6KUU | pdb_00006kuu

Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B3)

PDB DOI: https://doi.org/10.2210/pdb6KUU/pdb
Entry: 6KUU supersedes: 6ABG
NAKB: 6KUU
EM Map EMD-9582: EMDB EMDataResource

Classification: VIRAL PROTEIN/RNA
Organism(s): Influenza D virus (D/swine/Oklahoma/1334/2011), synthetic construct
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No

Deposited: 2019-09-02 Released: 2019-12-11
Deposition Author(s): Peng, Q., Peng, R., Qi, J., Gao, G.F., Shi, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6KUU

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

Literature

Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B3)

Peng, Q., Peng, R., Qi, J., Gao, G.F., Shi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 266.91 kDa
Atom Count: 12,364
Modeled Residue Count: 1,492
Deposited Residue Count: 2,264
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase 3	A	710	Influenza D virus (D/swine/Oklahoma/1334/2011)	Mutation(s): 0 Gene Names: P3
UniProt
Find proteins for K9LHJ4 (Influenza D virus) Explore K9LHJ4 Go to UniProtKB: K9LHJ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K9LHJ4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase catalytic subunit	B	753	Influenza D virus (D/swine/Oklahoma/1334/2011)	Mutation(s): 0 Gene Names: PB1 EC: 2.7.7.48
UniProt
Find proteins for K9LH03 (Influenza D virus) Explore K9LH03 Go to UniProtKB: K9LH03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K9LH03
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase PB2	C	772	Influenza D virus (D/swine/Oklahoma/1334/2011)	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for K9LHF3 (Influenza D virus) Explore K9LHF3 Go to UniProtKB: K9LHF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K9LHF3
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 4
3'-vRNA	D [auth R]	14	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 5
5'-vRNA	E [auth V]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

This entry supersedes: 6ABG

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB08020100

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references
Version 1.2: 2025-06-25
Changes: Data collection, 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.