8J71 | pdb_00008j71

Selenomethionine mutant (L601Sem/L654Sem) of SAND domain of protein SP140 with DNA

PDB DOI: https://doi.org/10.2210/pdb8J71/pdb
NAKB: 8J71

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2023-04-26 Released: 2024-05-01
Deposition Author(s): Li, H.T., Liu, W.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.224 (Depositor), 0.227 (DCC)
R-Value Work:
0.194 (Depositor), 0.198 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8J71

This is version 1.1 of the entry. See complete history.

Literature

Molecular basis for Speckled protein SP140 bivalent recognition of histone H3 and DNA

Li, H.T., Liu, W.Q.

To be published.

Macromolecule Content

Total Structure Weight: 30.94 kDa
Atom Count: 2,208
Modeled Residue Count: 207
Deposited Residue Count: 224
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear body protein SP140	A, B	99	Homo sapiens	Mutation(s): 2 Gene Names: SP140, LYSP100
UniProt & NIH Common Fund Data Resources
Find proteins for Q13342 (Homo sapiens) Explore Q13342 Go to UniProtKB: Q13342
PHAROS: Q13342 GTEx: ENSG00000079263
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13342
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(GPGPGPCPGPGPCPCPGPCPCPCP*T)-3')	C, D	13	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.224 (Depositor), 0.227 (DCC)
R-Value Work: 0.194 (Depositor), 0.198 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.131	α = 90
b = 59.748	β = 90
c = 124.956	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
SHELX	phasing
SHELX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-05-01
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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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.