5W51 | pdb_00005w51

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP

PDB DOI: https://doi.org/10.2210/pdb5W51/pdb
NAKB: 5W51

Classification: DNA BINDING PROTEIN/RNA/DNA
Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2017-06-13 Released: 2018-06-20
Deposition Author(s): Wang, W., Wang, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: 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

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.

Wang, W., Xu, L., Hu, L., Chong, J., He, C., Wang, D.

(2017) J Am Chem Soc 139: 14436-14442

PubMed: 28933854 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.7b06381
Primary Citation Related Structures:
5W4U, 5W51

PubMed Abstract:
N ⁶-Methyladenine (N ⁶-mA or 6 mA) is an epigenetic DNA modification in eukaryotic genomes. In contrast to the well-established roles of 5-methylcytosine for epigenetic regulation of gene expression, the functional roles of N ⁶-mA remain elusive. In particular, the impact of N ⁶-mA modification of the DNA template on RNA polymerase II (pol II) transcription elongation is not known. In this work, using the Saccharomyces cerevisiae pol II transcriptional elongation system as a model, we investigated the molecular mechanism of pol II recognition and processing of N ⁶-mA sites via both biochemical and structural approaches. We found that N ⁶-mA causes site-specific pol II pausing/stalling. Structural analysis revealed that while N ⁶-mA can reach the +1 template position, the stability of the N ⁶-mA and UTP base pairing is compromised. Taken together, we reveal that the presence of the 6-methyl group on adenine reduces incorporation efficiency and promotes backtracking translocation. Our studies with yeast pol II provide molecular insights into understanding the impacts of N ⁶-mA on pol II transcription dynamics in different organisms.

Organizational Affiliation

Department of Chemistry, Sun Yat-Sen University , Guangzhou 510275, China.

Macromolecule Content

Total Structure Weight: 486.81 kDa
Atom Count: 28,880
Modeled Residue Count: 3,543
Deposited Residue Count: 4,225
Unique protein chains: 10
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	A	1,733	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04050
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	B	1,224	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518 Go to UniProtKB: P08518
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08518
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	318	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370 Go to UniProtKB: P16370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16370
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	D [auth E]	215	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20434
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	E [auth F]	155	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20435
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	F [auth H]	146	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20436
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	G [auth I]	122	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999 Go to UniProtKB: P27999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27999
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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 RPABC5	H [auth J]	70	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22139
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	I [auth K]	120	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902 Go to UniProtKB: P38902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38902
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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 RPABC4	J [auth L]	70	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40422
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 11
29mer template DNA	K [auth T]	29	Saccharomyces cerevisiae
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 12
14mer non-template DNA	L [auth N]	14	Saccharomyces cerevisiae
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 13
9mer RNA	M [auth R]	9	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2KH Query on 2KH Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine C₉ H₁₆ N₃ O₁₄ P₃ OZIBFYOFLVBDIY-XVFCMESISA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth J] SDF format, chain V [auth I] SDF format, chain U [auth I] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain X [auth L] MOL2 format, chain W [auth J] MOL2 format, chain V [auth I] MOL2 format, chain U [auth I] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain X [auth L] mmCIF format, chain W [auth J] mmCIF format, chain V [auth I] mmCIF format, chain U [auth I] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A] O [auth A] S [auth B] T [auth C] U [auth I] N [auth A], O [auth A], S [auth B], T [auth C], U [auth I], V [auth I], W [auth J], X [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth I] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth L] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth I] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	P [auth A], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.254 (Depositor), 0.255 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.7	α = 90
b = 224	β = 101.04
c = 193.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Wang, W.

Wang, D.

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2019-07-03
Changes: Data collection, Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.

5W51 | pdb_00005w51

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP

Literature

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

Sequence Annotations

Entity ID: 12

Sequence Annotations

Entity ID: 13

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)