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- PDB-9odb: Clone 2.1 Fab in complex with chicken IgY CH2 domain (local refin... -

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Basic information

Entry
Database: PDB / ID: 9odb
TitleClone 2.1 Fab in complex with chicken IgY CH2 domain (local refinement)
Components
  • Clone 2.1 Fab heavy chain
  • Clone 2.1 Fab light chain
  • chicken IgY heavy chain,Ig-like domain-containing protein
KeywordsIMMUNE SYSTEM / germinal center evolution / antibody
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ig-like domain-containing protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsOzorowski, G. / Alkutkar, T. / Ward, A.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2025
Title: Replaying germinal center evolution on a quantified affinity landscape
Authors: DeWitt, W.S.S. / Vora, A.A. / Araki, T. / Galloway, J.G. / Alkutkar, T. / Bortolatto, J. / Castro, T.B. / Dumm, W. / Jennings-Schaffer, C. / Jia, T. / Mesin, L. / Ozorowski, G. / Pae, J. / ...Authors: DeWitt, W.S.S. / Vora, A.A. / Araki, T. / Galloway, J.G. / Alkutkar, T. / Bortolatto, J. / Castro, T.B. / Dumm, W. / Jennings-Schaffer, C. / Jia, T. / Mesin, L. / Ozorowski, G. / Pae, J. / Ralph, D.K. / Bloom, J.D. / Nourmohammad, A. / Song, Y.S. / Ward, A. / Starr, T.N. / Matsen, F.A. / Victora, G.D.
History
DepositionApr 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chicken IgY heavy chain,Ig-like domain-containing protein
H: Clone 2.1 Fab heavy chain
L: Clone 2.1 Fab light chain
B: Clone 2.1 Fab heavy chain
C: Clone 2.1 Fab light chain
D: chicken IgY heavy chain,Ig-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,4598
Polymers218,0176
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody chicken IgY heavy chain,Ig-like domain-containing protein


Mass: 59474.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human) / References: UniProt: A0A8V0XLK0
#2: Antibody Clone 2.1 Fab heavy chain


Mass: 25972.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Clone 2.1 Fab light chain


Mass: 23561.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Clone 2.1 Fab in complex with chicken IgY CH2 domain / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487model refinement
3Leginonimage acquisition
5GctfCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346259 / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0074971
ELECTRON MICROSCOPYf_angle_d1.2036762
ELECTRON MICROSCOPYf_dihedral_angle_d10.6891760
ELECTRON MICROSCOPYf_chiral_restr0.062768
ELECTRON MICROSCOPYf_plane_restr0.006854

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