7PMQ | pdb_00007pmq

DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3

PDB DOI: https://doi.org/10.2210/pdb7PMQ/pdb
NAKB: 7PMQ

Classification: RNA BINDING PROTEIN
Organism(s): Escherichia coli, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-09-02 Released: 2022-09-14
Deposition Author(s): Wurm, J.P.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.22 Å
R-Value Free:
0.264 (Depositor), 0.262 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.

Wurm, J.P.

(2023) RNA 29: 1339-1354

PubMed: 37221012 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1261/rna.079582.123
Primary Citation Related Structures:
7PLI, 7PMM, 7PMQ

PubMed Abstract:
DEAD-box RNA helicases are implicated in most aspects of RNA biology, where these enzymes unwind short RNA duplexes in an ATP-dependent manner. During the central step of the unwinding cycle, the two domains of the helicase core form a distinct closed conformation that destabilizes the RNA duplex, which ultimately leads to duplex melting. Despite the importance of this step for the unwinding process no high-resolution structures of this state are available. Here, I used nuclear magnetic resonance spectroscopy and X-ray crystallography to determine structures of the DEAD-box helicase DbpA in the closed conformation, complexed with substrate duplexes and single-stranded unwinding product. These structures reveal that DbpA initiates duplex unwinding by interacting with up to three base-paired nucleotides and a 5' single-stranded RNA duplex overhang. These high-resolution snapshots, together with biochemical assays, rationalize the destabilization of the RNA duplex and are integrated into a conclusive model of the unwinding process.

Organizational Affiliation

Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany jan-philip.wurm@ur.de.

Macromolecule Content

Total Structure Weight: 253.46 kDa
Atom Count: 17,493
Modeled Residue Count: 1,996
Deposited Residue Count: 2,004
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DbpA	A [auth C], B [auth A], C [auth B], D	459	Escherichia coli	Mutation(s): 0 Gene Names: dbpA, A8C65_19820, A9R57_00760, ACU57_03180, AUQ13_15600, BANRA_00847, BANRA_04171, BHS87_08505, BJJ90_11745, BMA87_07955... dbpA, A8C65_19820, A9R57_00760, ACU57_03180, AUQ13_15600, BANRA_00847, BANRA_04171, BHS87_08505, BJJ90_11745, BMA87_07955, BMT91_21590, BON75_24465, BUE81_14670, BvCms2454_02704, BvCmsHHP001_02300, BvCmsHHP019_03587, BW690_11350, BZL31_07520, C5F72_14440, C5F73_15055, C5N07_15770, C9E25_22300, CA593_21090, CG692_05575, CI694_17855, D0X26_18530, D2185_21600, D3821_15150, D3O91_18845, D3Y67_16695, D9C99_05435, D9D20_02105, D9G69_18010, D9H68_04755, D9I18_03165, D9J11_06735, D9J52_03565, D9Z28_17890, DAH34_14805, DJ503_15675, DNC98_04485, DT034_18155, E2127_03725, E2128_00120, E2134_01275, E2135_09020, E4K51_14550, E4K53_14175, E4K55_14180, E4K61_06710, E5P28_06285, EA213_25155, EC1094V2_2419, EC3234A_27c00310, ECTO6_02613, EEP23_08150, EG808_15015, EI032_01315, EI041_15270, EIZ93_05985, EPT01_22665, ERS150873_03851, ETECE1441_02540, EYD11_12000, EYV18_14670, FKC84_18670, FORC82_2579, FV293_11225, G5632_15630, G5688_06460, G6Z99_13300, G9P50_11500, GHD50_09530, GKF86_15135, GKF89_14975, GKG12_04280, GP720_20830, GP979_17935, GQE33_11520, GQE34_14030, GQE64_13275, GQE67_23825, GQM17_12000, GRW02_10210, GRW80_12795, HH707_003477, HJV81_000527, HLU13_09435, HMQ05_12610, HVV53_02995, HVX22_12385, HVX24_12180, HVY77_14250, HVY79_10190, HVY93_12730, HVZ24_12305, NCTC11126_00544, NCTC13148_00656, NCTC13216_03945, NCTC9045_03126, NCTC9062_00753, NCTC9706_03606, PGD_01899, RK56_010785, SAMEA3472047_04221, SAMEA3472080_01001, SAMEA3484427_04610, SAMEA3484429_04553, SAMEA3751407_04875, SAMEA3752557_05298, SAMEA3752559_01385, SK85_01554, WP2S18E08_25570, WP4S18E08_24570 EC: 3.6.4.13
UniProt
Find proteins for P21693 (Escherichia coli (strain K12)) Explore P21693 Go to UniProtKB: P21693
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21693
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (42-MER)	E, F, G, H	42	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain I [auth C] MOL2 format, chain R [auth D] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain I [auth C] mmCIF format, chain R [auth D] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain I [auth C]	I [auth C], L [auth A], O [auth B], R [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth C] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth D] Interactions & Density Focus chain I [auth C] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E]	U [auth E], V [auth F], W [auth G], X [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Interactions & Density Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H]
BEF Query on BEF Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain J [auth C] MOL2 format, chain S [auth D] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain J [auth C] mmCIF format, chain S [auth D] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain J [auth C]	J [auth C], M [auth A], P [auth B], S [auth D]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain J [auth C] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth D] Interactions & Density Focus chain J [auth C] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain K [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain K [auth C] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain K [auth C]	K [auth C], N [auth A], Q [auth B], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth D] Interactions & Density Focus chain K [auth C] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.22 Å
R-Value Free: 0.264 (Depositor), 0.262 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.644	α = 90
b = 159.644	β = 90
c = 204.682	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

Wurm, J.P.

Funding Organization	Location	Grant Number
Other government		WU 988/1-1

Revision History (Full details and data files)

Version 1.0: 2022-09-14
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-01-31
Changes: Refinement description