3P8B | pdb_00003p8b

X-ray crystal structure of Pyrococcus furiosus transcription elongation factor Spt4/5

PDB DOI: https://doi.org/10.2210/pdb3P8B/pdb

Classification: TRANSFERASE/TRANSCRIPTION
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-13 Released: 2011-01-26
Deposition Author(s): Murakami, K.S., Klein, B.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.292 (Depositor), 0.290 (DCC)
R-Value Work:
0.236 (Depositor), 0.237 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

RNA polymerase and transcription elongation factor Spt4/5 complex structure.

Klein, B.J., Bose, D., Baker, K.J., Yusoff, Z.M., Zhang, X., Murakami, K.S.

(2011) Proc Natl Acad Sci U S A 108: 546-550

PubMed: 21187417 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1013828108
Primary Citation Related Structures:
3P8B

PubMed Abstract:
Spt4/5 in archaea and eukaryote and its bacterial homolog NusG is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating RNA polymerase. Here, we present the crystal structure of Spt4/5 as well as the structure of RNA polymerase-Spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. The Spt4/5 binds in the middle of RNA polymerase claw and encloses the DNA, reminiscent of the DNA polymerase clamp and ring helicases. The transcription elongation complex model reveals that the Spt4/5 is an upstream DNA holder and contacts the nontemplate DNA in the transcription bubble. These structures reveal that the cellular RNA polymerases also use a strategy of encircling DNA to enhance its processivity as commonly observed for many nucleic acid processing enzymes including DNA polymerases and helicases.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

Macromolecule Content

Total Structure Weight: 52.97 kDa
Atom Count: 3,405
Modeled Residue Count: 414
Deposited Residue Count: 466
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase, subunit e''	A, C	81	Pyrococcus furiosus	Mutation(s): 0 Gene Names: PF0255, Spt4
UniProt
Find proteins for Q8U440 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U440 Go to UniProtKB: Q8U440
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U440
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription antitermination protein nusG	B, D	152	Pyrococcus furiosus	Mutation(s): 0 Gene Names: PF1990, Spt5
UniProt
Find proteins for Q8TZK1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZK1 Go to UniProtKB: Q8TZK1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain I [auth B]	G [auth B], H [auth B], I [auth B], N [auth D], O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D] Focus chain O [auth D]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A] J [auth B] K [auth B] L [auth B] P [auth D] F [auth A], J [auth B], K [auth B], L [auth B], P [auth D], Q [auth D]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth D] Focus chain Q [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.292 (Depositor), 0.290 (DCC)
R-Value Work: 0.236 (Depositor), 0.237 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.532	α = 90
b = 87.213	β = 90
c = 133.107	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-01-26

Deposition Author(s):

Murakami, K.S.

Klein, B.J.

Revision History (Full details and data files)

Version 1.0: 2011-01-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations