8W8E

human co-transcriptional RNA capping enzyme RNGTT

PDB DOI: https://doi.org/10.2210/pdb8W8E/pdb
EM Map EMD-37352: EMDB EMDataResource
NAKB: 8W8E

Classification: TRANSCRIPTION
Organism(s): Sus scrofa, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-09-02 Released: 2024-04-10
Deposition Author(s): Li, Y., Wang, Q., Xu, Y., Li, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 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

Strcutures of co-transcriptional RNA capping enzymes on paused transcription complex

Li, Y., Wang, Q., Xu, Y., Li, Z.

To be published.

Macromolecule Content

Total Structure Weight: 988.37 kDa
Atom Count: 50,912
Modelled Residue Count: 6,279
Deposited Residue Count: 8,572
Unique protein chains: 19
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	1,970	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa) Explore A0A8D1DPV6 Go to UniProtKB: A0A8D1DPV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D1DPV6
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,174	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A4X1TVZ5 (Sus scrofa) Explore A0A4X1TVZ5 Go to UniProtKB: A0A4X1TVZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TVZ5
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	271	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A481DF93 (Sus scrofa) Explore A0A481DF93 Go to UniProtKB: A0A481DF93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A481DF93
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	142	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A481BYI6 (Sus scrofa) Explore A0A481BYI6 Go to UniProtKB: A0A481BYI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A481BYI6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	E	210	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VTX4 (Sus scrofa) Explore A0A4X1VTX4 Go to UniProtKB: A0A4X1VTX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VTX4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit F	F	127	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VEK9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	172	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VKG7
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	150	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCB2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	125	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899 Go to UniProtKB: P60899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60899
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	67	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A493TD97 (Anas platyrhynchos platyrhynchos) Explore A0A493TD97 Go to UniProtKB: A0A493TD97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A493TD97
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11-a	K	117	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1RKE4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
RPB12	L	58	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TRS6
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor A	P [auth U]	528	Homo sapiens	Mutation(s): 0 Gene Names: NELFA, WHSC2, P/OKcl.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3P2 (Homo sapiens) Explore Q9H3P2 Go to UniProtKB: Q9H3P2
PHAROS: Q9H3P2 GTEx: ENSG00000185049
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H3P2
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor B	Q [auth V]	580	Homo sapiens	Mutation(s): 0 Gene Names: NELFB, COBRA1, KIAA1182
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WX92 (Homo sapiens) Explore Q8WX92 Go to UniProtKB: Q8WX92
PHAROS: Q8WX92 GTEx: ENSG00000188986
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WX92
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor C/D	R [auth W]	584	Homo sapiens	Mutation(s): 0 Gene Names: NELFCD
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXH7 (Homo sapiens) Explore Q8IXH7 Go to UniProtKB: Q8IXH7
PHAROS: Q8IXH7 GTEx: ENSG00000101158
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IXH7
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor E	S [auth X]	380	Homo sapiens	Mutation(s): 0 Gene Names: NELFE, RD, RDBP
UniProt & NIH Common Fund Data Resources
Find proteins for P18615 (Homo sapiens) Explore P18615 Go to UniProtKB: P18615
PHAROS: P18615 GTEx: ENSG00000204356
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18615
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT4	T [auth Y]	121	Homo sapiens	Mutation(s): 0 Gene Names: SUPT4H1, SPT4H, SUPT4H
UniProt & NIH Common Fund Data Resources
Find proteins for P63272 (Homo sapiens) Explore P63272 Go to UniProtKB: P63272
PHAROS: P63272 GTEx: ENSG00000213246
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63272
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT5	U [auth Z]	1,087	Homo sapiens	Mutation(s): 0 Gene Names: SUPT5H, SPT5, SPT5H
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens) Explore O00267 Go to UniProtKB: O00267
PHAROS: O00267 GTEx: ENSG00000196235
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00267
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA-capping enzyme	V [auth a]	597	Homo sapiens	Mutation(s): 0 Gene Names: RNGTT
UniProt & NIH Common Fund Data Resources
Find proteins for O60942 (Homo sapiens) Explore O60942 Go to UniProtKB: O60942
PHAROS: O60942 GTEx: ENSG00000111880
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60942
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	M [auth N]	48	Homo sapiens
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Length	Organism	Image
RNA (5'-D((GTP))-R(PAPGPAPGPAPGPGPGPAPAPCPCPCPAPCP*U)-3')	N [auth P]	16	Homo sapiens
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
DNA (45-MER)	O [auth T]	48	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain EA [auth P] MOL2 format, chain EA [auth P]	EA [auth P]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain EA [auth P] Interactions & Density Focus chain EA [auth P]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth I] SDF format, chain CA [auth I] SDF format, chain DA [auth L] SDF format, chain FA [auth Y] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth L] MOL2 format, chain FA [auth Y] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B]	AA [auth C] BA [auth I] CA [auth I] DA [auth L] FA [auth Y] AA [auth C], BA [auth I], CA [auth I], DA [auth L], FA [auth Y], X [auth A], Y [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth L] Focus chain FA [auth Y] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth L] Focus chain FA [auth Y] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A]	W [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-04-10
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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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8W8E

human co-transcriptional RNA capping enzyme RNGTT

Strcutures of co-transcriptional RNA capping enzymes on paused transcription complex

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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UniProt

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Entity ID: 11

UniProt

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Entity ID: 12

UniProt

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UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 20

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 21

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 22