8R61

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
R-Value Work: 0.232
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Andersen, G.R., Gandini, R.

To be published.

Macromolecule Content

Total Structure Weight: 442.67 kDa
Atom Count: 25,344
Modelled 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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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
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Reference Sequence

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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
R-Value Work: 0.232
R-Value Observed: 0.233
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

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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

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 R01GM133198.