PDB-6vvj: Cap1G-TPUA

ID or keywords:

Entry

Database: PDB / ID: 6vvj

Title

Cap1G-TPUA

Components

RNA (130-MER)

Keywords

RNA / capped RNA / viral / MAL strain / MAL / 5' leader / Leader RNA / covered cap

Function / homology

RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Human immunodeficiency virus 1

Method

SOLUTION NMR / simulated annealing

Authors

Summers, M.F. / Brown, J.D.

Funding support

United States, 5items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	8R01 AI50498	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	U54 AI150470	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	F31 GM123803	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	MARC U*STAR 2T34 GM008663	United States
Howard Hughes Medical Institute (HHMI)		United States

Citation

Journal: Science / Year: 2020
Title: Structural basis for transcriptional start site control of HIV-1 RNA fate.
Authors: Brown, J.D. / Kharytonchyk, S. / Chaudry, I. / Iyer, A.S. / Carter, H. / Becker, G. / Desai, Y. / Glang, L. / Choi, S.H. / Singh, K. / Lopresti, M.W. / Orellana, M. / Rodriguez, T. / Oboh, U. ...

History

Deposition	Feb 18, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2020	Group: Database references / Structure summary / Category: citation / citation_author / struct Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2	Jun 14, 2023	Group: Database references / Other / Category: database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.0	Mar 6, 2024	Group: Data collection / Non-polymer description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1	May 15, 2024	Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/6vvj ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vvj	HTTPS FTP

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Related structure data

Related structure data	6vu1C C: citing same article (ref.)
Similar structure data	2pis-d 7avt-d 6sfr-d 7avu-d 2o25-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	BMRB: 30724Cap3G-TAR-F1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

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Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#245 - May 2020
Spliceosomes
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: RNA (130-MER)

41.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	20 / 20	target function
Representative	Model #1	lowest energy

#1: RNA chain	RNA (130-MER) Mass: 41922.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
Has ligand of interest	Y

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Experiment

Experiment

Method: SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Sample state	Spectrometer-ID	Type
1	1	1	isotropic	1	2D 1H-1H NOESY
1	2	2	isotropic	1	2D 1H-1H NOESY
1	3	3	isotropic	1	2D 1H-1H NOESY
1	4	4	isotropic	1	2D 1H-1H NOESY
1	5	5	isotropic	1	2D 1H-1H NOESY
1	6	6	isotropic	1	2D 1H-1H NOESY
1	7	7	isotropic	1	2D 1H-1H NOESY
1	8	8	isotropic	1	2D 1H-1H NOESY
2	9	9	isotropic	1	2D 1H-1H NOESY
2	10	10	isotropic	1	2D 1H-1H NOESY
2	11	11	isotropic	1	2D 1H-1H NOESY
1	12	12	isotropic	1	2D 1H-1H NOESY
1	13	13	isotropic	1	2D 1H-1H NOESY
1	14	14	isotropic	1	2D 1H-1H NOESY
1	15	15	isotropic	1	2D 1H-1H NOESY
1	16	16	isotropic	1	2D 1H-1H NOESY
1	17	17	isotropic	1	2D 1H-1H NOESY
1	18	18	isotropic	1	2D 1H-1H NOESY
1	19	19	isotropic	1	2D 1H-1H NOESY
1	20	20	isotropic	1	2D 1H-1H NOESY
1	21	21	isotropic	1	2D 1H-1H NOESY
1	22	22	isotropic	1	2D 1H-1H NOESY
1	23	23	isotropic	1	2D 1H-1H NOESY
1	24	24	isotropic	1	2D 1H-1H NOESY

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Sample preparation

Details

Type	Solution-ID	Contents	Label	Solvent system
solution	1	150 uM 1H Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_1H	100% D2O
solution	2	150 uM Gh Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_Gh	100% D2O
solution	3	150 uM A2rGr Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_A2rGr	100% D2O
solution	4	150 uM GhU6r Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_GhU6r	100% D2O
solution	5	150 uM U6r Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_U6r	100% D2O
solution	6	150 uM C6r Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_C6r	100% D2O
solution	7	150 uM C6rU6r Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_C6rU6r	100% D2O
solution	8	150 uM AhCh Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	Cap1G-TPUA_AhCh	100% D2O
solution	9	150 uM U6r Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 90% H2O/10% D2O	Cap1G-TPUA_U6r-H2O	90% H2O/10% D2O
solution	10	150 uM 1H Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 90% H2O/10% D2O	Cap1G-TPUA_1H-H2O	90% H2O/10% D2O
solution	11	150 uM Gh Cap1G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 90% H2O/10% D2O	Cap1G-TPUA_Gh-H2O	90% H2O/10% D2O
solution	12	150 uM 1H 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_1H	100% D2O
solution	13	150 uM Ah 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_Ah	100% D2O
solution	14	150 uM Ch 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_Ch	100% D2O
solution	15	150 uM Uh 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_Uh	100% D2O
solution	16	150 uM A2rCr 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_A2rCr	100% D2O
solution	17	150 uM A2rUr 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_A2rUr	100% D2O
solution	18	150 uM C6rUr 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_C6rUr	100% D2O
solution	19	150 uM CrU6r 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_CrU6r	100% D2O
solution	20	150 uM AhCh 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_AhCh	100% D2O
solution	21	150 uM ChGh 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_ChGh	100% D2O
solution	22	150 uM GhUh 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_GhUh	100% D2O
solution	23	150 uM AhUh 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 mM KCl, 100% D2O	2G-TPUA_AhUh	100% D2O
solution	24	150 uM AhGh 2G-TPUA, 10 mM Deuterated KH2PO4, 1 mM MgCl2, 122 M KCl, 100% D2O	2G-TPUA_AhGh	100% D2O

