5N8U | pdb_00005n8u

Crystal Structure of Drosophila DHX36 helicase in complex with CTCTCCT

PDB DOI: https://doi.org/10.2210/pdb5N8U/pdb
NAKB: 5N8U

Classification: HYDROLASE
Organism(s): Drosophila melanogaster, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-24 Released: 2018-03-14
Deposition Author(s): Chen, W.-F., Rety, S., Guo, H.-L., Wu, W.-Q., Liu, N.-N., Liu, Q.-W., Dai, Y.-X., Xi, X.-G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.249 (Depositor), 0.252 (DCC)
R-Value Work:
0.182 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding

Chen, W.-F., Rety, S., Guo, H.-L., Wu, W.-Q., Liu, N.-N., Liu, Q.-W., Dai, Y.-X., Xi, X.-G.

To be published.

Macromolecule Content

Total Structure Weight: 221.62 kDa
Atom Count: 14,110
Modeled Residue Count: 1,714
Deposited Residue Count: 1,904
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CG9323, isoform A	A, B	944	Drosophila melanogaster	Mutation(s): 0 Gene Names: CG9323, Dmel_CG9323 EC: 3.6.1.3 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q8SWT2 (Drosophila melanogaster) Explore Q8SWT2 Go to UniProtKB: Q8SWT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8SWT2
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(PCPTPCPTPCPCPCPT)-3')	C, D	8	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.249 (Depositor), 0.252 (DCC)
R-Value Work: 0.182 (Depositor), 0.184 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 302.368	α = 90
b = 51.288	β = 114.7
c = 164.097	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.