8R61 | pdb_00008r61

Structure of IgE delta epsilon 3-4 in complex with a kappa binding nanobody

PDB DOI: https://doi.org/10.2210/pdb8R61/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2023-11-20 Released: 2023-11-29
Deposition Author(s): Andersen, G.R., Gandini, R.
Funding Organization(s): Danish Council for Independent Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.275 (Depositor), 0.280 (DCC)
R-Value Work:
0.232 (Depositor), 0.240 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The dynamics of hinge flexibility in receptor bound immunoglobulin E revealed by electron microscopy

Jensen, R.K., Miehe, M., Gandini, R., Jorgensen, M.H., Spillner, E., Andersen, G.R.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.02.17.528943

Macromolecule Content

Total Structure Weight: 442.67 kDa
Atom Count: 25,344
Modeled Residue Count: 3,360
Deposited Residue Count: 4,098
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin E VH-Ceps1-Ceps1	A, D, G, J, M A, D, G, J, M, P	346	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HMM5 IgE light chain	B, E, H, K, N B, E, H, K, N, Q	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
kappa binding nanobody	C, F, I, L, O C, F, I, L, O, R	120	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.275 (Depositor), 0.280 (DCC)
R-Value Work: 0.232 (Depositor), 0.240 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.1	α = 90
b = 132.49	β = 118.843
c = 154.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	0135-00061B

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release
Version 1.1: 2024-06-12
Changes: Database references
Version 1.2: 2024-11-13
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.