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- PDB-7x13: Structure of IgG-Fc hexamer -

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Basic information

Entry
Database: PDB / ID: 7x13
TitleStructure of IgG-Fc hexamer
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsSTRUCTURAL PROTEIN / IgG-Fc hexamer
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
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 ...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
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYuan, D. / Weixin, Y. / Xiao, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other private China
CitationJournal: To Be Published
Title: Structure of IgG-Fc hexamer
Authors: Yuan, D. / Weixin, Y. / Xiao, F.
History
DepositionFeb 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
C: Immunoglobulin gamma-1 heavy chain
D: Immunoglobulin gamma-1 heavy chain
E: Immunoglobulin gamma-1 heavy chain
F: Immunoglobulin gamma-1 heavy chain
G: Immunoglobulin gamma-1 heavy chain
H: Immunoglobulin gamma-1 heavy chain
I: Immunoglobulin gamma-1 heavy chain
J: Immunoglobulin gamma-1 heavy chain
K: Immunoglobulin gamma-1 heavy chain
L: Immunoglobulin gamma-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)330,81812
Polymers330,81812
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35370 Å2
ΔGint-192 kcal/mol
Surface area136590 Å2

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Components

#1: Antibody
Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 27568.195 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals) / References: UniProt: P0DOX5

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: IgG-Fc hexamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalia (mammals)
Buffer solutionpH: 7.5
SpecimenConc.: 1.93 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1900 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 1.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300561 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221824
ELECTRON MICROSCOPYf_angle_d0.48929705
ELECTRON MICROSCOPYf_dihedral_angle_d7.4512848
ELECTRON MICROSCOPYf_chiral_restr0.0423268
ELECTRON MICROSCOPYf_plane_restr0.0033821

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