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- PDB-6xh0: Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved... -

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Basic information

Entry
Database: PDB / ID: 6xh0
TitleCo-crystal structure of HIV-1 TAR RNA in complex with lab-evolved RRM TBP6.9
Components
  • TAR binding protein 6.9
  • TRANS-ACTIVATION RESPONSE ELEMENT
KeywordsRNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / TAR RNA / LAB-EVOLVED PROTEIN / ARGININE FORK / BETA HAIRPIN / MAJOR-GROOVE READOUT / BASE TRIPLE / U1A / HIV-1 / TRANS- ACTIVATION / RNA RECOGNITION MOTIF / RRM / RNA BINDING PROTEIN-RNA COMPLEX / RNA BINDING PROTEIN
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsChavali, S.S. / Jenkins, J.L. / Wedekind, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI150463 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.
Authors: Chavali, S.S. / Mali, S.M. / Jenkins, J.L. / Fasan, R. / Wedekind, J.E.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAR binding protein 6.9
D: TRANS-ACTIVATION RESPONSE ELEMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7774
Polymers18,7292
Non-polymers492
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.494, 40.494, 286.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TAR binding protein 6.9


Mass: 10071.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09012*PLUS
#2: RNA chain TRANS-ACTIVATION RESPONSE ELEMENT /


Mass: 8657.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 17.5% PEG 4000, 0.05 M MES Monohydrate pH 6.0, 0.005 M MgCl2(H20)6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2018
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→38.97 Å / Num. obs: 4920 / % possible obs: 99.7 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rpim(I) all: 0.071 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 858 / CC1/2: 0.743 / Rpim(I) all: 0.447 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
Aimless0.7.1 : 27/03/18data scaling
PDB_EXTRACT3.25data extraction
XDSJan 26, 2018data reduction
Blu-Icedata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.1→38.966 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 493 10.02 %
Rwork0.2282 4427 -
obs0.2339 4920 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.89 Å2 / Biso mean: 83.3428 Å2 / Biso min: 56.2 Å2
Refinement stepCycle: final / Resolution: 3.1→38.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 572 2 3 1286
Biso mean--65.92 65.52 -
Num. residues----114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.41190.38691180.33461060100
3.4119-3.90520.30021180.25731062100
3.9052-4.91860.28991230.22071105100
4.9186-38.960.25711340.1956120099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.92281.7198-2.44694.31261.58945.0029-0.24220.18180.12640.08010.10450.13020.41080.1082-0.00010.68450.01020.00650.67430.06960.761958.095917.5605316.2741
21.6061-1.902-1.08193.4090.19141.82330.34530.39020.385-0.5138-0.2205-0.4947-0.1708-0.10850.00010.8970.02580.08131.02650.05110.871167.785829.5363302.2904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 91)A5 - 91
2X-RAY DIFFRACTION2(chain 'D' and resid 18 through 44)D18 - 44

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