8VVD | pdb_00008vvd

Cryo-EM Structure of DHX36 bound to a RNA G-quadruplex derived from the cMyc G-quadruplex, Class 2

PDB DOI: https://doi.org/10.2210/pdb8VVD/pdb
NAKB: 8VVD
EM Map EMD-43555: EMDB EMDataResource

Classification: MOTOR PROTEIN/RNA
Organism(s): Bos taurus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-30 Released: 2025-07-30
Deposition Author(s): Banco, M.T., Ferre-D'Amare, A.R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8VVD

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

Literature

Inter-domain synergy enables both DNA and RNA G-quadruplex unwinding by the DEAH-box helicase DHX36

Banco, M.T., Paul, T., Jiang, J., Myong, S., Ferre-D'Amare, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 120.42 kDa
Atom Count: 6,980
Modeled Residue Count: 873
Deposited Residue Count: 999
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA/RNA helicase DHX36	A	972	Bos taurus	Mutation(s): 0 Gene Names: DHX36 EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q05B79 (Bos taurus) Explore Q05B79 Go to UniProtKB: Q05B79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05B79
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (27-MER)	B	27	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Ferre-D'Amare, A.R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release

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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.