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- PDB-6xh2: Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved... -

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Basic information

Entry
Database: PDB / ID: 6xh2
TitleCo-crystal structure of HIV-1 TAR RNA in complex with lab-evolved RRM 6.6
Components
  • TAR-BINDING PROTEIN 6.6
  • 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 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 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAR-BINDING PROTEIN 6.6
D: TRANS-ACTIVATION RESPONSE ELEMENT


Theoretical massNumber of molelcules
Total (without water)19,3522
Polymers19,3522
Non-polymers00
Water1,74797
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)40.300, 40.300, 288.683
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 6.6


Mass: 10694.442 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M Sodium Cacodylate pH 7.0, 0.1 M Sodium Chloride, 0.002 M Ammonium Sulfate, 17% (w/v) PEG-5000 MME

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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: May 10, 2017
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.71→39.91 Å / Num. obs: 26782 / % possible obs: 99.2 % / Redundancy: 8.2 % / Biso Wilson estimate: 32.65 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.033 / Net I/σ(I): 10.7
Reflection shellResolution: 1.71→1.74 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1245 / CC1/2: 0.635 / Rpim(I) all: 0.385

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CMN

6cmn


Resolution: 1.71→38.815 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 2000 7.47 %
Rwork0.1912 24782 -
obs0.1926 26782 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.72 Å2 / Biso mean: 45.2937 Å2 / Biso min: 21.2 Å2
Refinement stepCycle: final / Resolution: 1.71→38.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 572 0 98 1423
Biso mean---43.41 -
Num. residues----120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011428
X-RAY DIFFRACTIONf_angle_d1.2512060
X-RAY DIFFRACTIONf_chiral_restr0.063251
X-RAY DIFFRACTIONf_plane_restr0.009164
X-RAY DIFFRACTIONf_dihedral_angle_d11.374814
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.715-1.75780.27421260.2804157389
1.7578-1.80530.29611400.25911725100
1.8053-1.85850.24011350.249167998
1.8585-1.91840.26771440.23661776100
1.9184-1.9870.23191370.2311708100
1.987-2.06650.23431420.22151744100
2.0665-2.16060.20271420.2121765100
2.1606-2.27450.24981420.2116176199
2.2745-2.4170.21511420.20661762100
2.417-2.60360.21291460.20721797100
2.6036-2.86550.22241440.21191805100
2.8655-3.27990.1961460.1911797100
3.2799-4.13160.18981520.15851875100
4.1316-38.8150.2011620.17652015100
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)
18.5301-0.67931.05283.9510.10942.9717-0.2870.12820.73850.07370.1109-0.0978-0.20650.080.19620.2102-0.0250.01770.29830.04790.319156.448222.672319.231
22.8551.05840.62699.26091.27114.63520.03640.1254-0.10390.2438-0.066-0.10630.23770.5172-0.04050.23540.07290.02680.34310.08180.334161.154210.7247318.6877
35.37984.0858-4.20414.9494-2.1496.6003-0.22530.216-0.1243-0.00670.07550.05780.4327-0.03570.16720.16290.04610.02310.26890.04210.358655.364417.1381316.6246
46.6668-1.52240.82686.82690.13636.9916-0.22650.14210.17480.12770.0110.01330.0367-0.08230.1680.1322-0.02410.05960.2480.09690.283255.433119.235321.0798
52.1888-1.3458-0.45984.80070.82275.66950.01980.29680.4091-0.5821-0.0523-0.3973-0.1249-0.00840.00810.2589-0.06130.02840.42370.08240.269968.130129.5245305.6457
62.2848-2.0175-1.23.28391.75645.95290.22240.28580.1563-0.6826-0.02950.0847-0.06720.1698-0.1890.3206-0.0772-0.02840.38880.05240.32864.731329.1059303.766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )A2 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 37 )A23 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 72 )A38 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 94 )A73 - 94
5X-RAY DIFFRACTION5chain 'D' and (resid 18 through 32 )D18 - 32
6X-RAY DIFFRACTION6chain 'D' and (resid 33 through 44 )D33 - 44

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