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- PDB-8p2e: Homotypic interacting B1 fab bound to Chondroitin Sulfate A -

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Basic information

Entry
Database: PDB / ID: 8p2e
TitleHomotypic interacting B1 fab bound to Chondroitin Sulfate A
Components
  • B1 fab heavy
  • B1 fab light
KeywordsSUGAR BINDING PROTEIN / Chondroitin Sulfate A
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRaghavan, S.S.R. / Dagil, R. / Wang, K.T. / Salanti, A.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF22OC0076055 Denmark
Novo Nordisk FoundationNNF21OC0068192 Denmark
The Carlsberg FoundationCF20-0045 Denmark
CitationJournal: To Be Published
Title: Structure of homotypic B1 fabs bound to Chondroiting Sulfate A
Authors: Raghavan, S.S.R. / Vidal-Calvo, E.E. / Dagil, R. / Wang, K.T. / Salanti, A.
History
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B1 fab light
B: B1 fab heavy
C: B1 fab light
D: B1 fab heavy
E: B1 fab light
F: B1 fab heavy
G: B1 fab light
H: B1 fab heavy


Theoretical massNumber of molelcules
Total (without water)200,3288
Polymers200,3288
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17230 Å2
ΔGint-93 kcal/mol
Surface area72150 Å2

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Components

#1: Antibody
B1 fab light


Mass: 23662.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
B1 fab heavy


Mass: 26419.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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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: B1 fabs bound to chondroitin sulphate A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 50 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1250000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213275
ELECTRON MICROSCOPYf_angle_d0.81518048
ELECTRON MICROSCOPYf_dihedral_angle_d13.2594749
ELECTRON MICROSCOPYf_chiral_restr0.0382030
ELECTRON MICROSCOPYf_plane_restr0.0042316

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