[English] 日本語
Yorodumi
- PDB-6d2u: Solution structure of a ultra-high affinity macrocycle bound to H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d2u
TitleSolution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA
Components
  • DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO
  • RNA (29-MER)
KeywordsPeptide/RNA / Macrocycle inhibitor / complex / HIV-1 TAR / Tat / P-TEFb / RNA / Peptide-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsShortridge, M.D. / Varani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM110569 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.
Authors: Shortridge, M.D. / Wille, P.T. / Jones, A.N. / Davidson, A. / Bogdanovic, J. / Arts, E. / Karn, J. / Robinson, J.A. / Varani, G.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO
B: RNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)11,0052
Polymers11,0052
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO


Mass: 1697.087 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: RNA chain RNA (29-MER)


Mass: 9307.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic32D 1H-15N HSQC
222isotropic32D 1H-1H TOCSY
131isotropic32D 1H-1H NOESY
242isotropic32D 1H-1H NOESY
254isotropic32D 1H-13C HSQC
163isotropic33D 1H-15N NOESY
274isotropic33D 1H-13C NOESY

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.7 mM DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.2 mM RNA (29-MER), 0.01 mM EDTA, 20 mM potassium phosphate, 10 mM sodium chloride, 95% H2O/5% D2OSample conditions to record exchangeable proton distance information (imino, amino). 300uL volume in shigemi nmr tube.1H Peptide/1H RNA H2O95% H2O/5% D2O
solution21.7 mM DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.2 mM RNA (29-MER), 0.01 mM EDTA, 20 mM potassium phosphate, 10 mM sodium chloride, 100% D2OSample conditions to record non-exchangeable proton distance information. Same sample as id#1 lyophylized down and redissolved in 100% D2O1H Peptide/1H RNA D2O100% D2O
solution31.5 mM DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.0 mM [U-99% 13C; U-99% 15N] RNA (29-MER), 0.01 mM EDTA, 20 mM potassium phosphate, 10 mM sodium chloride, 95% H2O/5% D2OSample conditions to record exchangeable proton distance information (imino, amino). 300uL volume in shigemi nmr tube.1H Peptide/ 13C/15N RNA H2O95% H2O/5% D2O
solution41.5 mM DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.0 mM [U-99% 13C; U-99% 15N] RNA (29-MER), 0.01 mM EDTA, 20 mM potassium phosphate, 10 mM sodium chloride, 100% D2OSample conditions to record non-exchangeable proton distance information. Same sample as id#3 lyophylized down and redissolved in 100% D2O1H Peptide/ 13C/15N RNA D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMDAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PROnatural abundance1
1.2 mMRNA (29-MER)natural abundance1
0.01 mMEDTAnatural abundance1
20 mMpotassium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
1.7 mMDAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PROnatural abundance2
1.2 mMRNA (29-MER)natural abundance2
0.01 mMEDTAnatural abundance2
20 mMpotassium phosphatenatural abundance2
10 mMsodium chloridenatural abundance2
1.5 mMDAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PROnatural abundance3
1.0 mMRNA (29-MER)[U-99% 13C; U-99% 15N]3
0.01 mMEDTAnatural abundance3
20 mMpotassium phosphatenatural abundance3
10 mMsodium chloridenatural abundance3
1.5 mMDAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PROnatural abundance4
1.0 mMRNA (29-MER)[U-99% 13C; U-99% 15N]4
0.01 mMEDTAnatural abundance4
20 mMpotassium phosphatenatural abundance4
10 mMsodium chloridenatural abundance4
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Low temp sample conditions to record exchangeable proton information (imino, amino)10 mM NaCl, 20mM Na Phosphate mMlow_temp6.5 1 atm277 K
2high temp sample conditions to record difference in exchangeable proton information (imino, amino)10 mM NaCl, 20mM Na Phosphate mMhigh_temp6.5 1 atm303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker DRXBrukerDRX5001TCI cryoprobe
Bruker AVANCE IIBrukerAVANCE II6002TCI cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8003TCI cryoprobe

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more