: #2-911 Fab light chain
C: MEDI8852 Fab heavy chain
D: MEDI8852 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3566
Polymers93,8214
Non-polymers5342
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.283, 151.111, 176.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 4 types, 8 molecules EAFBGCHD

#1: Antibody #2-911 Fab heavy chain


Mass: 23311.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Expi 293 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody #2-911 Fab light chain


Mass: 23129.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Expi 293 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody MEDI8852 Fab heavy chain


Mass: 24470.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi 293 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Antibody MEDI8852 Fab light chain


Mass: 22910.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi 293 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Sugars , 1 types, 3 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 280 molecules

#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris (pH5.5), 13% PEG3350, 1% Tacsimate, 10 mM TCEP

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.374→48.43 Å / Num. obs: 91583 / % possible obs: 88.8 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 12.72
Reflection shellResolution: 2.374→2.459 Å / Rmerge(I) obs: 0.469 / Num. unique obs: 8971 / CC1/2: 0.748

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Processing

Software
NameVersionClassification
REFMACv5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JW3,2QHR

5jw3

2qhr


Resolution: 2.374→48.43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.838 / SU ML: 0.214 / Cross valid method: FREE R-VALUE / ESU R: 0.311 / ESU R Free: 0.243
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2543 4705 5.137 %
Rwork0.2 86878 -
all0.203 --
obs-91583 99.885 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.519 Å2
Baniso -1Baniso -2Baniso -3
1--3.726 Å20 Å2-0 Å2
2--3.532 Å20 Å2
3---0.195 Å2
Refinement stepCycle: LAST / Resolution: 2.374→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13180 0 95 278 13553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01213616
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612269
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.80418595
X-RAY DIFFRACTIONr_angle_other_deg0.5241.7328481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23551731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.987540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.467102115
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.80110508
X-RAY DIFFRACTIONr_chiral_restr0.0670.22141
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022971
X-RAY DIFFRACTIONr_nbd_refined0.1930.22017
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.211050
X-RAY DIFFRACTIONr_nbtor_refined0.1830.26446
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.27291
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2385
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.213
X-RAY DIFFRACTIONr_nbd_other0.150.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2580.211
X-RAY DIFFRACTIONr_mcbond_it5.3335.2146948
X-RAY DIFFRACTIONr_mcbond_other5.3255.2156948
X-RAY DIFFRACTIONr_mcangle_it7.8149.3568671
X-RAY DIFFRACTIONr_mcangle_other7.8159.3578672
X-RAY DIFFRACTIONr_scbond_it5.9855.5936668
X-RAY DIFFRACTIONr_scbond_other5.9755.5936667
X-RAY DIFFRACTIONr_scangle_it8.9810.0569924
X-RAY DIFFRACTIONr_scangle_other8.9810.0569925
X-RAY DIFFRACTIONr_lrange_it12.74162.56853852
X-RAY DIFFRACTIONr_lrange_other12.74162.56853853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.374-2.4350.4273420.3666294X-RAY DIFFRACTION99.0596
2.435-2.5020.3663180.3296174X-RAY DIFFRACTION99.9538
2.502-2.5740.3253250.2866040X-RAY DIFFRACTION99.9372
2.574-2.6530.313360.2655815X-RAY DIFFRACTION99.9837
2.653-2.740.3082880.2455696X-RAY DIFFRACTION99.9666
2.74-2.8360.2652970.2235513X-RAY DIFFRACTION99.9656
2.836-2.9420.313010.2275280X-RAY DIFFRACTION99.9821
2.942-3.0620.2842880.2175089X-RAY DIFFRACTION99.9814
3.062-3.1980.2742590.2154919X-RAY DIFFRACTION99.9035
3.198-3.3530.2592380.2124717X-RAY DIFFRACTION99.9597
3.353-3.5330.2732410.2114499X-RAY DIFFRACTION99.9578
3.533-3.7460.2572360.2044239X-RAY DIFFRACTION99.9777
3.746-4.0030.2492220.1744012X-RAY DIFFRACTION100
4.003-4.3220.182000.1513733X-RAY DIFFRACTION100
4.322-4.730.1741800.1243470X-RAY DIFFRACTION100
4.73-5.2820.2041770.1423149X-RAY DIFFRACTION100
5.282-6.0880.2331480.1712802X-RAY DIFFRACTION100
6.088-7.4270.2451430.1862367X-RAY DIFFRACTION99.9602
7.427-10.3820.2121080.1721902X-RAY DIFFRACTION99.9006
10.382-48.430.287580.2461168X-RAY DIFFRACTION99.9185

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