8HYL

Crystal structure of DO1 Fv-clasp fragment

PDB DOI: https://doi.org/10.2210/pdb8HYL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-06 Released: 2024-02-14
Deposition Author(s): Anan, Y., Lu, P., Nagata, K., Itakura, M., Uchida, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.298
R-Value Work: 0.241
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

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

Literature

Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins

Anan, Y., Itakura, M., Shimoda, T., Yamaguchi, K., Lu, P., Nagata, K., Dong, J., Ueda, H., Uchida, K.

(2024) Commun Biol 7: 149

DOI: https://doi.org/10.1038/s42003-024-05851-0

Macromolecule Content

Total Structure Weight: 75.76 kDa
Atom Count: 5,569
Modelled Residue Count: 651
Deposited Residue Count: 670
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VH-SARAH	A, C	170	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VL-SARAH	B, D	165	Mus musculus	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: 2.00 Å
R-Value Free: 0.298
R-Value Work: 0.241
R-Value Observed: 0.244
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.277	α = 90
b = 86.207	β = 90
c = 112.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP17H06170

Revision History (Full details and data files)

Version 1.0: 2024-02-14
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.