Sample

Conc. (mg/ml)	Component	Isotopic labeling	Solution-ID
150 uM	Cap1G-TPUA	1H	1
10 mM	KH2PO4	Deuterated	1
1 mM	MgCl2	natural abundance	1
122 mM	KCl	natural abundance	1
150 uM	Cap1G-TPUA	Gh	2
10 mM	KH2PO4	Deuterated	2
1 mM	MgCl2	natural abundance	2
122 mM	KCl	natural abundance	2
150 uM	Cap1G-TPUA	A2rGr	3
10 mM	KH2PO4	Deuterated	3
1 mM	MgCl2	natural abundance	3
122 mM	KCl	natural abundance	3
150 uM	Cap1G-TPUA	GhU6r	4
10 mM	KH2PO4	Deuterated	4
1 mM	MgCl2	natural abundance	4
122 mM	KCl	natural abundance	4
150 uM	Cap1G-TPUA	U6r	5
10 mM	KH2PO4	Deuterated	5
1 mM	MgCl2	natural abundance	5
122 mM	KCl	natural abundance	5
150 uM	Cap1G-TPUA	C6r	6
10 mM	KH2PO4	Deuterated	6
1 mM	MgCl2	natural abundance	6
122 mM	KCl	natural abundance	6
150 uM	Cap1G-TPUA	C6rU6r	7
10 mM	KH2PO4	Deuterated	7
1 mM	MgCl2	natural abundance	7
122 mM	KCl	natural abundance	7
150 uM	Cap1G-TPUA	AhCh	8
10 mM	KH2PO4	Deuterated	8
1 mM	MgCl2	natural abundance	8
122 mM	KCl	natural abundance	8
150 uM	Cap1G-TPUA	U6r	9
10 mM	KH2PO4	Deuterated	9
1 mM	MgCl2	natural abundance	9
122 mM	KCl	natural abundance	9
150 uM	Cap1G-TPUA	1H	10
10 mM	KH2PO4	Deuterated	10
1 mM	MgCl2	natural abundance	10
122 mM	KCl	natural abundance	10
150 uM	Cap1G-TPUA	Gh	11
10 mM	KH2PO4	Deuterated	11
1 mM	MgCl2	natural abundance	11
122 mM	KCl	natural abundance	11
150 uM	2G-TPUA	1H	12
10 mM	KH2PO4	Deuterated	12
1 mM	MgCl2	natural abundance	12
122 mM	KCl	natural abundance	12
150 uM	2G-TPUA	Ah	13
10 mM	KH2PO4	Deuterated	13
1 mM	MgCl2	natural abundance	13
122 mM	KCl	natural abundance	13
150 uM	2G-TPUA	Ch	14
10 mM	KH2PO4	Deuterated	14
1 mM	MgCl2	natural abundance	14
122 mM	KCl	natural abundance	14
150 uM	2G-TPUA	Uh	15
10 mM	KH2PO4	Deuterated	15
1 mM	MgCl2	natural abundance	15
122 mM	KCl	natural abundance	15
150 uM	2G-TPUA	A2rCr	16
10 mM	KH2PO4	Deuterated	16
1 mM	MgCl2	natural abundance	16
122 mM	KCl	natural abundance	16
150 uM	2G-TPUA	A2rUr	17
10 mM	KH2PO4	Deuterated	17
1 mM	MgCl2	natural abundance	17
122 mM	KCl	natural abundance	17
150 uM	2G-TPUA	C6rUr	18
10 mM	KH2PO4	Deuterated	18
1 mM	MgCl2	natural abundance	18
122 mM	KCl	natural abundance	18
150 uM	2G-TPUA	CrU6r	19
10 mM	KH2PO4	Deuterated	19
1 mM	MgCl2	natural abundance	19
122 mM	KCl	natural abundance	19
150 uM	2G-TPUA	AhCh	20
10 mM	KH2PO4	Deuterated	20
1 mM	MgCl2	natural abundance	20
122 mM	KCl	natural abundance	20
150 uM	2G-TPUA	ChGh	21
10 mM	KH2PO4	Deuterated	21
1 mM	MgCl2	natural abundance	21
122 mM	KCl	natural abundance	21
150 uM	2G-TPUA	GhUh	22
10 mM	KH2PO4	Deuterated	22
1 mM	MgCl2	natural abundance	22
122 mM	KCl	natural abundance	22
150 uM	2G-TPUA	AhUh	23
10 mM	KH2PO4	Deuterated	23
1 mM	MgCl2	natural abundance	23
122 mM	KCl	natural abundance	23
150 uM	2G-TPUA	AhGh	24
10 mM	KH2PO4	Deuterated	24
1 mM	MgCl2	natural abundance	24
122 M	KCl	natural abundance	24

Sample conditions

Ionic strength: 10 mM KH2PO4, 1 mM MgCl2, 122 mM KCl mM / Label: PI-D2O / pH: 7.4 Not defined / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer	Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software

Name	Developer	Classification
NMRFx	Johnson, One Moon Scientific	processing
NMRView	Johnson, One Moon Scientific	data analysis
NMRView	Johnson, One Moon Scientific	peak picking
NMRView	Johnson, One Moon Scientific	chemical shift assignment
CYANA	Guntert, Mumenthaler and Wuthrich	geometry optimization
CYANA	Guntert, Mumenthaler and Wuthrich	structure calculation
Amber	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman	structure calculation
Amber	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman	refinement
CYANA	Guntert, Mumenthaler and Wuthrich	refinement

Refinement

Method: simulated annealing / Software ordinal: 9 / Details: distance geometry, molecular dynamics

NMR representative

Selection criteria: lowest energy

NMR ensemble

Conformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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