9BCU

Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA

PDB DOI: https://doi.org/10.2210/pdb9BCU/pdb
NAKB: 9BCU
EM Map EMD-44439: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Thermococcus kodakarensis, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-09 Released: 2024-07-31
Deposition Author(s): You, L., Ebright, R.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of archaeal FttA-dependent transcription termination

You, L., Ebright, R.H.

To be published.

Macromolecule Content

Total Structure Weight: 591.6 kDa
Atom Count: 39,765
Modelled Residue Count: 4,862
Deposited Residue Count: 4,988
Unique protein chains: 14
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit A'	A	906	Thermococcus kodakarensis	Mutation(s): 0
UniProt
Find proteins for Q5JE33 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE33 Go to UniProtKB: Q5JE33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JE33
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit B	B	1,123	Thermococcus kodakarensis	Mutation(s): 0
UniProt
Find proteins for Q5JE32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE32 Go to UniProtKB: Q5JE32
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JE32
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit A"	C	391	Thermococcus kodakarensis	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5JE34 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE34 Go to UniProtKB: Q5JE34
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JE34
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit D	D	261	Thermococcus kodakarensis	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit E	E	190	Thermococcus kodakarensis	Mutation(s): 0
UniProt
Find proteins for Q5JIY4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JIY4 Go to UniProtKB: Q5JIY4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JIY4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit F	F	122	Thermococcus kodakarensis	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit H	G [auth H]	82	Thermococcus kodakarensis	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5JE31 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE31 Go to UniProtKB: Q5JE31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JE31
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit K	H [auth K]	60	Thermococcus kodakarensis	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit L	I [auth L]	94	Thermococcus kodakarensis	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5JE88 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE88 Go to UniProtKB: Q5JE88
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JE88
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit N	J [auth N]	65	Thermococcus kodakarensis	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5JJC9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJC9 Go to UniProtKB: Q5JJC9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JJC9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit P	K [auth P]	49	Thermococcus kodakarensis	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q5JDM8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDM8 Go to UniProtKB: Q5JDM8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JDM8
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor Spt5	L [auth G]	152	Thermococcus kodakarensis	Mutation(s): 0 Gene Names: spt5
UniProt
Find proteins for Q5JH33 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JH33 Go to UniProtKB: Q5JH33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JH33
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor Spt4	M [auth I]	73	Thermococcus kodakarensis	Mutation(s): 0 Gene Names: spt4, TK1698
UniProt
Find proteins for Q5JIY5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JIY5 Go to UniProtKB: Q5JIY5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JIY5
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination factor FttA	N [auth J], O [auth M]	648	Thermococcus kodakarensis	Mutation(s): 0 Gene Names: TK1428
UniProt
Find proteins for Q5JH24 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JH24 Go to UniProtKB: Q5JH24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JH24
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
non-template strand DNA	P [auth 5]	36	synthetic construct
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Length	Organism	Image
template strand DNA	Q [auth 6]	36	synthetic construct
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Length	Organism	Image
RNA (29-MER)	R [auth 7]	52	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth N] SDF format, chain X [auth P] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain AA [auth M] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth N] MOL2 format, chain X [auth P] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J]	AA [auth M] T [auth A] U [auth A] V [auth B] W [auth N] AA [auth M], T [auth A], U [auth A], V [auth B], W [auth N], X [auth P], Y [auth I], Z [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth N] Focus chain X [auth P] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth M] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth N] Focus chain X [auth P] Focus chain Y [auth I] Focus chain Z [auth J]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

You, L.

Ebright, R.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release

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 R01GM133198.

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Help and Resources

9BCU

Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA

Structural basis of archaeal FttA-dependent transcription termination

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)