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- PDB-6cmn: Co-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7 -

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Basic information

Entry
Database: PDB / ID: 6cmn
TitleCo-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7
Components
  • TAR-Binding Protein 6.7
  • Trans-Activation Response RNA 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
Function / homology
Function and homology information


U1 snRNP / U1 snRNA binding / spliceosomal complex / nucleoplasm / identical protein binding
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.796 Å
AuthorsBelashov, I.A. / Wedekind, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123864 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.
Authors: Belashov, I.A. / Crawford, D.W. / Cavender, C.E. / Dai, P. / Beardslee, P.C. / Mathews, D.H. / Pentelute, B.L. / McNaughton, B.R. / Wedekind, J.E.
History
DepositionMar 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
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
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 6.7
D: Trans-Activation Response RNA Element


Theoretical massNumber of molelcules
Total (without water)22,3832
Polymers22,3832
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, N-value = 0.99 +/- 0.02 (number of sites)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.422, 40.422, 284.558
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 6.7


Mass: 13725.837 Da / Num. of mol.: 1
Mutation: E19S, Y31H, Q36R, S46P, S48Q, L49R, K50T, M51P, R83A, S91K, D92R, I94P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: G1TM83
#2: RNA chain Trans-Activation Response RNA 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.: 153 / 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: 2.6 Å3/Da / Density % sol: 52.63 % / Description: Half-octagon plate habit
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: NaCl, ammonium sulfate, PEG-mme 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2016
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: 1.796→38.9 Å / Num. obs: 23297 / % possible obs: 99.4 % / Redundancy: 8.8 % / Biso Wilson estimate: 31.74 Å2 / CC1/2: 0.987 / Net I/σ(I): 19.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2140 / CC1/2: 0.692 / % possible all: 91.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URN

1urn


Resolution: 1.796→37.187 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.2213 1164 5 %
Rwork0.1891 --
obs0.1907 23278 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.45 Å2 / Biso mean: 46.1147 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 1.796→37.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms741 572 0 153 1466
Biso mean---46.69 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051401
X-RAY DIFFRACTIONf_angle_d0.7592021
X-RAY DIFFRACTIONf_chiral_restr0.042247
X-RAY DIFFRACTIONf_plane_restr0.005159
X-RAY DIFFRACTIONf_dihedral_angle_d13.806798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.796-1.87780.28241360.26962577271396
1.8778-1.97680.31511420.257427022844100
1.9768-2.10060.25581430.225727202863100
2.1006-2.26280.2791440.21227232867100
2.2628-2.49050.24551450.2127342879100
2.4905-2.85070.25671440.215727832927100
2.8507-3.59110.21211480.171128262974100
3.5911-37.19450.18241620.165830493211100
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)
10.68920.33260.31243.41590.3242.9265-0.28860.09380.3036-0.05630.06840.0807-0.12570.0172-0.00130.2161-0.03180.01170.24650.04050.279856.611321.4279314.2891
21.5061-0.46020.33381.52070.56591.4141-0.26460.1771-0.55-0.0224-0.0106-0.04750.21690.13950.00020.2414-0.00430.06770.25920.05890.308159.621610.8385312.395
30.4621-0.1215-0.78650.65211.19352.8115-0.27210.1616-0.1473-0.03230.0513-0.05780.305-0.0538-0.01440.1884-0.00940.03360.22820.05650.29256.016418.7367313.0744
43.1760.0682-2.23883.8358-0.41251.6104-0.04070.5427-0.0829-0.1163-0.02310.07120.24370.08920.00080.25010.00050.0110.29860.04540.300255.54619.2016315.565
51.7154-0.39260.05592.6293-0.0823.2543-0.00860.2080.2876-0.41330.0577-0.4560.0047-0.03370.02230.3155-0.07690.01870.39710.0640.262368.55529.5203301.1427
60.0715-0.1776-0.02160.4310.05670.0049-0.2231-0.1126-0.1651-0.26860.40820.26710.0839-0.2126-0.0030.3438-0.0651-0.04040.40980.04140.4460.01834.3691310.4973
70.5148-0.03070.56040.3113-0.06630.84270.39050.5297-0.0782-0.9489-0.1818-0.27810.13730.11090.00030.6356-0.03720.01320.51890.01680.286469.036525.069290.7905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 22 )A5 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 44 )A23 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 72 )A45 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 95 )A73 - 95
5X-RAY DIFFRACTION5chain 'D' and (resid 18 through 32 )D18 - 32
6X-RAY DIFFRACTION6chain 'D' and (resid 33 through 37 )D33 - 37
7X-RAY DIFFRACTION7chain 'D' and (resid 38 through 44 )D38 - 44

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